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공공누리This item is licensed Korea Open Government License

Title
Free-Energy Landscape of a Thrombin-Binding DNA Aptamer in Aqueous Environment
Author(s)
김은애
Publication Year
2012-10-08
Abstract
Thrombin-bindingaptamer(TBA-15)isasingle-stranded15-meroligonucleotidethathasawiderangeof
biomedicalapplications.Inthepresenceofmetalcationsofpropersizes,thisaptamerdisplaysG-quadruplexeswithasingle
cationenclosedatitscentralbindingsitewhenitiscompletelyfolded.Tounderstandhowthisaptamerfoldsintoitsstablethreedimensional
structureinthepresenceofK+ions,wecarriedoutfree-energycalculationsusingthestate-of-artreplicaexchange
moleculardynamicssimulation(REMD)attheall-atomlevel.TheresultingfreeenergymaprevealedthatTBA-15followsatwostate
foldingbehaviorwithasubstantiallylargefoldingbarrierof6kcal/molatambienttemperature.Oursimulationshowedthat
theinterveningTGT-loop,whichislocatedinthemiddleoftheTBA-15sequence,virtuallyremainsintactregardlessoffolding
andunfoldingstates.Furthermore,intheconservedTGT-loopstructure,thebase-pairstackingofG8andT9inducesthenativelike
baseorientationsofG6andG10pertainingtotheupperG-quadrant.Thisstackinginteractionenhancestheloopstability
andreducesitsdynamicfluctuations.Interestingly,fortheG-stemtofoldintoitsnativestate,theaggregationoftheG8andT9
residuesintheTGT-loopisakeystepforinitiatingthefoldingeventoftheG-stembycapturingabulkycation.
Keyword
Thrombin-Binding; DNAAptamer; Free-Energy
Journal Title
Journalofchemicaltheoryandcomputation
Citation Volume
8
ISSN
1549-9618
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Appears in Collections:
7. KISTI 연구성과 > 학술지 발표논문
URI
https://repository.kisti.re.kr/handle/10580/14047
http://www.ndsl.kr/ndsl/search/detail/article/articleSearchResultDetail.do?cn=NART64959155
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