{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,19]],"date-time":"2025-10-19T05:56:29Z","timestamp":1760853389565},"reference-count":53,"publisher":"Elsevier BV","issue":"5","license":[{"start":{"date-parts":[[2001,5,1]],"date-time":"2001-05-01T00:00:00Z","timestamp":988675200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2013,7,16]],"date-time":"2013-07-16T00:00:00Z","timestamp":1373932800000},"content-version":"vor","delay-in-days":4459,"URL":"https:\/\/www.elsevier.com\/open-access\/userlicense\/1.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biophysical Journal"],"published-print":{"date-parts":[[2001,5]]},"DOI":"10.1016\/s0006-3495(01)76205-4","type":"journal-article","created":{"date-parts":[[2009,1,6]],"date-time":"2009-01-06T12:41:34Z","timestamp":1231245694000},"page":"2350-2363","source":"Crossref","is-referenced-by-count":26,"title":["Conformational Analysis of DNA-Trinucleotide-Hairpin-Loop Structures Using a Continuum Solvent Model"],"prefix":"10.1016","volume":"80","author":[{"given":"Martin","family":"Zacharias","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/S0006-3495(01)76205-4_bib1","doi-asserted-by":"crossref","first-page":"776","DOI":"10.1006\/jmbi.1996.0615","article-title":"The hairpin structure of a topoisomerase II site DNA strand analysed by combined NMR and energy minimization methods","volume":"263","author":"Aslani","year":"1996","journal-title":"J. Mol. Biol"},{"key":"10.1016\/S0006-3495(01)76205-4_bib2","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1128\/JVI.54.1.171-177.1985","article-title":"Sequence analysis of the termini of virion and replicative forms of minute virus of mice DNA suggests a modified rolling hairpin model for autonomous parvovirus replication","volume":"54","author":"Astell","year":"1985","journal-title":"J. Virol."},{"key":"10.1016\/S0006-3495(01)76205-4_bib3","doi-asserted-by":"crossref","first-page":"3218","DOI":"10.1016\/S0006-3495(99)77152-3","article-title":"Abasic sites in duplex DNA: molecular modeling of sequence-dependent effects on conformation","volume":"77","author":"Ayadi","year":"1999","journal-title":"Biophys. J."},{"key":"10.1016\/S0006-3495(01)76205-4_bib4","doi-asserted-by":"crossref","first-page":"5179","DOI":"10.1021\/ja00124a002","article-title":"A second generation force field for the simulation of proteins, nucleic acids and organic molecules","volume":"117","author":"Cornell","year":"1995","journal-title":"J. Am. Chem. Soc."},{"key":"10.1016\/S0006-3495(01)76205-4_bib5","doi-asserted-by":"crossref","first-page":"5199","DOI":"10.1073\/pnas.92.11.5199","article-title":"Hairpins are formed by the single DNA strands of the fragile X triplet repeats: structure and biological implications","volume":"92","author":"Chen","year":"1995","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"10.1016\/S0006-3495(01)76205-4_bib6","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1006\/jmbi.1999.2564","article-title":"Stable sheared A C pair in DNA hairpins","volume":"287","author":"Chou","year":"1999","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S0006-3495(01)76205-4_bib7","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1006\/jmbi.1999.3066","article-title":"Stable formation of a pyrimidine-rich loop hairpin in a cruciform promoter","volume":"292","author":"Chou","year":"1999","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S0006-3495(01)76205-4_bib8","doi-asserted-by":"crossref","first-page":"981","DOI":"10.1006\/jmbi.1996.0691","article-title":"Hairpin loops consisting of single adenine residues closed by sheared A:A or G:G pairs formed by DNA triplets AAA and GAG: solution structures of the d(GTACAAAGTAC) hairpin","volume":"264","author":"Chou","year":"1996","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S0006-3495(01)76205-4_bib9","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1016\/S0959-440X(99)80009-8","article-title":"RNA-protein complexes","volume":"9","author":"Cusack","year":"1999","journal-title":"Curr. Opin. Struct. Biol."