{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T21:44:39Z","timestamp":1784238279085,"version":"3.55.0"},"reference-count":65,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2025,6,30]],"date-time":"2025-06-30T00:00:00Z","timestamp":1751241600000},"content-version":"vor","delay-in-days":10,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100009122","name":"Ministry of Education","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009122","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["(21K05283"],"award-info":[{"award-number":["(21K05283"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["24K01631"],"award-info":[{"award-number":["24K01631"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["22H04975"],"award-info":[{"award-number":["22H04975"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["JPJSCCA20220005"],"award-info":[{"award-number":["JPJSCCA20220005"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["120233509"],"award-info":[{"award-number":["120233509"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Konan New Century Strategic Research Project"},{"DOI":"10.13039\/100007684","name":"Asahi Glass Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007684","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Chubei Itoh Foundation"},{"name":"CERIC-ERIC consortium","award":["20227082"],"award-info":[{"award-number":["20227082"]}]},{"DOI":"10.13039\/501100004329","name":"Slovenian Research and Innovation Agency","doi-asserted-by":"crossref","award":["P1-0242"],"award-info":[{"award-number":["P1-0242"]}],"id":[{"id":"10.13039\/501100004329","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100004329","name":"Slovenian Research and Innovation Agency","doi-asserted-by":"crossref","award":["J1-60019"],"award-info":[{"award-number":["J1-60019"]}],"id":[{"id":"10.13039\/501100004329","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,6,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Intercalated motif (i-motif) tetraplex DNA plays a crucial role in gene expression and diseases. However, due to the limited number of i-motif binding proteins in human cells, the chemical mechanisms regulating i-motifs within cell remain currently unknown. Thus, molecular environment should have a main factor to control i-motif formation and functions in cells. Here, we systematically investigated the stability and functions of i-motif DNAs by using various polyethylene glycols (PEGs) and oligoethylene glycols (OEGs) that mimicked diverse cellular crowding environments. We found that the human telomere i-motif was significantly stabilized by PEGs and OEGs having six or more ethylene glycol units, whereas it was destabilized by those having less than six units. As these stabilization effects coincided with the drastic changes in hypochromicity by i-motif helixes, we quantitatively validated these effects through changes in solution properties and by assessing the twisting of the tetraplex structure using nuclear magnetic resonance (NMR) and molecular dynamics simulations. Furthermore, cosolute-induced twisting dynamics controlled by different cosolutes changed the activation energy barrier of replication by a twofold magnitude along the i-motif-forming DNAs. Our findings indicate that regulatory mechanisms underlying the biological roles of i-motifs across different cellular phases may exist by molecular environments.<\/jats:p>","DOI":"10.1093\/nar\/gkaf500","type":"journal-article","created":{"date-parts":[[2025,6,30]],"date-time":"2025-06-30T10:31:17Z","timestamp":1751279477000},"source":"Crossref","is-referenced-by-count":7,"title":["Twisting tetraplex DNA: A strand dynamics regulating i-motif function in diverse molecular crowding environments"],"prefix":"10.1093","volume":"53","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7569-1761","authenticated-orcid":false,"given":"Shuntaro","family":"Takahashi","sequence":"first","affiliation":[{"name":"FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University , 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047 ,","place":["Japan"]},{"name":"FIRST (Graduate School of Frontiers of Innovative Research in Science and Technology), Konan