{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T01:06:55Z","timestamp":1778634415552,"version":"3.51.4"},"reference-count":219,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T00:00:00Z","timestamp":1667260800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"the Department of Science and Technology, New Delhi","award":["EMR\/2017\/002451"],"award-info":[{"award-number":["EMR\/2017\/002451"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Entropy"],"abstract":"<jats:p>Deoxyribonucleic acid (DNA) is a fundamental biomolecule for correct cellular functioning and regulation of biological processes. DNA\u2019s structure is dynamic and has the ability to adopt a variety of structural conformations in addition to its most widely known double-stranded DNA (dsDNA) helix structure. Stability and structural dynamics of dsDNA play an important role in molecular biology. In vivo, DNA molecules are folded in a tightly confined space, such as a cell chamber or a channel, and are highly dense in solution; their conformational properties are restricted, which affects their thermodynamics and mechanical properties. There are also many technical medical purposes for which DNA is placed in a confined space, such as gene therapy, DNA encapsulation, DNA mapping, etc. Physiological conditions and the nature of confined spaces have a significant influence on the opening or denaturation of DNA base pairs. In this review, we summarize the progress of research on the stability and dynamics of dsDNA in cell-like environments and discuss current challenges and future directions. We include studies on various thermal and mechanical properties of dsDNA in ionic solutions, molecular crowded environments, and confined spaces. By providing a better understanding of melting and unzipping of dsDNA in different environments, this review provides valuable guidelines for predicting DNA thermodynamic quantities and for designing DNA\/RNA nanostructures.<\/jats:p>","DOI":"10.3390\/e24111587","type":"journal-article","created":{"date-parts":[[2022,11,2]],"date-time":"2022-11-02T03:36:44Z","timestamp":1667360204000},"page":"1587","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":35,"title":["Structure and Dynamics of dsDNA in Cell-like Environments"],"prefix":"10.3390","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9582-670X","authenticated-orcid":false,"given":"Amar","family":"Singh","sequence":"first","affiliation":[{"name":"Department of Physics, Birla Institute of Technology & Science, Pilani 333031, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6992-9473","authenticated-orcid":false,"given":"Arghya","family":"Maity","sequence":"additional","affiliation":[{"name":"Department of Physics, Birla Institute of Technology & Science, Pilani 333031, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5213-6741","authenticated-orcid":false,"given":"Navin","family":"Singh","sequence":"additional","affiliation":[{"name":"Department of Physics, Birla Institute of Technology & Science, Pilani 333031, India"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,11,1]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Vologodskii, A. (2015). Biophysics of DNA, Cambridge University Press. [1st ed.].","DOI":"10.1017\/CBO9781139542371"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1038\/171737a0","article-title":"Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid","volume":"171","author":"Watson","year":"1953","journal-title":"Nature"},{"key":"ref_3","unstructured":"Sinden, R.R. (1994). DNA Structure and Function, Academic Press. [1st ed.]."},{"key":"ref_4","unstructured":"Bloomfield, V.A., Crothers, D.M., Tinoco, I., Hearst, J.E., Wemmer, D.E., Killman, P.A., and Turner, D.H. (2000). Nucleic Acids: Structures, Properties, and Functions, University Science Books. [1st ed.]."},{"key":"ref_5","unstructured":"Omoto, C. (2004). Genes and DNA: A Beginner\u2019s Guide to Genetics and Its Applications, Columbia University Press."},{"key":"ref_6","unstructured":"Anders, M. (2018). DNA, Genes, and Chromosomes, Capstone."},{"key":"ref_7","unstructured":"Calladine, C.R., Drew, H., Luisi, B., and Travers, A. (2004). Understanding DNA, Third Edition: The Molecule and How it Works, Academic Press."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Carlberg, C., and Molnar, F. (2014). Mechanisms of Gene Regulation, Springer. [1st ed.].","DOI":"10.1007\/978-94-007-7905-1"},{"key":"ref_9","unstructured":"Watson, J., Myers, R., Myers, U., Caudy, A., and Witkowski, J. (2007). Recombinant DNA: Genes and Genomes: A Short Course, W. H. Freeman."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1023\/A:1005158503806","article-title":"Results and Limitations of the Soliton Theory of DNA Transcription","volume":"24","author":"Gaeta","year":"1999","journal-title":"J. Biol. Phys."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"640","DOI":"10.1002\/bip.22432","article-title":"The role of molecular structure of sugar-phosphate backbone and nucleic acid bases in the formation of single-stranded and double-stranded DNA structures","volume":"101","author":"Poltev","year":"2014","journal-title":"Biopolymers"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"4539","DOI":"10.1093\/nar\/gkq250","article-title":"Quantitative design and experimental validation for a single-molecule DNA nanodevice transformable among three structural states","volume":"38","author":"Komiya","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"5335","DOI":"10.1002\/anie.200460789","article-title":"A DNA Nanomachine Based on a Duplex\u2013Triplex Transition","volume":"43","author":"Chen","year":"2004","journal-title":"Angew. Chem. Int. Ed."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1244","DOI":"10.1002\/smll.200600237","article-title":"Hairpin-DNA memory Using Molecular Addressing","volume":"2","author":"Takinoue","year":"2006","journal-title":"Small"},{"key":"ref_15","first-page":"93","article-title":"Molecular reactions for a molecular memory based on hairpin DNA","volume":"4","author":"Takinoue","year":"2004","journal-title":"Chem-Bio Inf. J."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"5734","DOI":"10.1002\/anie.200352402","article-title":"A Proton-Fuelled DNA Nanomachine","volume":"42","author":"Liu","year":"2003","journal-title":"Angew. Chem. Int. Ed."},{"key":"ref_17","unstructured":"Cantor, C.R., and Schimmel, P.R. (1980). Biophysical Chemistry: Part III: The Behavior of Biological Macromolecules (Their Biophysical Chemistry), W. H. Freeman. [1st ed.]."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1016\/0370-1573(85)90060-2","article-title":"Thermal denaturation of {DNA} molecules: A comparison of theory with experiment","volume":"126","author":"Wartell","year":"1985","journal-title":"Phys. Rep."},{"key":"ref_19","unstructured":"Nelson, P. (2003). Biological Physics: Energy, Information, Life, W. H. Freeman. [1st ed.]."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1349","DOI":"10.1063\/1.1731411","article-title":"Theory of Melting of the Helical Form in Double Chains of the DNA","volume":"33","author":"Zimm","year":"1960","journal-title":"J. Chem. Phys."},{"key":"ref_21","unstructured":"Poland, D., and Scheraga, H.A. (1970). Theory of Helix-Coil Transitions in Biopolymers; Statistical Mechanical Theory of Order-Disorder Transitions in Biological Macromolecules, Academic Press."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.physrep.2009.11.001","article-title":"Biomolecules under mechanical force","volume":"486","author":"Kumar","year":"2010","journal-title":"Phys. Rep."