Lattice model of oligonucleotide hybridization in solution. II. Specificity and cooperativity

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dc.citation.articleNumber125101en_US
dc.citation.issueNumber12en_US
dc.citation.journalTitleThe Journal of Chemical Physicsen_US
dc.citation.volumeNumber144en_US
dc.contributor.authorAraque, J.C.en_US
dc.contributor.authorRobert, M.A.en_US
dc.date.accessioned2017-05-09T20:16:06Zen_US
dc.date.available2017-05-09T20:16:06Zen_US
dc.date.issued2016en_US
dc.description.abstractBecause oligonucleotides are short sequences of nucleic acid bases, their association in solution with complementary strands (hybridization) is often seen to conform to a simple two-state model. However, experimental evidence suggests that, despite their short length, oligonucleotides may hybridize through multiple states involving intermediates. We investigate whether these apparently contradictory scenarios are possible by imposing different levels of sequence specificity on a lattice model of oligonucleotides in solution, which we introduced in Part I [J. C. Araque et al., J. Chem. Phys. 134, 165103 (2011)]. We find that both multiple-intermediate (weakly cooperative) and two-state (strongly cooperative) transitions are possible and that these are directly linked to the level of sequence specificity. Sequences with low specificity hybridize (base-by-base) by way of multiple stable intermediates with increasing number of paired bases. Such intermediate states are weakly cooperative because the energetic gain from adding an additional base pair is outweighed by the conformational entropy loss. Instead, sequences with high specificity hybridize through multiple metastable intermediates which easily bridge the configurational and energetic gaps between single- and double-stranded states. These metastable intermediates interconvert with minimal loss of conformational entropy leading to a strongly cooperative hybridization. The possibility of both scenarios, multiple- and two-states, is therefore encoded in the specificity of the sequence which in turn defines the level of cooperativity.en_US
dc.identifier.citationAraque, J.C. and Robert, M.A.. "Lattice model of oligonucleotide hybridization in solution. II. Specificity and cooperativity." <i>The Journal of Chemical Physics,</i> 144, no. 12 (2016) AIP Publishing LLC: http://dx.doi.org/10.1063/1.4943577.en_US
dc.identifier.doihttp://dx.doi.org/10.1063/1.4943577en_US
dc.identifier.urihttps://hdl.handle.net/1911/94206en_US
dc.language.isoengen_US
dc.publisherAIP Publishing LLCen_US
dc.rightsArticle is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.en_US
dc.titleLattice model of oligonucleotide hybridization in solution. II. Specificity and cooperativityen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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