University , 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saptarshi","family":"Ghosh","sequence":"additional","affiliation":[{"name":"FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University , 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marko","family":"Trajkovski","sequence":"additional","affiliation":[{"name":"National Institute of Chemistry Slovenian NMR Centre, , Hajdrihova 19, SI-1000 Ljubljana ,","place":["Slovenia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tatsuya","family":"Ohyama","sequence":"additional","affiliation":[{"name":"FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University , 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1570-8602","authenticated-orcid":false,"given":"Janez","family":"Plavec","sequence":"additional","affiliation":[{"name":"National Institute of Chemistry Slovenian NMR Centre, , Hajdrihova 19, SI-1000 Ljubljana ,","place":["Slovenia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naoki","family":"Sugimoto","sequence":"additional","affiliation":[{"name":"FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University , 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,6,30]]},"reference":[{"key":"2025063006311255000_B1","doi-asserted-by":"publisher","first-page":"8627","DOI":"10.1093\/nar\/gkv862","article-title":"G-quadruplexes and their regulatory roles in biology","volume":"43","author":"Rhodes","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2025063006311255000_B2","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1016\/j.trechm.2019.07.002","article-title":"The Structure and Function of DNA G-Quadruplexes","volume":"2","author":"Spiegel","year":"2020","journal-title":"Trends Chem"},{"key":"2025063006311255000_B3","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1038\/s42003-018-0237-x","article-title":"Z-DNA and Z-RNA in human disease","volume":"2","author":"Herbert","year":"2019","journal-title":"Commun Biol"},{"key":"2025063006311255000_B4","doi-asserted-by":"publisher","first-page":"459","DOI":"10.1038\/s41580-020-0236-x","article-title":"The regulation and functions of DNA and RNA G-quadruplexes","volume":"21","author":"Varshney","year":"2020","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2025063006311255000_B5","doi-asserted-by":"publisher","first-page":"10450","DOI":"10.1073\/pnas.88.23.10450","article-title":"A triplex DNA-binding protein from human cells: purification and characterization","volume":"88","author":"Kiyama","year":"1991","journal-title":"Proc Natl Acad Sci USA"},{"key":"2025063006311255000_B6","doi-asserted-by":"publisher","first-page":"631","DOI":"10.1038\/s41557-018-0046-3","article-title":"I-Motif DNA structures are formed in the nuclei of human cells","volume":"10","author":"Zeraati","year":"2018","journal-title":"Nat Chem"},{"key":"2025063006311255000_B7","doi-asserted-by":"publisher","first-page":"2165","DOI":"10.1002\/anie.201712284","article-title":"Evaluation of the stability of DNA i-motifs in the nuclei of living mammalian cells","volume":"57","author":"Dzatko","year":"2018","journal-title":"Angew Chem Int Ed"},{"key":"2025063006311255000_B8","doi-asserted-by":"publisher","first-page":"20600","DOI":"10.1021\/jacs.0c11708","article-title":"DNA G-quadruplex and i-motif structure formation is interdependent in human cells","volume":"142","author":"King","year":"2020","journal-title":"J Am Chem Soc"},{"key":"2025063006311255000_B9","doi-asserted-by":"publisher","first-page":"8038","DOI":"10.1093\/nar\/gky735","article-title":"i-Motif DNA: structural features and significance to cell biology","volume":"46","author":"Abou","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2025063006311255000_B10","doi-asserted-by":"publisher","first-page":"9630","DOI":"10.1021\/acsomega.8b01551","article-title":"Rapid screen of potential i-motif forming sequences in DNA repair gene promoters","volume":"3","author":"Rogers","year":"2018","journal-title":"ACS Omega"},{"key":"2025063006311255000_B11","doi-asserted-by":"publisher","first-page":"1624","DOI":"10.1093\/nar\/gky035","article-title":"i-Motif of cytosine-rich human telomere DNA fragments containing natural base