},{"key":"10.1016\/S0006-3495(01)76205-4_bib10","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1016\/0022-2836(89)90324-0","article-title":"Definitions and nomenclature of nucleic acid structure parameters","volume":"205","author":"Dickerson","year":"1989","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S0006-3495(01)76205-4_bib11","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1021\/bi00053a008","article-title":"Theoretical predictions of DNA hairpin loop conformations: correlations with thermodynamic and spectroscopic data","volume":"32","author":"Erie","year":"1993","journal-title":"Biochemistry"},{"key":"10.1016\/S0006-3495(01)76205-4_bib12","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1016\/0092-8674(95)90074-8","article-title":"Trinucleotide repeats that expand in human disease form hairpin structures in vitro","volume":"81","author":"Gacy","year":"1995","journal-title":"Cell"},{"key":"10.1016\/S0006-3495(01)76205-4_bib13","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.1006\/jmbi.1993.1104","article-title":"Modeling the three-dimensional structure of RNA using discrete nucleotide conformational sets","volume":"229","author":"Gautheret","year":"1993","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S0006-3495(01)76205-4_bib14","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1016\/S0092-8674(00)81001-6","article-title":"E. coli SSB activates N4 virion RNA polymerase promoters by stabilizing a DNA hairpin required for promoter recognition","volume":"84","author":"Glucksmann-Kuis","year":"1996","journal-title":"Cell"},{"key":"10.1016\/S0006-3495(01)76205-4_bib15","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1016\/0092-8674(92)90173-A","article-title":"Specific sequences and a hairpin structure in the template strand are required for N4 virion RNA polymerase promoter recognition","volume":"70","author":"Glucksmann-Kuis","year":"1992","journal-title":"Cell"},{"key":"10.1016\/S0006-3495(01)76205-4_bib16","doi-asserted-by":"crossref","first-page":"19824","DOI":"10.1021\/jp961710n","article-title":"Parameterized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium","volume":"100","author":"Hawkins","year":"1996","journal-title":"J. Phys. Chem."},{"key":"10.1016\/S0006-3495(01)76205-4_bib17","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1126\/science.1712983","article-title":"Structural features that give rise to the unusual stability of RNA hairpins containing GNRA tetraloops","volume":"253","author":"Heus","year":"1991","journal-title":"Science"},{"key":"10.1016\/S0006-3495(01)76205-4_bib18","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1093\/nar\/22.4.576","article-title":"Most compact hairpin-turn structure exerted by a short DNA fragment, d(GCGAAGC) in solution: an extraordinarily stable structure resistant to nuclease and heat","volume":"22","author":"Hirao","year":"1994","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/S0006-3495(01)76205-4_bib19","doi-asserted-by":"crossref","first-page":"3891","DOI":"10.1093\/nar\/20.15.3891","article-title":"Extraordinarily stable mini-hairpins: electrophoretical and thermal properties of the various sequence variants of d(GCGAAAGC) and their effects on DNA sequencing","volume":"20","author":"Hirao","year":"1992","journal-title":"Nucleic Acids Res"},{"key":"10.1016\/S0006-3495(01)76205-4_bib20","doi-asserted-by":"crossref","first-page":"9571","DOI":"10.1021\/jp982007x","article-title":"Solvation free energies of biomacromolecules: parameters for a modified generalized Born model consistent with the Amber force field","volume":"102","author":"Jayaram","year":"1998","journal-title":"J. Phys. Chem."},{"key":"10.1016\/S0006-3495(01)76205-4_bib21","first-page":"219","article-title":"GNRA tetraloops make a U-turn","volume":"1","author":"Jucker","year":"1995","journal-title":"RNA"},{"key":"10.1016\/S0006-3495(01)76205-4_bib22","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1021\/ma50003a019","article-title":"Method for estimating the configurational entropy of macromolecules","volume":"14","author":"Karplus","year":"1981","journal-title":"Macromolecules"},{"key":"10.1016\/S0006-3495(01)76205-4_bib23","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1016\/0010-4655(95)00046-I","article-title":"JUMNA (junction minimization of nucleic acids)","volume":"91","author":"Lavery","year":"1995","journal-title":"Comput. Phys. Commun."},{"key":"10.1016\/S0006-3495(01)76205-4_bib24","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1016\/0022-2836(85)90230-X","article-title":"Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme","volume":"181","author":"Levitt","year":"1985","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S0006-3495(01)76205-4_bib25","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/0010-4655(95)00043-F","article-title":"Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program","volume":"91","author":"Madura","year":"1995","journal-title":"Comput. Phys. Commun."},{"key":"10.1016\/S0006-3495(01)76205-4_bib26","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1007\/s002490050238","article-title":"Force field based conformational analysis of RNA structural motifs: GNRA tetraloops and their pyrimidine relatives","volume":"28","author":"Maier","year":"1999","journal-title":"Eur. Biophys. J."