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1016\/j.plrev.2014.01.005","article-title":"Fluctuations in the {DNA} double helix: A critical review","volume":"11","author":"Prakash","year":"2014","journal-title":"Phys. Life Rev."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"11935","DOI":"10.1073\/pnas.94.22.11935","article-title":"Mechanical separation of the complementary strands of DNA","volume":"94","author":"Bockelmann","year":"1997","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1128","DOI":"10.1103\/PhysRevE.62.1128","article-title":"Pulling a polymer out of a potential well and the mechanical unzipping of DNA","volume":"62","author":"Sebastian","year":"2000","journal-title":"Phys. Rev. E"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1572","DOI":"10.1103\/PhysRevLett.85.1572","article-title":"Pulling Pinned Polymers and Unzipping DNA","volume":"85","author":"Lubensky","year":"2000","journal-title":"Phys. Rev. Lett."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"L423","DOI":"10.1088\/0305-4470\/33\/45\/101","article-title":"Unzipping DNAs: Towards the first step of replication","volume":"33","author":"Bhattacharjee","year":"2000","journal-title":"J. Phys. A Math. Gen."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"248102","DOI":"10.1103\/PhysRevLett.93.248102","article-title":"Complete Phase Diagram of DNA Unzipping: Eye, Y Fork, and Triple Point","volume":"93","author":"Kapri","year":"2004","journal-title":"Phys. Rev. Lett."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"115102","DOI":"10.1063\/1.3563633","article-title":"The probability analysis of opening of DNA","volume":"134","author":"Srivastava","year":"2011","journal-title":"J. Chem. Phys."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"3831","DOI":"10.1021\/jp808232p","article-title":"Shear Unzipping of DNA","volume":"113","author":"Chakrabarti","year":"2009","journal-title":"J. Phys. Chem. B"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"034113","DOI":"10.1088\/0953-8984\/21\/3\/034113","article-title":"Force induced DNA melting","volume":"21","author":"Santosh","year":"2009","journal-title":"J. Phys. Condens. Matter"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"031905","DOI":"10.1103\/PhysRevE.84.031905","article-title":"Shear unzipping of double-stranded DNA","volume":"84","author":"Prakash","year":"2011","journal-title":"Phys. Rev. E"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"174910","DOI":"10.1063\/1.4919646","article-title":"On the rupture of DNA molecule","volume":"142","author":"Mishra","year":"2015","journal-title":"J. Chem. Phys."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1021\/acsomega.7b01692","article-title":"How Well Can DNA Rupture DNA? Shearing and Unzipping Forces inside DNA Nanostructures","volume":"3","author":"Tee","year":"2018","journal-title":"ACS Omega"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1002\/masy.201400189","article-title":"Pulling DNA: The Effect of Chain Length on the Mechanical Stability of DNA Chain","volume":"357","author":"Singh","year":"2015","journal-title":"Macromol. Symp."},{"key":"ref_36","first-page":"18","article-title":"Force induced unzipping of dsDNA: The solvent effect","volume":"3","author":"Singh","year":"2013","journal-title":"Phys. Express"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1140\/epje\/i2004-10100-7","article-title":"Statistical theory of force-induced unzipping of DNA","volume":"17","author":"Singh","year":"2005","journal-title":"Eur. Phys. J. E"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1813","DOI":"10.1016\/S0006-3495(96)79746-1","article-title":"Quantitative measurements of force and displacement using an optical trap","volume":"70","author":"Simmons","year":"1996","journal-title":"Biophys. J."},{"key":"ref_39","first-page":"100067","article-title":"Temperature-dependent elastic properties of DNA","volume":"2","author":"Ritort","year":"2022","journal-title":"Biophys. Rep."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"930","DOI":"10.1103\/PhysRevLett.56.930","article-title":"Atomic Force Microscope","volume":"56","author":"Binnig","year":"1986","journal-title":"Phys. Rev. Lett."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"2752","DOI":"10.1529\/biophysj.104.047340","article-title":"Pause Point Spectra in {DNA} Constant-Force Unzipping","volume":"88","author":"Weeks","year":"2005","journal-title":"Biophys. J."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"113030","DOI":"10.1016\/j.bios.2021.113030","article-title":"G-quadruplex: Flexible conformational changes by cations, pH, crowding and its applications to biosensing","volume":"178","author":"Nishio","year":"2021","journal-title":"Biosens. Bioelectron."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"8976","DOI":"10.1021\/acsomega.0c06350","article-title":"Opposite Effects of Potassium Ions on the Thermal Stability of i-Motif DNA in Different Buffer Systems","volume":"6","author":"Gao","year":"2021","journal-title":"ACS Omega"},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Brown, S.L., and Kendrick, S. (2021). The i-Motif as a Molecular Target: More Than a Complementary DNA Secondary Structure. Pharmaceuticals, 14.","DOI":"10.3390\/ph14020096"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"5217","DOI":"10.1007\/s00216-022-04058-8","article-title":"Applications of triplex DNA nanostructures in sensor development","volume":"414","author":"Lin","year":"2022","journal-title":"Anal. Bioanal. Chem."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"064903","DOI":"10.1063\/5.0059153","article-title":"Efimov-DNA phase diagram: Three stranded DNA on a cubic lattice","volume":"155","author":"Bhattacharjee","year":"2021","journal-title":"J. Chem. Phys."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"012121","DOI":"10.1103\/PhysRevE.89.012121","article-title":"Melting behavior and different bound states in three-stranded DNA models","volume":"89","author":"Maji","year":"2014","journal-title":"Phys. Rev. E"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1002\/humu.20951","article-title":"High-resolution DNA melting analysis: Advancements and limitations","volume":"30","author":"Wittwer","year":"2009","journal-title":"Hum. Mutat."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1002\/bip.360030207","article-title":"Dependence of the melting temperature of DNA on salt concentration","volume":"3","author":"Schildkraut","year":"1965","journal-title":"Biopolymers"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"2623","DOI":"10.1002\/bip.360101223","article-title":"Simplification of the empirical relationship between melting temperature of DNA, its GC content and concentration of sodium ions in solution","volume":"10","year":"1971","journal-title":"Biopolymers"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"806","DOI":"10.1209\/epl\/i2005-10466-6","article-title":"Sharp DNA denaturation due to solvent interaction","volume":"73","author":"Weber","year":"2006","journal-title":"EPL Europhys. Lett."