lesions","volume":"46","author":"Dvorakova","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2025063006311255000_B12","doi-asserted-by":"publisher","first-page":"9605","DOI":"10.1073\/pnas.1704258114","article-title":"Topological impact of noncanonical DNA structures on Klenow fragment of DNA polymerase","volume":"114","author":"Takahashi","year":"2017","journal-title":"Proc Natl Acad Sci USA"},{"key":"2025063006311255000_B13","doi-asserted-by":"publisher","first-page":"4161","DOI":"10.1021\/ja410934b","article-title":"The dynamic character of the BCL2 promoter i-motif provides a mechanism for modulation of gene expression by compounds that bind selectively to the alternative DNA hairpin structure","volume":"136","author":"Kendrick","year":"2014","journal-title":"J Am Chem Soc"},{"key":"2025063006311255000_B14","doi-asserted-by":"publisher","first-page":"18097","DOI":"10.1038\/srep18097","article-title":"GC-elements controlling HRAS transcription form i-motif structures unfolded by heterogeneous ribonucleoprotein particle A1","volume":"5","author":"Miglietta","year":"2015","journal-title":"Sci Rep"},{"key":"2025063006311255000_B15","doi-asserted-by":"publisher","first-page":"1078","DOI":"10.1002\/cbic.201800021","article-title":"Structural characterization of i-motif structure in the human acetyl-CoA carboxylase 1 gene promoters and their role in the regulation of gene expression","volume":"19","author":"Kaulage","year":"2018","journal-title":"ChemBioChem"},{"key":"2025063006311255000_B16","doi-asserted-by":"publisher","first-page":"2504","DOI":"10.1038\/s41598-020-59343-2","article-title":"Preferential targeting cancer-related i-motif DNAs by the plant flavonol fisetin for theranostics applications","volume":"10","author":"Takahashi","year":"2020","journal-title":"Sci Rep"},{"key":"2025063006311255000_B17","doi-asserted-by":"publisher","first-page":"7119","DOI":"10.1038\/s41467-024-50553-0","article-title":"Structural insights into i-motif DNA structures in sequences from the insulin-linked polymorphic region","volume":"15","author":"Guneri","year":"2024","journal-title":"Nat Commun"},{"key":"2025063006311255000_B18","doi-asserted-by":"publisher","first-page":"10395","DOI":"10.1093\/nar\/gkad764","article-title":"Telomeric i-motifs and C-strands inhibit parallel G-quadruplex extension by telomerase","volume":"51","author":"El-Khoury","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025063006311255000_B19","doi-asserted-by":"publisher","first-page":"3445","DOI":"10.1093\/nar\/gkac158","article-title":"i-Motif formation and spontaneous deletions in human cells","volume":"50","author":"Martella","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2025063006311255000_B20","doi-asserted-by":"publisher","first-page":"4172","DOI":"10.1021\/ja4109352","article-title":"The transcriptional complex between the BCL2 i-motif and hnRNP LL is a molecular switch for control of gene expression that can be modulated by small molecules","volume":"136","author":"Kang","year":"2014","journal-title":"J Am Chem Soc"},{"key":"2025063006311255000_B21","doi-asserted-by":"publisher","first-page":"14138","DOI":"10.1021\/jacs.6b09196","article-title":"A mechanosensor mechanism controls the G-quadruplex\/i-motif molecular switch in the MYC promoter NHE III1","volume":"138","author":"Sutherland","year":"2016","journal-title":"J Am Chem Soc"},{"key":"2025063006311255000_B22","doi-asserted-by":"publisher","first-page":"103575","DOI":"10.1016\/j.isci.2021.103575","article-title":"Remodeling the conformational dynamics of I-motif DNA by helicases in ATP-independent mode at acidic environment","volume":"25","author":"Gao","year":"2022","journal-title":"iScience"},{"key":"2025063006311255000_B23","doi-asserted-by":"publisher","first-page":"13530","DOI":"10.1093\/nar\/gkae1001","article-title":"Profiling of i-motif-binding proteins reveals functional roles of nucleolin in regulation of high-order DNA structures","volume":"52","author":"Ban","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2025063006311255000_B24","doi-asserted-by":"publisher","first-page":"10286","DOI":"10.1002\/anie.202016801","article-title":"Thermal and pH stabilities of i-DNA: confronting in vitro experiments with