{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T11:43:27Z","timestamp":1790682207149,"version":"4.1.0"},"reference-count":79,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2020,4,25]],"date-time":"2020-04-25T00:00:00Z","timestamp":1587772800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["GM072462"],"award-info":[{"award-number":["GM072462"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Retroviral nucleocapsid (NC) proteins are nucleic acid chaperones that play distinct roles in the viral life cycle. During reverse transcription, HIV-1 NC facilitates the rearrangement of nucleic acid secondary structures, allowing the transactivation response (TAR) RNA hairpin to be transiently destabilized and annealed to a complementary RNA hairpin. In contrast, during viral assembly, NC, as a domain of the group-specific antigen (Gag) polyprotein, binds the genomic RNA and facilitates packaging into new virions. It is not clear how the same protein, alone or as part of Gag, performs such different RNA binding functions in the viral life cycle. By combining single-molecule optical tweezers measurements with a quantitative mfold-based model, we characterize the equilibrium stability and unfolding barrier for TAR RNA. Comparing measured results with a model of discrete protein binding allows us to localize affected binding sites, in addition to quantifying hairpin stability. We find that, while both NCp7 and Gag\u2206p6 destabilize the TAR hairpin, Gag\u2206p6 binding is localized to two sites in the stem, while NCp7 targets sites near the top loop. Unlike Gag\u2206p6, NCp7 destabilizes this loop, shifting the location of the reaction barrier toward the folded state and increasing the natural rate of hairpin opening by ~104. Thus, our results explain why Gag cleavage and NC release is an essential prerequisite for reverse transcription within the virion.<\/jats:p>","DOI":"10.3390\/v12050484","type":"journal-article","created":{"date-parts":[[2020,4,28]],"date-time":"2020-04-28T05:05:32Z","timestamp":1588050332000},"page":"484","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["Significant Differences in RNA Structure Destabilization by HIV-1 Gag\u2206p6 and NCp7 Proteins"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2115-2989","authenticated-orcid":false,"given":"Micah J.","family":"McCauley","sequence":"first","affiliation":[{"name":"Department of Physics, Northeastern University, Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4651-5264","authenticated-orcid":false,"given":"Ioulia","family":"Rouzina","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Biochemistry, The Ohio State University, Center for Retroviral Research, and Center for RNA Biology, Columbus, OH 43210, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jasmine","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Program in Biochemistry, Wellesley College, Wellesley, MA 02481, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4576-6926","authenticated-orcid":false,"given":"Megan E.","family":"N\u00fa\u00f1ez","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Program in Biochemistry, Wellesley College, Wellesley, MA 02481, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3219-376X","authenticated-orcid":false,"given":"Mark C.","family":"Williams","sequence":"additional","affiliation":[{"name":"Department of Physics, Northeastern University, Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2020,4,25]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1016\/0092-8674(81)90390-1","article-title":"In vitro splicing of the ribosomal RNA precursor of Tetrahymena: Involvement of a guanosine nucleotide in the excision of the intervening sequence","volume":"27","author":"Cech","year":"1981","journal-title":"Cell"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1485","DOI":"10.1073\/pnas.1115045109","article-title":"Folding energy landscape of the thiamine pyrophosphate riboswitch aptamer","volume":"109","author":"Anthony","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1126\/science.1151298","article-title":"Direct Observation of Hierarchical Folding in Single Riboswitch Aptamers","volume":"319","author":"Greenleaf","year":"2008","journal-title":"Science"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"15847","DOI":"10.1073\/pnas.0607202103","article-title":"Unusual mechanical stability of a minimal RNA kissing complex","volume":"103","author":"Li","year":"2006","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1892","DOI":"10.1126\/science.1081338","article-title":"Identifying kinetic barriers to mechanical unfolding of the T. thermophila ribozyme","volume":"299","author":"Onoa","year":"2003","journal-title":"Science"},{"key":"ref_6","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":"Dai","year":"1996","journal-title":"Cell"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1016\/j.jmb.2006.08.039","article-title":"Mechanistic studies of mini-TAR RNA\/DNA annealing in the absence and presence of HIV-1 nucleocapsid