},{"key":"10.1016\/S0006-3495(01)76205-4_bib27","doi-asserted-by":"crossref","first-page":"1255","DOI":"10.1126\/science.1716375","article-title":"The combination of symbolic and numerical computation for three-dimensional modeling of RNA","volume":"253","author":"Major","year":"1991","journal-title":"Science"},{"key":"10.1016\/S0006-3495(01)76205-4_bib28","doi-asserted-by":"crossref","first-page":"12803","DOI":"10.1021\/bi00039a041","article-title":"The trinucleotide repeat d(CGG)15 forms a heat-stable hairpin containing Gsyn:Ganti base pairs","volume":"34","author":"Mitas","year":"1995","journal-title":"Biochemistry"},{"key":"10.1016\/S0006-3495(01)76205-4_bib29","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1016\/S0959-440X(99)80010-4","article-title":"Adaptive recognition in RNA complexes with peptides and protein modules","volume":"9","author":"Patel","year":"1999","journal-title":"Curr. Opin. Struct. Biol."},{"key":"10.1016\/S0006-3495(01)76205-4_bib30","doi-asserted-by":"crossref","first-page":"3005","DOI":"10.1021\/jp961992r","article-title":"The GB\/SA continuum model for solvation: a fast analytical method for the calculation of approximate Born radii","volume":"101","author":"Qui","year":"1997","journal-title":"J. Phys. Chem."},{"key":"10.1016\/S0006-3495(01)76205-4_bib31","doi-asserted-by":"crossref","first-page":"2860","DOI":"10.1021\/ja992966k","article-title":"Methylene blue binding to DNA with alternating GC base sequence: a modeling study","volume":"122","author":"Rohs","year":"2000","journal-title":"J. Am. Chem. Soc."},{"key":"10.1016\/S0006-3495(01)76205-4_bib32","series-title":"Principles of Nucleic Acids Structure","author":"Saenger","year":"1984"},{"key":"10.1016\/S0006-3495(01)76205-4_bib33","doi-asserted-by":"crossref","first-page":"4717","DOI":"10.1093\/nar\/23.22.4717","article-title":"Occurrence, solution structure and stability of DNA hairpins stabilized by a GA\/CG helix unit","volume":"23","author":"Sandusky","year":"1995","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/S0006-3495(01)76205-4_bib34","doi-asserted-by":"crossref","first-page":"7684","DOI":"10.1021\/j100382a068","article-title":"Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation","volume":"94","author":"Sharp","year":"1990","journal-title":"J. Phys. Chem."},{"key":"10.1016\/S0006-3495(01)76205-4_bib35","doi-asserted-by":"crossref","first-page":"1978","DOI":"10.1021\/j100058a043","article-title":"Accurate calculation of hydration free energies using macroscopic solvent models","volume":"98","author":"Sitkoff","year":"1994","journal-title":"J. Phys. Chem."},{"key":"10.1016\/S0006-3495(01)76205-4_bib36","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1080\/07391102.1998.10508279","article-title":"Continuum solvent studies of the stability of RNA hairpin loops and helices","volume":"16","author":"Srinivasan","year":"1998","journal-title":"J. Biomol. Struct. Dyn."},{"key":"10.1016\/S0006-3495(01)76205-4_bib37","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1007\/s002140050460","article-title":"Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt effects","volume":"101","author":"Srinivasan","year":"1999","journal-title":"Theor. Chem. Acc."},{"key":"10.1016\/S0006-3495(01)76205-4_bib38","doi-asserted-by":"crossref","first-page":"6127","DOI":"10.1021\/ja00172a038","article-title":"Semianalytical treatment of solvation for molecular mechanics and dynamics","volume":"112","author":"Still","year":"1990","journal-title":"J. Am. Chem. Soc."},{"key":"10.1016\/S0006-3495(01)76205-4_bib39","doi-asserted-by":"crossref","first-page":"2489","DOI":"10.1021\/ja9939385","article-title":"Molecular dynamics simulations of nucleic acids with a generalized Born solvation model","volume":"122","author":"Tsui","year":"2000","journal-title":"J. Am. Chem. Soc."},{"key":"10.1016\/S0006-3495(01)76205-4_bib40","doi-asserted-by":"crossref","first-page":"1537","DOI":"10.1093\/nar\/25.8.1537","article-title":"Structural features of the DNA hairpin d(ATCCTA-GTTA-TAGGAT): formation of a G-A base pair in the loop","volume":"25","author":"van Dongen","year":"1997","journal-title":"Nucleic Acid Res."},{"key":"10.1016\/S0006-3495(01)76205-4_bib41","doi-asserted-by":"crossref","first-page":"3192","DOI":"10.1016\/S0006-3495(99)77471-0","article-title":"Unrestrained stochastic dynamics simulations of the UUCG tetraloop using an implicit solvation model","volume":"76","author":"Williams","year":"1999","journal-title":"Biophys. J."