models and in-cell NMR data","volume":"60","author":"Cheng","year":"2021","journal-title":"Angew Chem Int Ed"},{"key":"2025063006311255000_B25","doi-asserted-by":"publisher","first-page":"599","DOI":"10.1016\/0022-2836(91)90499-V","article-title":"Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli","volume":"222","author":"Zimmerman","year":"1991","journal-title":"J Mol Biol"},{"key":"2025063006311255000_B26","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1002\/bip.22163","article-title":"Quantitative assessment of the relative contributions of steric repulsion and chemical interactions to macromolecular crowding","volume":"99","author":"Minton","year":"2013","journal-title":"Biopolymers"},{"key":"2025063006311255000_B27","doi-asserted-by":"publisher","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":"2025063006311255000_B28","doi-asserted-by":"publisher","first-page":"8439","DOI":"10.1039\/D0CS00594K","article-title":"Stability prediction of canonical and non-canonical structures of nucleic acids in various molecular environments and cells","volume":"49","author":"Takahashi","year":"2020","journal-title":"Chem Soc Rev"},{"key":"2025063006311255000_B29","doi-asserted-by":"publisher","first-page":"7792","DOI":"10.1021\/jacs.1c02209","article-title":"Drivers of i-DNA formation in a variety of environments revealed by four-dimensional UV melting and annealing","volume":"143","author":"Cheng","year":"2021","journal-title":"J Am Chem Soc"},{"key":"2025063006311255000_B30","doi-asserted-by":"publisher","first-page":"2586","DOI":"10.1021\/acs.analchem.8b04177","article-title":"Characterization of intracellular crowding environments with topology-based DNA quadruplex sensors","volume":"91","author":"Takahashi","year":"2019","journal-title":"Anal Chem"},{"key":"2025063006311255000_B31","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1038\/nchem.2519","article-title":"Membraneless organelles can melt nucleic acid duplexes and act as biomolecular filters","volume":"8","author":"Nott","year":"2016","journal-title":"Nat Chem"},{"key":"2025063006311255000_B32","doi-asserted-by":"publisher","first-page":"3224","DOI":"10.1002\/anie.201510847","article-title":"RNA hairpin folding in the crowded cell","volume":"55","author":"Gao","year":"2016","journal-title":"Angew Chem Int Ed"},{"key":"2025063006311255000_B33","doi-asserted-by":"publisher","first-page":"1299","DOI":"10.1039\/b922050j","article-title":"Molecular crowding of the cosolutes induces an intramolecular i-motif structure of triplet repeat DNA oligomers at neutral pH","volume":"46","author":"Rajendran","year":"2010","journal-title":"Chem Commun"},{"key":"2025063006311255000_B34","doi-asserted-by":"publisher","first-page":"2229","DOI":"10.1021\/jacs.7b11537","article-title":"Probing the ionic atmosphere and hydration of the c-MYC i-motif","volume":"140","author":"Liu","year":"2018","journal-title":"J Am Chem Soc"},{"key":"2025063006311255000_B35","doi-asserted-by":"publisher","first-page":"8309","DOI":"10.1093\/nar\/gkad626","article-title":"Genome-wide mapping of i-motifs reveals their association with transcription regulation in live human cells","volume":"51","author":"Zanin","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025063006311255000_B36","doi-asserted-by":"publisher","first-page":"7.19.1-7.19.17","DOI":"10.1002\/0471142700.nc0719s53","article-title":"Quantitative analyses of nucleic acid stability under the molecular crowding condition induced by cosolutes","volume":"53","author":"Tateishi-Karimata","year":"2013","journal-title":"Curr Protoc Nucleic Acid Chem"},{"key":"2025063006311255000_B37","doi-asserted-by":"publisher","first-page":"7400","DOI":"10.1021\/acs.analchem.2c01075","article-title":"Volumetric strategy for quantitatively elucidating a local hydration network around a G-quadruplex","volume":"94","author":"Matsumoto","year":"2022","journal-title":"Anal Chem"},{"key":"2025063006311255000_B38","doi-asserted-by":"publisher","first-page":"33052","DOI":"10.1039\/D0RA06502A","article-title":"Molecular crowding induces primer extension by RNA polymerase through base stacking beyond Watson\u2013Crick rules","volume":"10","author":"Takahashi","year":"2020","journal-title":"RSC