protein","volume":"363","author":"Vo","year":"2006","journal-title":"J. Mol. Biol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1016\/j.jmb.2008.12.070","article-title":"HIV-1 nucleocapsid protein switches the pathway of transactivation response element RNA\/DNA annealing from loop-loop \u201ckissing\u201d to \u201czipper\u201d","volume":"386","author":"Vo","year":"2009","journal-title":"J. Mol. Biol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1128\/jvi.66.1.139-149.1992","article-title":"Functional roles for the TATA promoter and enhancers in basal and Tat-induced expression of the human immunodeficiency virus type 1 long terminal repeat","volume":"66","author":"Berkhout","year":"1992","journal-title":"J. Virol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1016\/S0079-6603(05)80006-6","article-title":"Nucleic acid chaperone activity of HIV-1 nucleocapsid protein: Critical role in reverse transcription and molecular mechanism","volume":"80","author":"Levin","year":"2005","journal-title":"Prog. Nucleic Acid. Res. Mol. Biol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"867","DOI":"10.1016\/j.jmb.2006.08.070","article-title":"Rapid kinetics of protein-nucleic acid interaction is a major component of HIV-1 nucleocapsid protein\u2019s nucleic acid chaperone function","volume":"363","author":"Cruceanu","year":"2006","journal-title":"J. Mol. Biol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1006\/jmbi.1995.0635","article-title":"First Glimpses at Structure-function Relationships of the Nucleocapsid Protein of Retroviruses","volume":"254","author":"Darlix","year":"1995","journal-title":"J. Mol. Biol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1093\/nar\/21.4.831","article-title":"Interaction between HIV-1 nucleocapsid protein and viral DNA may have important functions in the viral life cycle","volume":"21","author":"Roques","year":"1993","journal-title":"Nucleic Acids Res."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"2434","DOI":"10.1093\/nar\/23.13.2434","article-title":"Analysis of the nucleic acid annealing activities of nucleocapsid protein from HIV-1","volume":"23","author":"Pernelle","year":"1995","journal-title":"Nucleic Acids Res."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.virusres.2007.12.006","article-title":"Nucleocapsid protein function in early infection processes","volume":"134","author":"Thomas","year":"2008","journal-title":"Virus Res."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1016\/j.virusres.2012.07.008","article-title":"Aromatic residue mutations reveal direct correlation between HIV-1 nucleocapsid protein\u2019s nucleic acid chaperone activity and retroviral replication","volume":"171","author":"Wu","year":"2013","journal-title":"Virus Res."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1126\/science.279.5349.384","article-title":"Structure of the HIV-1 Nucleocapsid Protein Bound to the SL3 psi-RNA Recognition Element","volume":"279","author":"Wu","year":"1998","journal-title":"Science"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1099\/0022-1317-82-3-581","article-title":"Extended nucleocapsid protein is cleaved from the Gag-Pol precursor of human immunodeficiency virus type 1","volume":"82","author":"Chen","year":"2001","journal-title":"J. Gen. Virol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"9156","DOI":"10.1128\/JVI.75.19.9156-9164.2001","article-title":"Proteolytic processing of the p2\/nucleocapsid cleavage site is critical for human immunodeficiency virus type 1 RNA dimer maturation","volume":"75","author":"Krausslich","year":"2001","journal-title":"J. Virol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1016\/S0968-0004(98)01256-0","article-title":"Nucleic-acid-chaperone activity of retroviral nucleocapsid proteins: Significance for viral replication","volume":"23","author":"Rein","year":"1998","journal-title":"Trends Biochem. Sci."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"5863","DOI":"10.1128\/jvi.68.9.5863-5870.1994","article-title":"DNA strand exchange and selective DNA annealing promoted by the human immunodeficiency virus type 1 nucleocapsid protein","volume":"68","author":"Tsuchihashi","year":"1994","journal-title":"J. Virol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1261\/rna.054445.115","article-title":"Insights into the mechanisms of RNA secondary structure destabilization by the HIV-1 nucleocapsid protein","volume":"22","author":"Belfetmi","year":"2016","journal-title":"RNA"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"13555","DOI":"10.1073\/pnas.1510100112","article-title":"Targeted binding of nucleocapsid protein transforms the folding landscape of HIV-1 TAR RNA","volume":"112","author":"McCauley","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"7050","DOI":"10.1128\/JVI.73.8.7050-7055.1999","article-title":"Mass determination of Rous sarcoma virus virions by scanning transmission electron microscopy","volume":"73","author":"Vogt","year":"1999","journal-title":"J. Virol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"672","DOI":"10.1038\/nsmb785","article-title":"The