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"4650","DOI":"10.1021\/ma010159b","article-title":"Counterion Condensation on a Helical Charge Lattice","volume":"34","author":"Manning","year":"2001","journal-title":"Macromolecules"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"1460","DOI":"10.1073\/pnas.95.4.1460","article-title":"A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics","volume":"95","author":"SantaLucia","year":"1998","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"106189","DOI":"10.1016\/j.bpc.2019.106189","article-title":"Nearest-neighbour parameters optimized for melting temperature prediction of DNA\/RNA hybrids at high and low salt concentrations","volume":"251","author":"Weber","year":"2019","journal-title":"Biophys. Chem."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"8273","DOI":"10.1039\/D0SC01700K","article-title":"Melting temperature measurement and mesoscopic evaluation of single, double and triple DNA mismatches","volume":"11","author":"Oliveira","year":"2020","journal-title":"Chem. Sci."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"2052","DOI":"10.1016\/j.physa.2013.01.029","article-title":"Phase diagram of mechanically stretched DNA: The salt effect","volume":"392","author":"Singh","year":"2013","journal-title":"Physics A"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"R44","DOI":"10.1103\/PhysRevE.47.R44","article-title":"Entropy-driven DNA denaturation","volume":"47","author":"Dauxois","year":"1993","journal-title":"Phys. Rev. E"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"2755","DOI":"10.1103\/PhysRevLett.62.2755","article-title":"Statistical mechanics of a nonlinear model for DNA denaturation","volume":"62","author":"Peyrard","year":"1989","journal-title":"Phys. Rev. Lett."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"137781","DOI":"10.1016\/j.cplett.2020.137781","article-title":"Sharp DNA denaturation in a helicoidal mesoscopic model","volume":"755","author":"Weber","year":"2020","journal-title":"Chem. Phys. Lett."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"194102","DOI":"10.1063\/5.0046891","article-title":"Base pair fluctuations in helical models for nucleic acids","volume":"154","author":"Zoli","year":"2021","journal-title":"J. Chem. Phys."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"113017","DOI":"10.1088\/1367-2630\/16\/11\/113017","article-title":"Thermal denaturation of A-DNA","volume":"16","author":"Wildes","year":"2014","journal-title":"New J. Phys."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"032703","DOI":"10.1103\/PhysRevE.92.032703","article-title":"Pulling short DNA molecules having defects on different locations","volume":"92","author":"Singh","year":"2015","journal-title":"Phys. Rev. E"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"115101","DOI":"10.1063\/1.3631564","article-title":"Thermodynamics of twisted DNA with solvent interaction","volume":"135","author":"Zoli","year":"2011","journal-title":"J. Chem. Phys."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1016\/j.physa.2014.10.029","article-title":"Effect of salt concentration on the stability of heterogeneous {DNA}","volume":"419","author":"Singh","year":"2015","journal-title":"Physics A"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"11B602_1","DOI":"10.1063\/1.4934783","article-title":"DNA terminal base pairs have weaker hydrogen bonds especially for AT under low salt concentration","volume":"143","author":"Ferreira","year":"2015","journal-title":"J. Chem. Phys."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1016\/j.physa.2014.02.029","article-title":"Thermal properties of a DNA denaturation with solvent interaction","volume":"404","author":"Macedo","year":"2014","journal-title":"Physics A"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"1394","DOI":"10.1016\/S0006-3495(93)81505-4","article-title":"Salt dependent premelting base pair opening probabilities of B and Z {DNA} Poly [d(G-C)] and significance for the B-Z transition","volume":"64","author":"Chen","year":"1993","journal-title":"Biophys. J."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"2242","DOI":"10.1063\/1.446921","article-title":"A modified self-consistent phonon theory of hydrogen bond melting","volume":"80","author":"Gao","year":"1984","journal-title":"J. Chem. Phys."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"6291","DOI":"10.1063\/1.446732","article-title":"A self-consistent microscopic theory of hydrogen bond melting with application to poly(dG).poly(dC)","volume":"80","author":"Gao","year":"1984","journal-title":"J. Chem. Phys."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"17166","DOI":"10.1002\/chem.201703518","article-title":"Metal-Mediated Base Pairs: From Characterization to Application","volume":"23","author":"Jash","year":"2017","journal-title":"Chem.\u2014A Eur. J."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"044903","DOI":"10.1063\/1.1842059","article-title":"Electrostatic correlations and fluctuations for ion binding to a finite length polyelectrolyte","volume":"122","author":"Tan","year":"2005","journal-title":"J. Chem. Phys."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"1175","DOI":"10.1529\/biophysj.105.070904","article-title":"Nucleic Acid Helix Stability: Effects of Salt Concentration, Cation Valence and Size, and Chain Length","volume":"90","author":"Tan","year":"2006","journal-title":"Biophys. J."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"139847","DOI":"10.1016\/j.cplett.2022.139847","article-title":"Mesoscopic model confirms strong base pair metal mediated bonding for T\u2013Hg2+\u2013T and weaker for C\u2013Ag+\u2013C","volume":"803","author":"Silva","year":"2022","journal-title":"Chem. Phys. Lett."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"106845","DOI":"10.1016\/j.bpc.2022.106845","article-title":"Transformation characteristics of A-DNA in salt solution revealed through molecular dynamics simulations","volume":"288","author":"Xue","year":"2022","journal-title":"Biophys. Chem."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1016\/j.pbiomolbio.2018.01.007","article-title":"Forces maintaining the DNA double helix and its complexes with transcription factors","volume":"135","author":"Privalov","year":"2018","journal-title":"Prog. Biophys. Mol. Biol."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"048702","DOI":"10.1088\/1674-1056\/ac3caa","article-title":"Molecular dynamics simulations of A-DNA in bivalent metal ions salt solution","volume":"31","author":"Xue","year":"2022","journal-title":"Chin. Phys. B"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"8138","DOI":"10.1093\/nar\/gku504","article-title":"Analyzing ion distributions around DNA","volume":"42","author":"Lavery","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"2412","DOI":"10.1093\/nar\/gkv080","article-title":"Analyzing ion distributions around DNA: Sequence-dependence of potassium ion distributions from microsecond molecular dynamics","volume":"43","author":"Pasi","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1002\/bip.1969.360070408","article-title":"Determination of DNA base compositions from melting profiles in dilute buffers","volume":"7","author":"Owen","year":"1969","journal-title":"Biopolymers"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"3537","DOI":"10.1021\/bi034621r","article-title":"Effects of Sodium Ions on DNA Duplex Oligomers: Improved Predictions of Melting Temperatures","volume":"43","author":"Owczarzy","year":"2004","journal-title":"Biochemistry"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"5336","DOI":"10.1021\/bi702363u","article-title":"Predicting Stability of DNA Duplexes in Solutions Containing Magnesium and Monovalent Cations","volume":"47","author":"Owczarzy","year":"2008","journal-title":"Biochemistry"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1093\/nar\/gkj454","article-title":"Base-stacking and base-pairing contributions into thermal stability of the DNA double helix","volume":"34","author":"Yakovchuk","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"041803","DOI":"10.1103\/PhysRevE.83.041803","article-title":"Manning free counterion fraction for a rodlike polyion: Aqueous solutions of short DNA fragments in presence of very low added salt","volume":"83","author":"Aumiler","year":"2011","journal-title":"Phys. Rev. E"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"1464","DOI":"10.1063\/1.1727786","article-title":"Occurrence of a Phase Transition in Nucleic Acid Models","volume":"45","author":"Poland","year":"1966","journal-title":"J. Chem. Phys."