},{"key":"10.1016\/S0006-3495(01)76205-4_bib42","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1006\/jmbi.2000.3547","article-title":"Experimental and theoretical studies of the effects of desoxyribose substitutions on the stability of the UUCG tetraloop","volume":"297","author":"Williams","year":"2000","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S0006-3495(01)76205-4_bib43","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1006\/jmbi.2000.3623","article-title":"Experimental and computational studies of the G[UUCG]C RNA tetraloop","volume":"297","author":"Williams","year":"2000","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S0006-3495(01)76205-4_bib44","doi-asserted-by":"crossref","first-page":"4761","DOI":"10.1021\/bi961738p","article-title":"GNA trinucleotide loop sequences producing extraordinary stable DNA minihairpins","volume":"36","author":"Yoshizawa","year":"1997","journal-title":"Biochemistry"},{"key":"10.1016\/S0006-3495(01)76205-4_bib45","doi-asserted-by":"crossref","first-page":"4055","DOI":"10.1093\/nar\/23.20.4055","article-title":"The purine-rich trinucleotide repeat sequences d(CAG)15 and d(GAC)15 form hairpins","volume":"23","author":"Yu","year":"1995","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/S0006-3495(01)76205-4_bib46","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1016\/S0959-440X(00)00089-0","article-title":"Simulation of the structure and dynamics of nonhelical RNA motifs","volume":"10","author":"Zacharias","year":"2000","journal-title":"Curr. Opin. Struct. Biol"},{"key":"10.1016\/S0006-3495(01)76205-4_bib47","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1002\/1097-0282(200012)54:7<547::AID-BIP70>3.0.CO;2-N","article-title":"Comparison of molecular dynamics and harmonic mode calculations on RNA","volume":"54","author":"Zacharias","year":"2000","journal-title":"Biopolymers"},{"key":"10.1016\/S0006-3495(01)76205-4_bib48","doi-asserted-by":"crossref","first-page":"2990","DOI":"10.1016\/S0006-3495(97)78328-0","article-title":"Analysis of the stability of looped-out and stacked-in conformations of an adenine bulge in DNA using a continuum model for solvent and ions","volume":"73","author":"Zacharias","year":"1997","journal-title":"Biophys. J."},{"key":"10.1016\/S0006-3495(01)76205-4_bib49","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1006\/jmbi.1999.2760","article-title":"Conformational analysis of single-base bulges in A-form DNA and RNA using a hierarchical approach and energetic evaluation with a continuum solvent model","volume":"289","author":"Zacharias","year":"1999","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S0006-3495(01)76205-4_bib50","doi-asserted-by":"crossref","first-page":"2528","DOI":"10.1016\/S0006-3495(00)76798-1","article-title":"Conformational deformability of RNA: a harmonic mode analysis","volume":"78","author":"Zacharias","year":"2000","journal-title":"Biophys. J."},{"key":"10.1016\/S0006-3495(01)76205-4_bib51","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1016\/0301-0104(95)00345-2","article-title":"Poisson-Boltzmann calculations for nucleic acids and nucleic acid complexes","volume":"204","author":"Zakrzewska","year":"1996","journal-title":"Chem. Phys."},{"key":"10.1016\/S0006-3495(01)76205-4_bib52","doi-asserted-by":"crossref","first-page":"1012","DOI":"10.1038\/nsb1195-1012","article-title":"Structure of a single-cytidine hairpin loop formed by the DNA triplet GCA","volume":"2","author":"Zhu","year":"1995","journal-title":"Nat. Struct. Biol."},{"key":"10.1016\/S0006-3495(01)76205-4_bib53","doi-asserted-by":"crossref","first-page":"12159","DOI":"10.1073\/pnas.93.22.12159","article-title":"A single G-to-C change causes human centromere TGGAA repeats to fold back into hairpins","volume":"93","author":"Zhu","year":"1996","journal-title":"Proc. Natl. Acad. Sci. U.S.A."}],"container-title":["Biophysical Journal"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0006349501762054?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0006349501762054?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2020,5,14]],"date-time":"2020-05-14T10:44:19Z","timestamp":1589453059000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0006349501762054"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2001,5]]},"references-count":53,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2001,5]]}},"alternative-id":["S0006349501762054"],"URL":"https:\/\/doi.org\/10.1016\/s0006-3495(01)76205-4","relation":{},"ISSN":["0006-3495"],"issn-type":[{"value":"0006-3495","type":"print"}],"subject":[],"published":{"date-parts":[[2001,5]]}}}