stoichiometry of Gag protein in HIV-1","volume":"11","author":"Briggs","year":"2004","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"9039","DOI":"10.1128\/JVI.01013-06","article-title":"Proteomic and biochemical analysis of purified human immunodeficiency virus type 1 produced from infected monocyte-derived macrophages","volume":"80","author":"Chertova","year":"2006","journal-title":"J. Virol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"17488","DOI":"10.1074\/jbc.M501310200","article-title":"A HIV-1 minimal gag protein is superior to nucleocapsid at in vitro annealing and exhibits multimerization-induced inhibition of reverse transcription","volume":"280","author":"Roldan","year":"2005","journal-title":"J. Biol. Chem."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"8980","DOI":"10.1128\/JVI.74.19.8980-8988.2000","article-title":"Zinc finger structures in the human immunodeficiency virus type 1 nucleocapsid protein facilitate efficient minus- and plus-strand transfer","volume":"74","author":"Guo","year":"2000","journal-title":"J. Virol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"4370","DOI":"10.1128\/JVI.76.9.4370-4378.2002","article-title":"Subtle alterations of the native zinc finger structures have dramatic effects on the nucleic acid chaperone activity of human immunodeficiency virus type 1 nucleocapsid protein","volume":"76","author":"Guo","year":"2002","journal-title":"J. Virol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"754","DOI":"10.4161\/rna.7.6.14115","article-title":"Role of HIV-1 nucleocapsid protein in HIV-1 reverse transcription","volume":"7","author":"Levin","year":"2010","journal-title":"RNA Biol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"556","DOI":"10.1016\/j.virol.2010.06.042","article-title":"Fundamental differences between the nucleic acid chaperone activities of HIV-1 nucleocapsid protein and Gag or Gag-derived proteins: Biological implications","volume":"405","author":"Wu","year":"2010","journal-title":"Virology"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"4033","DOI":"10.1093\/nar\/gky148","article-title":"Quantifying the stability of oxidatively damaged DNA by single-molecule DNA stretching","volume":"46","author":"McCauley","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"2270","DOI":"10.1128\/JVI.73.3.2270-2279.1999","article-title":"In vitro assembly properties of human immunodeficiency virus type 1 Gag protein lacking the p6 domain","volume":"73","author":"Campbell","year":"1999","journal-title":"J. Virol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"4425","DOI":"10.1128\/jvi.71.6.4425-4435.1997","article-title":"In vitro assembly of virus-like particles with Rous sarcoma virus Gag deletion mutants: Identification of the p10 domain as a morphological determinant in the formation of spherical particles","volume":"71","author":"Campbell","year":"1997","journal-title":"J. Virol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1093\/nar\/gkj458","article-title":"Nucleic acid binding and chaperone properties of HIV-1 Gag and nucleocapsid proteins","volume":"34","author":"Cruceanu","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1016\/j.plrev.2010.06.001","article-title":"Biophysical characterization of DNA binding from single molecule force measurements","volume":"7","author":"Chaurasiya","year":"2010","journal-title":"Phys. Life Rev."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"208102","DOI":"10.1103\/PhysRevLett.95.208102","article-title":"Passive all-optical force clamp for high-resolution laser trapping","volume":"95","author":"Greenleaf","year":"2005","journal-title":"Phys. Rev. Lett."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"250","DOI":"10.1529\/biophysj.105.068049","article-title":"Probing the mechanical folding kinetics of TAR RNA by hopping, force-jump, and force-ramp methods","volume":"90","author":"Li","year":"2006","journal-title":"Biophys. J."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1002\/bip.21123","article-title":"Optical tweezers experiments resolve distinct modes of DNA-protein binding","volume":"91","author":"McCauley","year":"2009","journal-title":"Biopolymers"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/nmeth.1218","article-title":"Single-molecule force spectroscopy: Optical tweezers, magnetic tweezers and atomic force microscopy","volume":"5","author":"Neuman","year":"2008","journal-title":"Nat. Methods"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1146\/annurev-biophys-051013-022754","article-title":"Reconstructing folding energy landscapes by single-molecule force spectroscopy","volume":"43","author":"Woodside","year":"2014","journal-title":"Ann. Rev. Biophys."