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"1056","DOI":"10.1529\/biophysj.108.134031","article-title":"A Unified Poland-Scheraga Model of Oligo- and Polynucleotide DNA Melting: Salt Effects and Predictive Power","volume":"96","author":"Jost","year":"2009","journal-title":"Biophys. J."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"021905","DOI":"10.1103\/PhysRevE.82.021905","article-title":"Melting of genomic DNA: Predictive modeling by nonlinear lattice dynamics","volume":"82","author":"Theodorakopoulos","year":"2010","journal-title":"Phys. Rev. E"},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"882","DOI":"10.1016\/S0006-3495(01)76067-5","article-title":"Force-Induced Melting of the {DNA} Double Helix 1. Thermodynamic Analysis","volume":"80","author":"Rouzina","year":"2001","journal-title":"Biophys. J."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"894","DOI":"10.1016\/S0006-3495(01)76068-7","article-title":"Force-Induced Melting of the {DNA} Double Helix. 2. Effect of Solution Conditions","volume":"80","author":"Rouzina","year":"2001","journal-title":"Biophys. J."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"3160","DOI":"10.1016\/S0006-3495(02)75658-0","article-title":"Salt Dependence of the Elasticity and Overstretching Transition of Single {DNA} Molecules","volume":"82","author":"Wenner","year":"2002","journal-title":"Biophys. J."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"1248","DOI":"10.1529\/biophysj.108.132688","article-title":"{DNA} Overstretching in the Presence of Glyoxal: Structural Evidence of Force-Induced {DNA} Melting","volume":"95","author":"Shokri","year":"2008","journal-title":"Biophys. J."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"874","DOI":"10.1016\/S0006-3495(01)76066-3","article-title":"Effect of pH on the Overstretching Transition of Double-Stranded DNA: Evidence of Force-Induced {DNA} Melting","volume":"80","author":"Williams","year":"2001","journal-title":"Biophys. J."},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1002\/(SICI)1097-0282(19991005)50:4<425::AID-BIP8>3.0.CO;2-B","article-title":"Melting studies of short DNA hairpins: Influence of loop sequence and adjoining base pair identity on hairpin thermodynamic stability","volume":"50","author":"Vallone","year":"1999","journal-title":"Biopolymers"},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"7491","DOI":"10.1021\/bi00444a049","article-title":"Effects of base sequence on the loop folding in DNA hairpins","volume":"28","author":"Blommers","year":"1989","journal-title":"Biochemistry"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"5901","DOI":"10.1093\/nar\/19.21.5901","article-title":"A thermodynamic study of unusually stable RNA and DNA hairpins","volume":"19","author":"Antao","year":"1991","journal-title":"Nucleic Acids Res."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"3084","DOI":"10.1021\/bi1015524","article-title":"Monovalent Cation Size and DNA Conformational Stability","volume":"50","author":"Stellwagen","year":"2011","journal-title":"Biochemistry"},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"4489","DOI":"10.1103\/PhysRevLett.79.4489","article-title":"Molecular Stick-Slip Motion Revealed by Opening DNA with Piconewton Forces","volume":"79","author":"Bockelmann","year":"1997","journal-title":"Phys. Rev. Lett."},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"2386","DOI":"10.1103\/PhysRevE.58.2386","article-title":"DNA strand separation studied by single molecule force measurements","volume":"58","author":"Bockelmann","year":"1998","journal-title":"Phys. Rev. E"},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/S0301-4622(98)00231-2","article-title":"Folding and unfolding of a giant duplex-DNA in a mixed solution with polycations, polyanions and crowding neutral polymers","volume":"76","author":"Kidoaki","year":"1999","journal-title":"Biophys. Chem."},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"R531","DOI":"10.1088\/0953-8984\/18\/32\/R01","article-title":"Single-molecule experiments in biological physics: Methods and applications","volume":"18","author":"Ritort","year":"2006","journal-title":"J. Phys. Condens. Matter"},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1093\/nar\/gkm1014","article-title":"Measurement of the salt-dependent stabilization of partially open DNA by Escherichia coli SSB protein","volume":"36","author":"Hatch","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"15431","DOI":"10.1073\/pnas.1001454107","article-title":"Single-molecule derivation of salt dependent base-pair free energies in DNA","volume":"107","author":"Huguet","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"2064","DOI":"10.1093\/nar\/gkt1089","article-title":"Elastic properties and secondary structure formation of single-stranded DNA at monovalent and divalent salt conditions","volume":"42","author":"Bosco","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"1301","DOI":"10.1006\/jmbi.1999.2798","article-title":"{DNA} stretching and compression: Large-scale simulations of double helical structures1","volume":"289","author":"Kosikov","year":"1999","journal-title":"J. Mol. Biol."},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"9343","DOI":"10.1063\/1.1319380","article-title":"Elastic moduli renormalization in self-interacting stretchable polyelectrolytes","volume":"113","author":"Podgornik","year":"2000","journal-title":"J. Chem. Phys."},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1039\/B919808C","article-title":"Interactions between planar polyelectrolyte brushes: Effects of stiffness and salt","volume":"6","author":"Wynveen","year":"2010","journal-title":"Soft Matter"},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"085101","DOI":"10.1063\/1.4792252","article-title":"Coarse-grained simulations of DNA overstretching","volume":"138","author":"Romano","year":"2013","journal-title":"J. Chem. Phys."},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"234901","DOI":"10.1063\/1.4921957","article-title":"Introducing improved structural properties and salt dependence into a coarse-grained model of DNA","volume":"142","author":"Snodin","year":"2015","journal-title":"J. Chem. Phys."},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1007\/s10867-017-9468-1","article-title":"Ionic effects on the temperature\u2013force phase diagram of DNA","volume":"43","author":"Amnuanpol","year":"2017","journal-title":"J. Biol. Phys."},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"5544","DOI":"10.1021\/ja960495l","article-title":"Ionic Effects on the Stability and Conformation of Peptide Nucleic Acid Complexes","volume":"118","author":"Sebastian","year":"1996","journal-title":"J. Am. Chem. Soc."