Adv"},{"key":"2025063006311255000_B39","doi-asserted-by":"publisher","first-page":"1325","DOI":"10.1093\/bioinformatics\/btu830","article-title":"NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy","volume":"31","author":"Lee","year":"2015","journal-title":"Bioinformatics"},{"key":"2025063006311255000_B40","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1006\/jmbi.2000.3613","article-title":"The solution structure and internal motions of a fragment of the cytidine-rich strand of the human telomere","volume":"299","author":"Phan","year":"2000","journal-title":"J Mol Biol"},{"key":"2025063006311255000_B41","doi-asserted-by":"publisher","first-page":"3817","DOI":"10.1529\/biophysj.106.097782","article-title":"Refinement of the AMBER force field for nucleic acids: improving the description of \u03b1\/\u03b3 conformers","volume":"92","author":"P\u00e9rez","year":"2007","journal-title":"Biophys J"},{"key":"2025063006311255000_B42","doi-asserted-by":"publisher","first-page":"1157","DOI":"10.1002\/jcc.20035","article-title":"Development and testing of a general amber force field","volume":"25","author":"Wang","year":"2004","journal-title":"J Comput Chem"},{"key":"2025063006311255000_B43","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1016\/j.jmgm.2005.12.005","article-title":"Automatic atom type and bond type perception in molecular mechanical calculations","volume":"25","author":"Wang","year":"2006","journal-title":"J Mol Graph Model"},{"key":"2025063006311255000_B44","article-title":"Gaussian 09Rev. D.01","author":"Frisch","year":"2016"},{"key":"2025063006311255000_B45","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1186\/1756-0500-5-367","article-title":"ACPYPE\u2014AnteChamber PYthon Parser interfacE","volume":"5","author":"Sousa","year":"2012","journal-title":"BMC Res Notes"},{"key":"2025063006311255000_B46","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","article-title":"GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers","volume":"1\u20132","author":"Abraham","year":"2015","journal-title":"SoftwareX"},{"key":"2025063006311255000_B47","doi-asserted-by":"publisher","first-page":"926","DOI":"10.1063\/1.445869","article-title":"Comparison of simple potential functions for simulating liquid water","volume":"79","author":"Jorgensen","year":"1983","journal-title":"J Chem Phys"},{"key":"2025063006311255000_B48","doi-asserted-by":"publisher","first-page":"12699","DOI":"10.1073\/pnas.1103382108","article-title":"Separation of preferential interaction and excluded volume effects on DNA duplex and hairpin stability","volume":"108","author":"Knowles","year":"2011","journal-title":"Proc Natl Acad Sci USA"},{"key":"2025063006311255000_B49","doi-asserted-by":"publisher","first-page":"2193","DOI":"10.1063\/1.444026","article-title":"Excluded-volume theory of polymer\u2013protein interactions based on polymer chain statistics","volume":"77","author":"Hermans","year":"1982","journal-title":"J Chem Phys"},{"key":"2025063006311255000_B50","doi-asserted-by":"publisher","first-page":"3522","DOI":"10.1021\/ja805972a","article-title":"Hydration of Watson\u2013Crick base pairs and dehydration of Hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions","volume":"131","author":"Miyoshi","year":"2009","journal-title":"J Am Chem Soc"},{"key":"2025063006311255000_B51","doi-asserted-by":"publisher","first-page":"518","DOI":"10.1016\/S0022-2836(62)80106-5","article-title":"The hypochromism of helical polynucleotides","volume":"4","author":"Devoe","year":"1962","journal-title":"J Mol Biol"},{"key":"2025063006311255000_B52","doi-asserted-by":"publisher","first-page":"2268","DOI":"10.1002\/cbic.201800425","article-title":"Analysis of interactions between Telomeric i-motif DNA and a cyclic tetraoxazole compound","volume":"19","author":"Sedghi","year":"2018","journal-title":"ChemBioChem"},{"key":"2025063006311255000_B53","doi-asserted-by":"publisher","first-page":"4101","DOI":"10.1093\/nar\/gkad020","article-title":"Nearest-neighbor parameters for the prediction of RNA duplex stability in diverse in vitro and cellular-like crowding