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"3406","DOI":"10.1093\/nar\/gkg595","article-title":"Mfold web server for nucleic acid folding and hybridization prediction","volume":"31","author":"Zuker","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/978-1-60327-429-6_1","article-title":"UNAFold: Software for nucleic acid folding and hybridization","volume":"453","author":"Markham","year":"2008","journal-title":"Methods Mol. Biol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1126\/science.1133601","article-title":"Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid","volume":"314","author":"Woodside","year":"2006","journal-title":"Science"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"6190","DOI":"10.1073\/pnas.0511048103","article-title":"Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins","volume":"103","author":"Woodside","year":"2006","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"5036","DOI":"10.1093\/nar\/gkt164","article-title":"Site-selective probing of cTAR destabilization highlights the necessary plasticity of the HIV-1 nucleocapsid protein to chaperone the first strand transfer","volume":"41","author":"Godet","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1126\/science.1230715","article-title":"A guanosine-centric mechanism for RNA chaperone function","volume":"340","author":"Grohman","year":"2013","journal-title":"Science"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"7145","DOI":"10.1093\/nar\/gku335","article-title":"Distinct nucleic acid interaction properties of HIV-1 nucleocapsid protein precursor NCp15 explain reduced viral infectivity","volume":"42","author":"Wang","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1016\/j.virusres.2014.06.004","article-title":"Selection of fully processed HIV-1 nucleocapsid protein is required for optimal nucleic acid chaperone activity in reverse transcription","volume":"193","author":"Wu","year":"2014","journal-title":"Virus Res."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"10796","DOI":"10.1128\/JVI.74.22.10796-10800.2000","article-title":"Roles of Pr55(gag) and NCp7 in tRNA(3)(Lys) genomic placement and the initiation step of reverse transcription in human immunodeficiency virus type 1","volume":"74","author":"Cen","year":"2000","journal-title":"J. Virol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"8099","DOI":"10.1128\/JVI.00488-09","article-title":"Roles of Gag and NCp7 in facilitating tRNA(Lys)(3) Annealing to viral RNA in human immunodeficiency virus type 1","volume":"83","author":"Guo","year":"2009","journal-title":"J. Virol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"1594","DOI":"10.1128\/JVI.01809-10","article-title":"Matrix domain modulates HIV-1 Gag\u2019s nucleic acid chaperone activity via inositol phosphate binding","volume":"85","author":"Jones","year":"2011","journal-title":"J. Virol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"e38438","DOI":"10.7554\/eLife.38438","article-title":"Efficient support of virus-like particle assembly by the HIV-1 packaging signal","volume":"7","author":"Kroupa","year":"2018","journal-title":"Elife"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"1078","DOI":"10.1261\/rna.038869.113","article-title":"Distinct binding interactions of HIV-1 Gag to Psi and non-Psi RNAs: Implications for viral genomic RNA packaging","volume":"19","author":"Webb","year":"2013","journal-title":"RNA"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"6121","DOI":"10.1073\/pnas.101033198","article-title":"Mechanism for nucleic acid chaperone activity of HIV-1 nucleocapsid protein revealed by single molecule stretching","volume":"98","author":"Williams","year":"2001","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1186\/s12977-016-0287-4","article-title":"Characterization of the interaction between the HIV-1 Gag structural polyprotein and the cellular ribosomal protein L7 and its implication in viral nucleic acid remodeling","volume":"13","author":"Mekdad","year":"2016","journal-title":"Retrovirology"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"3577","DOI":"10.1128\/JVI.03353-13","article-title":"A conformational transition observed in single HIV-1 Gag molecules during in vitro assembly of virus-like particles","volume":"88","author":"Munro","year":"2014","journal-title":"J. Virol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1038\/s41586-018-0396-4","article-title":"Inositol phosphates are assembly co-factors for HIV-1","volume":"560","author":"Dick","year":"2018","journal-title":"Nature"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1261\/rna.058453.116","article-title":"Inhibition of HIV-1 Gag-membrane interactions by specific RNAs","volume":"23","author":"Todd","year":"2017","journal-title":"RNA"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"14369","DOI":"10.1038\/srep14369","article-title":"A novel combined RNA-protein interaction analysis distinguishes HIV-1 Gag protein binding sites from structural change in the viral RNA leader","volume":"5","author":"Kenyon","year":"2015","journal-title":"Sci. Rep."