},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"1306","DOI":"10.1039\/c2cc38627e","article-title":"DNA duplex stabilization in crowded polyanion solutions","volume":"49","author":"Khimji","year":"2013","journal-title":"Chem. Commun."},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1007\/s00249-016-1132-3","article-title":"Differential stability of DNA based on salt concentration","volume":"46","author":"Maity","year":"2017","journal-title":"Eur. Biophys. J."},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"045604","DOI":"10.1088\/1361-6528\/abc037","article-title":"Stabilization of DNA by sodium and magnesium ions during the synthesis of DNA-bridged gold nanoparticles","volume":"32","author":"Sokolov","year":"2020","journal-title":"Nanotechnology"},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1016\/0092-8674(82)90231-8","article-title":"How crowded is the cytoplasm?","volume":"30","author":"Fulton","year":"1982","journal-title":"Cell"},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1146\/annurev.bb.22.060193.000331","article-title":"Macromolecular Crowding: Biochemical, Biophysical, and Physiological Consequences","volume":"22","author":"Zimmerman","year":"1993","journal-title":"Annu. Rev. Biophys. Biomol. Struct."},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"1040","DOI":"10.1016\/j.biochi.2008.02.009","article-title":"Molecular crowding effects on structure and stability of DNA","volume":"90","author":"Miyoshi","year":"2008","journal-title":"Biochimie"},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"53","DOI":"10.3389\/fphy.2014.00053","article-title":"Structures and functions in the crowded nucleus: New biophysical insights","volume":"2","author":"Hancock","year":"2014","journal-title":"Front. Phys."},{"key":"ref_117","doi-asserted-by":"crossref","first-page":"7537","DOI":"10.1021\/acs.jpcb.0c04846","article-title":"Macromolecular Crowding: How Shape and Interactions Affect Diffusion","volume":"124","author":"Vaghefikia","year":"2020","journal-title":"J. Phys. Chem. B"},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1016\/S0968-0004(01)01938-7","article-title":"Macromolecular crowding: Obvious but underappreciated","volume":"26","author":"Ellis","year":"2001","journal-title":"Trends Biochem. Sci."},{"key":"ref_119","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1016\/S0959-440X(00)00172-X","article-title":"Macromolecular crowding: An important but neglected aspect of the intracellular environment","volume":"11","author":"Ellis","year":"2001","journal-title":"Curr. Opin. Struct. Biol."},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"13107","DOI":"10.1021\/jp402922q","article-title":"Force-Induced Unzipping Transitions in an Athermal Crowded Environment","volume":"117","author":"Pincus","year":"2013","journal-title":"J. Phys. Chem. B"},{"key":"ref_121","doi-asserted-by":"crossref","first-page":"2733","DOI":"10.1021\/cr400113m","article-title":"Effects of Molecular Crowding on the Structures, Interactions, and Functions of Nucleic Acids","volume":"114","author":"Nakano","year":"2014","journal-title":"Chem. Rev."},{"key":"ref_122","doi-asserted-by":"crossref","first-page":"19452","DOI":"10.1039\/C7CP03624H","article-title":"DNA melting in the presence of molecular crowders","volume":"19","author":"Singh","year":"2017","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1016\/j.bpc.2006.07.013","article-title":"Enthalpies of {DNA} melting in the presence of osmolytes","volume":"126","author":"Spink","year":"2007","journal-title":"Biophys. Chem."},{"key":"ref_124","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1093\/nar\/gkp884","article-title":"Understanding how the crowded interior of cells stabilizes DNA\/DNA and DNA\/RNA hybrids\u2013in silico predictions and in vitro evidence","volume":"38","author":"Harve","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"ref_125","doi-asserted-by":"crossref","first-page":"14330","DOI":"10.1021\/ja0463029","article-title":"The Effect of Molecular Crowding with Nucleotide Length and Cosolute Structure on DNA Duplex Stability","volume":"126","author":"Nakano","year":"2004","journal-title":"J. Am. Chem. Soc."},{"key":"ref_126","doi-asserted-by":"crossref","first-page":"4782","DOI":"10.1093\/nar\/gkab264","article-title":"Water structure around a left-handed Z-DNA fragment analyzed by cryo neutron crystallography","volume":"49","author":"Harp","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_127","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1021\/bi9820154","article-title":"Effects of Hydration, Ion Release, and Excluded Volume on the Melting of Triplex and Duplex DNA","volume":"38","author":"Spink","year":"1999","journal-title":"Biochemistry"},{"key":"ref_128","doi-asserted-by":"crossref","first-page":"12887","DOI":"10.1021\/ja00156a038","article-title":"Selective Stabilization of Triplex DNA by Poly(ethylene glycols)","volume":"117","author":"Spink","year":"1995","journal-title":"J. Am. Chem. Soc."},{"key":"ref_129","doi-asserted-by":"crossref","first-page":"1987","DOI":"10.1246\/bcsj.80.1987","article-title":"Effects of Polyethylene Glycol on DNA Duplex Stability at Different NaCl Concentrations","volume":"80","author":"Karimata","year":"2007","journal-title":"Bull. Chem. Soc. Jpn."},{"key":"ref_130","doi-asserted-by":"crossref","first-page":"963","DOI":"10.1021\/jp308402v","article-title":"Thermodynamics-Hydration Relationships within Loops That Affect G-Quadruplexes under Molecular Crowding Conditions","volume":"117","author":"Fujimoto","year":"2013","journal-title":"J. Phys. Chem. B"},{"key":"ref_131","doi-asserted-by":"crossref","first-page":"11969","DOI":"10.1021\/acs.jpcb.5b03787","article-title":"Stabilization of DNA Structures with Poly(ethylene sodium phosphate)","volume":"119","author":"Moriyama","year":"2015","journal-title":"J. Phys. Chem. B"},{"key":"ref_132","doi-asserted-by":"crossref","first-page":"10246","DOI":"10.1021\/la048434l","article-title":"Effect of Macromolecular Crowding on DNA:Au Nanoparticle Bioconjugate Assembly","volume":"20","author":"Goodrich","year":"2004","journal-title":"Langmuir"},{"key":"ref_133","doi-asserted-by":"crossref","first-page":"14194","DOI":"10.1073\/pnas.1920886117","article-title":"Nearest-neighbor parameters for predicting DNA duplex stability in diverse molecular crowding conditions","volume":"117","author":"Ghosh","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_134","doi-asserted-by":"crossref","first-page":"2873","DOI":"10.1016\/j.bpj.2022.07.003","article-title":"Evaluation of weak interactions of proteins and organic cations with DNA duplex structures","volume":"121","author":"Morimoto","year":"2022","journal-title":"Biophys. J."},{"key":"ref_135","doi-asserted-by":"crossref","first-page":"031919","DOI":"10.1103\/PhysRevE.81.031919","article-title":"Generalized fundamental measure theory for atomistic modeling of macromolecular crowding","volume":"81","author":"Qin","year":"2010","journal-title":"Phys. Rev. E"},{"key":"ref_136","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1016\/j.bpj.2009.10.009","article-title":"Dependence of Protein Folding Stability and Dynamics on the Density and Composition of Macromolecular Crowders","volume":"98","author":"Mittal","year":"2010","journal-title":"Biophys. J."