conditions","volume":"51","author":"Ghosh","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025063006311255000_B54","doi-asserted-by":"publisher","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":"2025063006311255000_B55","doi-asserted-by":"publisher","first-page":"1586","DOI":"10.1021\/bi401523b","article-title":"Epigenetic modification, dehydration, and molecular crowding effects on the thermodynamics of i-motif structure formation from C-rich DNA","volume":"53","author":"Bhavsar-Jog","year":"2014","journal-title":"Biochemistry"},{"key":"2025063006311255000_B56","doi-asserted-by":"publisher","first-page":"8887","DOI":"10.1021\/ja00140a001","article-title":"Intramolecular folding of pyrimidine oligodeoxynucleotides into an i-DNA motif","volume":"117","author":"Mergny","year":"1995","journal-title":"J Am Chem Soc"},{"key":"2025063006311255000_B57","doi-asserted-by":"publisher","first-page":"3284","DOI":"10.1093\/nar\/gkz071","article-title":"Validation of the nearest-neighbor model for Watson\u2013Crick self-complementary DNA duplexes in molecular crowding condition","volume":"47","author":"Ghosh","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2025063006311255000_B58","doi-asserted-by":"publisher","first-page":"3658","DOI":"10.1093\/nar\/gkz019","article-title":"Thermodynamic characterization and nearest neighbor parameters for RNA duplexes under molecular crowding conditions","volume":"47","author":"Adams","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2025063006311255000_B59","doi-asserted-by":"publisher","first-page":"14719","DOI":"10.1021\/bi9809425","article-title":"Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson\u2013Crick base pairs","volume":"37","author":"Xia","year":"1998","journal-title":"Biochemistry"},{"key":"2025063006311255000_B60","doi-asserted-by":"publisher","first-page":"7266","DOI":"10.1021\/acs.jpcb.3c03687","article-title":"Base dynamics in the HhaI protein binding site","volume":"127","author":"Pederson","year":"2023","journal-title":"J Phys Chem B"},{"key":"2025063006311255000_B61","doi-asserted-by":"publisher","first-page":"5774","DOI":"10.1021\/jacs.8b01577","article-title":"Recovery of the formation and function of oxidized G-quadruplexes by a pyrene-modified guanine tract","volume":"140","author":"Takahashi","year":"2018","journal-title":"J Am Chem Soc"},{"key":"2025063006311255000_B62","doi-asserted-by":"publisher","first-page":"16458","DOI":"10.1021\/jacs.1c05468","article-title":"Chemical modulation of DNA replication along G-quadruplex based on topology-dependent ligand binding","volume":"143","author":"Takahashi","year":"2021","journal-title":"J Am Chem Soc"},{"key":"2025063006311255000_B63","doi-asserted-by":"publisher","first-page":"10864","DOI":"10.1073\/pnas.0504744102","article-title":"Human POT1 disrupts telomeric G-quadruplexes allowing telomerase extension in vitro","volume":"102","author":"Zaug","year":"2005","journal-title":"Proc Natl Acad Sci USA"},{"key":"2025063006311255000_B64","doi-asserted-by":"publisher","first-page":"910","DOI":"10.15252\/embr.201540607","article-title":"G4-associated human diseases","volume":"16","author":"Maizels","year":"2015","journal-title":"EMBO Rep"},{"key":"2025063006311255000_B65","doi-asserted-by":"publisher","first-page":"101","DOI":"10.21873\/cgp.20171","article-title":"Duplex DNA from sites of helicase-polymerase uncoupling links non-B DNA structure formation to replicative stress","volume":"17","author":"Amparo","year":"2020","journal-title":"Cancer Genomics Proteomics"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/53\/12\/gkaf500\/63626080\/gkaf500.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/53\/12\/gkaf500\/63626080\/gkaf500.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,30]],"date-time":"2025-06-30T10:31:18Z","timestamp":1751279478000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/doi\/10.1093\/nar\/gkaf500\/8178390"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,6,20]]},"references-count":65,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2025,6,20]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkaf500","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,7,8]]},"published":{"date-parts":[[2025,6,20]]},"article-number":"gkaf500"}}