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"866","DOI":"10.1038\/nmeth.3490","article-title":"Mutational interference mapping experiment (MIME) for studying RNA structure and function","volume":"12","author":"Smyth","year":"2015","journal-title":"Nat. Methods"},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Wilkinson, K.A., Gorelick, R.J., Vasa, S.M., Guex, N., Rein, A., Mathews, D.H., Giddings, M.C., and Weeks, K.M. (2008). High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states. PLoS Biol., 6.","DOI":"10.1371\/journal.pbio.0060096"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1016\/S0006-3495(99)77207-3","article-title":"Estimating the persistence length of a Worm-Like Chain molecule from Force-Extension measurements","volume":"76","author":"Bouchiat","year":"1999","journal-title":"Biophys. J."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"7016","DOI":"10.1021\/ma00124a044","article-title":"Stiff chains and filaments under tension","volume":"28","author":"Odijk","year":"1995","journal-title":"Macromolecules"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"795","DOI":"10.1126\/science.271.5250.795","article-title":"Overstretching B-DNA: The elastic response of individual double-stranded and single-stranded DNA molecules","volume":"271","author":"Smith","year":"1996","journal-title":"Science"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"4360","DOI":"10.1529\/biophysj.107.112995","article-title":"Elasticity of short DNA molecules: Theory and experiment for contour lengths of 0.6\u20137 microns","volume":"93","author":"Seol","year":"2007","journal-title":"Biophys. J."},{"key":"ref_67","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_68","doi-asserted-by":"crossref","first-page":"6185","DOI":"10.1073\/pnas.94.12.6185","article-title":"Ionic effects on the elasticity of single DNA molecules","volume":"94","author":"Baumann","year":"1997","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"1122","DOI":"10.1126\/science.1439819","article-title":"Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads","volume":"258","author":"Smith","year":"1992","journal-title":"Science"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1007\/978-1-0716-0231-7_4","article-title":"Specific Nucleic Acid Chaperone Activity of HIV-1 Nucleocapsid Protein Deduced from Hairpin Unfolding","volume":"2106","author":"McCauley","year":"2020","journal-title":"Methods Mol. Biol."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"2721","DOI":"10.1103\/PhysRevE.60.2721","article-title":"Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences","volume":"60","author":"Crooks","year":"1999","journal-title":"Phys. Rev. E"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"2361","DOI":"10.1103\/PhysRevE.61.2361","article-title":"Path-ensemble averages in systems driven far from equilibrium","volume":"61","author":"Crooks","year":"2000","journal-title":"Phys. Rev. E"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1016\/0021-9991(76)90078-4","article-title":"Efficient estimation of free energy differences from Monte Carlo data","volume":"22","author":"Bennett","year":"1976","journal-title":"J. Comput. Phys."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"2690","DOI":"10.1103\/PhysRevLett.78.2690","article-title":"Nonequilibrium Equality for Free Energy Differences","volume":"78","author":"Jarzynski","year":"1997","journal-title":"Phys. Rev. Lett."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"11378","DOI":"10.1073\/pnas.1534554100","article-title":"Beyond the conventional description of dynamic force spectroscopy of adhesion bonds","volume":"100","author":"Dudko","year":"2003","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"108101","DOI":"10.1103\/PhysRevLett.96.108101","article-title":"Intrinsic rates and activation free energies from single-molecule pulling experiments","volume":"96","author":"Dudko","year":"2006","journal-title":"Phys. Rev. Lett."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"15755","DOI":"10.1073\/pnas.0806085105","article-title":"Theory, analysis, and interpretation of single-molecule force spectroscopy experiments","volume":"105","author":"Dudko","year":"2008","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"088101","DOI":"10.1103\/PhysRevLett.118.088101","article-title":"Distinguishing Signatures of Multipathway Conformational Transitions","volume":"118","author":"Pierse","year":"2017","journal-title":"Phys. Rev. Lett."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1007\/978-1-4939-8582-1_21","article-title":"Constructing Free Energy Landscapes of Nucleic Acid Hairpin Unfolding","volume":"1811","author":"McCauley","year":"2018","journal-title":"Methods Mol. Biol."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/12\/5\/484\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,13]],"date-time":"2025-10-13T13:23:44Z","timestamp":1760361824000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/12\/5\/484"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,4,25]]},"references-count":79,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2020,5]]}},"alternative-id":["v12050484"],"URL":"https:\/\/doi.org\/10.3390\/v12050484","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,4,25]]}}}