},{"key":"ref_137","doi-asserted-by":"crossref","first-page":"3491","DOI":"10.1039\/b924236h","article-title":"Macromolecular crowding induces polypeptide compaction and decreases folding cooperativity","volume":"12","author":"Tsao","year":"2010","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1002\/prot.22425","article-title":"Nonadditive effects of mixed crowding on protein stability","volume":"77","author":"Batra","year":"2009","journal-title":"Proteins Struct. Funct. Bioinform."},{"key":"ref_139","doi-asserted-by":"crossref","first-page":"051801","DOI":"10.1103\/PhysRevE.79.051801","article-title":"Effects of molecular crowding on stretching of polymers in poor solvent","volume":"79","author":"Singh","year":"2009","journal-title":"Phys. Rev. E"},{"key":"ref_140","doi-asserted-by":"crossref","first-page":"2156","DOI":"10.1110\/ps.037325.108","article-title":"The effects of macromolecular crowding on the mechanical stability of protein molecules","volume":"17","author":"Yuan","year":"2008","journal-title":"Protein Sci."},{"key":"ref_141","doi-asserted-by":"crossref","first-page":"4595","DOI":"10.1039\/c0sm01110j","article-title":"Stretching single stranded DNA","volume":"7","author":"Kumar","year":"2011","journal-title":"Soft Matter"},{"key":"ref_142","doi-asserted-by":"crossref","first-page":"9905","DOI":"10.1021\/jp104121q","article-title":"Molecular Thermodynamic Model for DNA Melting in Ionic and Crowded Solutions","volume":"114","author":"Liu","year":"2010","journal-title":"J. Phys. Chem. B"},{"key":"ref_143","doi-asserted-by":"crossref","first-page":"15400","DOI":"10.1039\/c2cp42138k","article-title":"Crowding effect on DNA melting: A molecular thermodynamic model with explicit solvent","volume":"14","author":"Liu","year":"2012","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"108101","DOI":"10.1103\/PhysRevLett.111.108101","article-title":"Intracellular Facilitated Diffusion: Searchers, Crowders, and Blockers","volume":"111","author":"Brackley","year":"2013","journal-title":"Phys. Rev. Lett."},{"key":"ref_145","doi-asserted-by":"crossref","first-page":"10726","DOI":"10.1093\/nar\/gkaa854","article-title":"Understanding DNA interactions in crowded environments with a coarse-grained model","volume":"48","author":"Hong","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref_146","doi-asserted-by":"crossref","first-page":"12566","DOI":"10.1039\/C9CP01098J","article-title":"DNA size in confined environments","volume":"21","author":"Zoli","year":"2019","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_147","doi-asserted-by":"crossref","first-page":"23090","DOI":"10.3390\/ijms151223090","article-title":"What Macromolecular Crowding Can Do to a Protein","volume":"15","author":"Kuznetsova","year":"2014","journal-title":"Int. J. Mol. Sci."},{"key":"ref_148","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/S0006-3495(00)76576-3","article-title":"Effect of a Concentrated \u201cInert\u201d Macromolecular Cosolute on the Stability of a Globular Protein with Respect to Denaturation by Heat and by Chaotropes: A Statistical-Thermodynamic Model","volume":"78","author":"Minton","year":"2000","journal-title":"Biophys. J."},{"key":"ref_149","doi-asserted-by":"crossref","first-page":"044911","DOI":"10.1063\/1.4891219","article-title":"Denaturation and renaturation behaviors of short DNA in a confined space","volume":"141","author":"Li","year":"2014","journal-title":"J. Chem. Phys."},{"key":"ref_150","doi-asserted-by":"crossref","first-page":"28001","DOI":"10.1209\/0295-5075\/118\/28001","article-title":"Statistical mechanics of a polymer chain attached to the interface of a cone-shaped channel","volume":"118","author":"Kumar","year":"2017","journal-title":"EPL Europhys. Lett."},{"key":"ref_151","doi-asserted-by":"crossref","first-page":"128103","DOI":"10.1103\/PhysRevLett.88.128103","article-title":"Confinement-Induced Entropic Recoil of Single DNA Molecules in a Nanofluidic Structure","volume":"88","author":"Turner","year":"2002","journal-title":"Phys. Rev. Lett."},{"key":"ref_152","doi-asserted-by":"crossref","first-page":"8394","DOI":"10.1021\/acsnano.6b03159","article-title":"DNA Translocation through Nanopores at Physiological Ionic Strengths Requires Precise Nanoscale Engineering","volume":"10","author":"Franceschini","year":"2016","journal-title":"ACS Nano"},{"key":"ref_153","doi-asserted-by":"crossref","first-page":"1615","DOI":"10.1038\/ncomms2620","article-title":"Impact of macromolecular crowding on DNA replication","volume":"4","author":"Akabayov","year":"2013","journal-title":"Nat. Commun."},{"key":"ref_154","doi-asserted-by":"crossref","first-page":"5898","DOI":"10.1039\/c0sm01517b","article-title":"Biopolymers in nanopores: Challenges and opportunities","volume":"7","author":"Kumar","year":"2011","journal-title":"Soft Matter"},{"key":"ref_155","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1007\/s11033-018-4174-z","article-title":"Thermal stability and conformation of DNA and proteins under the confined condition in the matrix of hydrogels","volume":"45","author":"Nakano","year":"2018","journal-title":"Mol. Biol. Rep."},{"key":"ref_156","doi-asserted-by":"crossref","first-page":"28002","DOI":"10.1209\/0295-5075\/130\/28002","article-title":"Stretching DNA in hard-wall potential channels","volume":"130","author":"Zoli","year":"2020","journal-title":"EPL Europhys. Lett."},{"key":"ref_157","doi-asserted-by":"crossref","first-page":"16060","DOI":"10.1073\/pnas.1001831107","article-title":"Nanopore DNA sequencing with MspA","volume":"107","author":"Derrington","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_158","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1016\/j.cplett.2005.05.129","article-title":"Dynamics of DNA Encapsulated in a Hydrophobic Nanotube","volume":"412","author":"Lau","year":"2005","journal-title":"Chem. Phys. Lett."},{"key":"ref_159","doi-asserted-by":"crossref","first-page":"034901","DOI":"10.1063\/1.4773302","article-title":"Translocation and encapsulation of siRNA inside carbon nanotubes","volume":"138","author":"Mogurampelly","year":"2013","journal-title":"J. Chem. Phys."},{"key":"ref_160","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1016\/j.plrev.2012.05.010","article-title":"Nanopores: A journey towards DNA sequencing","volume":"9","author":"Wanunu","year":"2012","journal-title":"Phys. Life Rev."},{"key":"ref_161","doi-asserted-by":"crossref","first-page":"1722","DOI":"10.1021\/nl300372a","article-title":"Electronic Barcoding of a Viral Gene at the Single-Molecule Level","volume":"12","author":"Singer","year":"2012","journal-title":"Nano Lett."},{"key":"ref_162","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1038\/nnano.2016.50","article-title":"Digitally encoded DNA nanostructures for multiplexed, single-molecule protein sensing with nanopores","volume":"11","author":"Bell","year":"2016","journal-title":"Nat. Nanotechnol."},{"key":"ref_163","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1038\/s41467-017-00423-9","article-title":"Asymmetric dynamics of DNA entering and exiting a strongly confining nanopore","volume":"8","author":"Bell","year":"2017","journal-title":"Nat. Commun."},{"key":"ref_164","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1007\/s00232-010-9328-4","article-title":"DNA Strands Attached Inside Single Conical Nanopores: Ionic Pore Characteristics and Insight into DNA Biophysics","volume":"239","author":"Nguyen","year":"2011","journal-title":"J Membr. Biol."},{"key":"ref_165","doi-asserted-by":"crossref","first-page":"1191","DOI":"10.1021\/acsmacrolett.1c00470","article-title":"Diffusion of Short Semiflexible DNA Polymer Chains in Strong and Moderate Confinement","volume":"10","author":"Morrin","year":"2021","journal-title":"ACS Macro Lett."},{"key":"ref_166","doi-asserted-by":"crossref","first-page":"10042","DOI":"10.1021\/jacs.0c01978","article-title":"Duplex DNA Is Weakened in Nanoconfinement","volume":"142","author":"Jonchhe","year":"2020","journal-title":"J. Am. Chem. Soc."},{"key":"ref_167","first-page":"1476","article-title":"Polymers for gene delivery across length scales","volume":"5","year":"2006","journal-title":"Nat. Mater."},{"key":"ref_168","doi-asserted-by":"crossref","first-page":"1309","DOI":"10.1021\/bp0400240","article-title":"DNA Microarrays: Experimental Issues, Data Analysis, and Application to Bacterial Systems","volume":"20","author":"Dharmadi","year":"2004","journal-title":"Biotechnol. Prog."},{"key":"ref_169","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1038\/35020524","article-title":"A DNA-fuelled molecular machine made of DNA","volume":"406","author":"Yurke","year":"2000","journal-title":"Nature"},{"key":"ref_170","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1021\/bp050422i","article-title":"Compaction Agent Protection of Nucleic Acids during Mechanical Lysis","volume":"22","author":"Murphy","year":"2006","journal-title":"Biotechnol. Prog."},{"key":"ref_171","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1016\/S0169-409X(01)00110-7","article-title":"Cationic lipid\u2013DNA complexes in gene delivery: From biophysics to biological applications","volume":"47","author":"Pires","year":"2001","journal-title":"Adv. Drug Deliv. Rev."},{"key":"ref_172","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1021\/bc034159n","article-title":"Cross-Linked Microparticles as Carriers for the Delivery of Plasmid DNA for Vaccine Development","volume":"15","author":"Goh","year":"2004","journal-title":"Bioconjugate Chem."},{"key":"ref_173","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1016\/j.jconrel.2009.02.004","article-title":"Fibrin hydrogels for non-viral vector delivery in vitro","volume":"136","author":"Shikanov","year":"2009","journal-title":"J. Control. Release"},{"key":"ref_174","doi-asserted-by":"crossref","first-page":"2884","DOI":"10.1039\/c2sm07029d","article-title":"DNA encapsulation via nanotemplates from cationic block copolymer micelles","volume":"8","author":"Haladjova","year":"2012","journal-title":"Soft Matter"},{"key":"ref_175","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1021\/bm049577p","article-title":"PLGA:Poloxamer and PLGA:Poloxamine Blend Nanoparticles: New Carriers for Gene Delivery","volume":"6","author":"Csaba","year":"2005","journal-title":"Biomacromolecules"},{"key":"ref_176","doi-asserted-by":"crossref","first-page":"8002","DOI":"10.1039\/c1sm05805c","article-title":"A mild and versatile approach for DNA encapsulation","volume":"7","author":"Dimitrov","year":"2011","journal-title":"Soft Matter"},{"key":"ref_177","doi-asserted-by":"crossref","first-page":"16735","DOI":"10.1021\/ja105809e","article-title":"DNA Core@Inorganic Shell","volume":"132","author":"Park","year":"2010","journal-title":"J. Am. Chem. Soc."},{"key":"ref_178","doi-asserted-by":"crossref","first-page":"225103","DOI":"10.1063\/1.4881422","article-title":"Endohedral confinement of a DNA dodecamer onto pristine carbon nanotubes and the stability of the canonical B form","volume":"140","author":"Cruz","year":"2014","journal-title":"J. Chem. Phys."},{"key":"ref_179","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.bej.2015.04.027","article-title":"Nanoscopic Characterization of DNA within Hydrophobic Pores: Thermodynamics and Kinetics","volume":"104","author":"Cruz","year":"2015","journal-title":"Biochem. Eng. J."},{"key":"ref_180","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1007\/s00249-020-01462-9","article-title":"Melting of DNA in confined geometries","volume":"49","author":"Maity","year":"2020","journal-title":"Eur. Biophys. J."},{"key":"ref_181","doi-asserted-by":"crossref","unstructured":"Maity, A., Mathur, N., Imhof, P., and Singh, N. (2022). Structural Analysis of DNA molecule in a confined shell. arXiv.","DOI":"10.1016\/j.physa.2022.128382"},{"key":"ref_182","doi-asserted-by":"crossref","first-page":"106601","DOI":"10.1088\/0034-4885\/75\/10\/106601","article-title":"DNA confinement in nanochannels: Physics and biological applications","volume":"75","author":"Reisner","year":"2012","journal-title":"Rep. Prog. Phys."},{"key":"ref_183","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1016\/S0022-2836(66)80037-2","article-title":"A denaturation map of the lambda phage DNA molecule determined by electron microscopy","volume":"18","author":"Inman","year":"1966","journal-title":"J. Mol. Biol."},{"key":"ref_184","doi-asserted-by":"crossref","first-page":"13294","DOI":"10.1073\/pnas.1007081107","article-title":"Single-molecule denaturation mapping of DNA in nanofluidic channels","volume":"107","author":"Reisner","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_185","doi-asserted-by":"crossref","first-page":"28001","DOI":"10.1209\/0295-5075\/127\/28001","article-title":"Stability of DNA passing through different geometrical pores","volume":"127","author":"Maity","year":"2019","journal-title":"EPL Europhys. Lett."},{"key":"ref_186","doi-asserted-by":"crossref","first-page":"2045","DOI":"10.1038\/s41598-018-27517-8","article-title":"Conic shapes have higher sensitivity than cylindrical ones in nanopore DNA sequencing","volume":"8","author":"Tu","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_187","doi-asserted-by":"crossref","first-page":"1146","DOI":"10.1038\/nbt.1495","article-title":"The potential and challenges of nanopore sequencing","volume":"26","author":"Ranton","year":"2008","journal-title":"Nat. Biotechnol."},{"key":"ref_188","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1038\/nbt.2171","article-title":"Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase","volume":"30","author":"Elizabeth","year":"2012","journal-title":"Nat. Biotechnol."},{"key":"ref_189","doi-asserted-by":"crossref","first-page":"684","DOI":"10.1038\/srep00684","article-title":"PEG-Labeled Nucleotides and Nanopore Detection for Single Molecule DNA Sequencing by Synthesis","volume":"2","author":"Kumar","year":"2012","journal-title":"Sci. Rep."},{"key":"ref_190","doi-asserted-by":"crossref","first-page":"5233","DOI":"10.1073\/pnas.1601782113","article-title":"Real-time single-molecule electronic DNA sequencing by synthesis using polymer-tagged nucleotides on a nanopore array","volume":"113","author":"Fuller","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_191","doi-asserted-by":"crossref","first-page":"3227","DOI":"10.1016\/S0006-3495(99)77153-5","article-title":"Microsecond Time-Scale Discrimination Among Polycytidylic Acid, Polyadenylic Acid, and Polyuridylic Acid as Homopolymers or as Segments Within Single RNA Molecules","volume":"77","author":"Akeson","year":"1999","journal-title":"Biophys. J."},{"key":"ref_192","doi-asserted-by":"crossref","first-page":"081104","DOI":"10.1063\/1.4894401","article-title":"Communication: Charge, diffusion, and mobility of proteins through nanopores","volume":"141","author":"Muthukumar","year":"2014","journal-title":"J. Chem. Phys."},{"key":"ref_193","doi-asserted-by":"crossref","first-page":"195101","DOI":"10.1063\/1.3429882","article-title":"Theory of capture rate in polymer translocation","volume":"132","author":"Muthukumar","year":"2010","journal-title":"J. Chem. Phys."},{"key":"ref_194","doi-asserted-by":"crossref","first-page":"044001","DOI":"10.1088\/0957-4484\/26\/4\/044001","article-title":"The effects of geometry and stability of solid-state nanopores on detecting single DNA molecules","volume":"26","author":"Rollings","year":"2015","journal-title":"Nanotechnology"},{"key":"ref_195","doi-asserted-by":"crossref","unstructured":"(2011). Venkatesan, Bala Murali; Bashir, Rashid Nanopore sensors for nucleic acid analysis. Nat. Nanotechnol., 6, 1\u201333.","DOI":"10.1007\/978-1-4419-8252-0_1"},{"key":"ref_196","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1016\/j.copbio.2010.05.002","article-title":"Applications of biological pores in nanomedicine, sensing, and nanoelectronics","volume":"21","author":"Majd","year":"2010","journal-title":"Curr. Opin. Biotechnol."},{"key":"ref_197","doi-asserted-by":"crossref","first-page":"3163","DOI":"10.1021\/nl102069z","article-title":"DNA Translocation through Graphene Nanopores","volume":"10","author":"Schneider","year":"2010","journal-title":"Nano Lett."},{"key":"ref_198","doi-asserted-by":"crossref","first-page":"2915","DOI":"10.1021\/nl101046t","article-title":"DNA Translocation through Graphene Nanopores","volume":"10","author":"Merchant","year":"2010","journal-title":"Nano Lett."},{"key":"ref_199","doi-asserted-by":"crossref","first-page":"1098","DOI":"10.1529\/biophysj.105.070672","article-title":"The Electromechanics of DNA in a Synthetic Nanopore","volume":"90","author":"Heng","year":"2006","journal-title":"Biophys. J."},{"key":"ref_200","doi-asserted-by":"crossref","first-page":"3057","DOI":"10.1103\/PhysRevLett.85.3057","article-title":"Driven DNA Transport into an Asymmetric Nanometer-Scale Pore","volume":"85","author":"Henrickson","year":"2000","journal-title":"Phys. Rev. Lett."},{"key":"ref_201","doi-asserted-by":"crossref","first-page":"135101","DOI":"10.1063\/1.3328875","article-title":"Probing single nanometer-scale pores with polymeric molecular rulers","volume":"132","author":"Henrickson","year":"2010","journal-title":"J. Chem. Phys."},{"key":"ref_202","doi-asserted-by":"crossref","first-page":"13770","DOI":"10.1073\/pnas.93.24.13770","article-title":"Characterization of individual polynucleotide molecules using a membrane channel","volume":"93","author":"Kasianowicz","year":"1996","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_203","doi-asserted-by":"crossref","first-page":"074002","DOI":"10.1088\/0957-4484\/26\/7\/074002","article-title":"Detection of benzo[a]pyrene-guanine adducts in single-stranded DNA using the \u03b1-hemolysin nanopore","volume":"26","author":"Perera","year":"2015","journal-title":"Nanotechnology"},{"key":"ref_204","doi-asserted-by":"crossref","first-page":"11410","DOI":"10.1039\/c2cc36366f","article-title":"Modulation of the current signatures of DNA abasic site adducts in the [small alpha]-hemolysin ion channel","volume":"48","author":"An","year":"2012","journal-title":"Chem. Commun."},{"key":"ref_205","doi-asserted-by":"crossref","first-page":"4296","DOI":"10.1021\/acsnano.5b00722","article-title":"Nanopore Detection of 8-Oxoguanine in the Human Telomere Repeat Sequence","volume":"9","author":"An","year":"2015","journal-title":"ACS Nano"},{"key":"ref_206","first-page":"1","article-title":"Solid-State Nanopore-Based DNA Sequencing Technology","volume":"13","author":"Liu","year":"2016","journal-title":"J. Nanomater."},{"key":"ref_207","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1002\/sca.21003","article-title":"Direct and Transmission Milling of Suspended Silicon Nitride Membranes With a Focused Helium Ion Beam","volume":"34","author":"Marshall","year":"2012","journal-title":"Scanning"},{"key":"ref_208","doi-asserted-by":"crossref","first-page":"1266","DOI":"10.1002\/adfm.200902128","article-title":"DNA Sensing Using Nanocrystalline Surface-Enhanced Al2O3 Nanopore Sensors","volume":"20","author":"Venkatesan","year":"2010","journal-title":"Adv. Funct. Mater."},{"key":"ref_209","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1021\/nl9029237","article-title":"Rapid Sequencing of Individual DNA Molecules in Graphene Nanogaps","volume":"10","author":"Postma","year":"2010","journal-title":"Nano Lett."},{"key":"ref_210","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1021\/nl202870y","article-title":"DNA Base-Specific Modulation of Microampere Transverse Edge Currents through a Metallic Graphene Nanoribbon with a Nanopore","volume":"12","author":"Saha","year":"2012","journal-title":"Nano Lett."},{"key":"ref_211","doi-asserted-by":"crossref","first-page":"2533","DOI":"10.1021\/nn900441x","article-title":"Discrimination of Single Base Substitutions in a DNA Strand Immobilized in a Biological Nanopore","volume":"3","author":"Purnell","year":"2009","journal-title":"ACS Nano"},{"key":"ref_212","doi-asserted-by":"crossref","first-page":"1079","DOI":"10.1073\/pnas.97.3.1079","article-title":"Rapid nanopore discrimination between single polynucleotide molecules","volume":"97","author":"Meller","year":"2000","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_213","doi-asserted-by":"crossref","unstructured":"Kwok, H., Briggs, K., and Tabard-Cossa, V. (2014). Nanopore Fabrication by Controlled Dielectric Breakdown. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0092880"},{"key":"ref_214","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1038\/nature09379","article-title":"Graphene as a subnanometre trans-electrode membrane","volume":"467","author":"Garaj","year":"2010","journal-title":"Nature"},{"key":"ref_215","doi-asserted-by":"crossref","first-page":"11812","DOI":"10.1021\/acsnano.5b03923","article-title":"Characterization of Interstrand DNA\u2013DNA Cross-Links Using the \u03b1-Hemolysin Protein Nanopore","volume":"9","author":"Zhang","year":"2015","journal-title":"ACS Nano"},{"key":"ref_216","doi-asserted-by":"crossref","first-page":"1859","DOI":"10.1126\/science.274.5294.1859","article-title":"Structure of Staphylococcal \u03b1-Hemolysin, a Heptameric Transmembrane Pore","volume":"274","author":"Song","year":"1996","journal-title":"Science"},{"key":"ref_217","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1021\/ar000138m","article-title":"Characterization of Nucleic Acids by Nanopore Analysis","volume":"35","author":"Deamer","year":"2002","journal-title":"Accounts Chem. Res."},{"key":"ref_218","doi-asserted-by":"crossref","first-page":"3205","DOI":"10.1529\/biophysj.104.047274","article-title":"Nanopore Unzipping of Individual DNA Hairpin Molecules","volume":"87","author":"Visram","year":"2004","journal-title":"Biophys. J."},{"key":"ref_219","doi-asserted-by":"crossref","first-page":"3539","DOI":"10.1039\/C7CC00060J","article-title":"Characterization of DNA duplex unzipping through a sub-2 nm solid-state nanopore","volume":"53","author":"Lin","year":"2017","journal-title":"Chem. Commun."}],"container-title":["Entropy"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1099-4300\/24\/11\/1587\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T01:08:54Z","timestamp":1760144934000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1099-4300\/24\/11\/1587"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,11,1]]},"references-count":219,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2022,11]]}},"alternative-id":["e24111587"],"URL":"https:\/\/doi.org\/10.3390\/e24111587","relation":{},"ISSN":["1099-4300"],"issn-type":[{"value":"1099-4300","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,11,1]]}}}