DC Field | Value | Language |
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dc.contributor.author | KIM, HYUN WOO | - |
dc.contributor.author | RHEE, YOUNG MIN | - |
dc.contributor.author | SHIN, SEUNG KOO | - |
dc.date.accessioned | 2018-11-12T01:45:18Z | - |
dc.date.available | 2018-11-12T01:45:18Z | - |
dc.date.created | 2018-11-02 | - |
dc.date.issued | 2018-08 | - |
dc.identifier.issn | 1463-9076 | - |
dc.identifier.uri | https://oasis.postech.ac.kr/handle/2014.oak/94121 | - |
dc.description.abstract | DNAs form various structures through hydrogen-bonding, base-stacking and electrostatic interactions. Although these noncovalent interactions are known to be cooperative in stabilizing a G-quadruplex (G4) structure of DNA, we find from all-atom molecular dynamics simulations that the electrostatic charge-dipole interaction is competitive with both hydrogen-bonding and base-stacking interactions. For the thrombin-binding aptamer (TBA) forming a chair-type antiparallel G4 structure, we have examined effects of an intercalating metal ion [K+, Sr2+, Mn+: an ion having a charge of n(+) (n = 1-4) with the ionic radius of K+] on structural properties and noncovalent interactions. When K+ in the TBA center dot K+ complex is replaced with Sr2+, guanine dipoles in the two G-tetrads are realigned toward the central metal ion, thereby distorting the planar G4 geometry. Replacing K+ with Sr2+ significantly enhances the charge-dipole interaction but substantially reduces the number of hydrogen bonds in the G-tetrads. In the case of TBA center dot Mn+ complexes, as the charge n increases, the charge-dipole interaction increases but both of the hydrogen-bonding and base-stacking interactions decrease. These results suggest that the charge-dipole interaction realigning guanine dipoles in the G-tetrads is not cooperative but competitive with both hydrogen-bonding and base-stacking interactions favoring the planar G-tetrad geometry. Obviously, the charge state of an intercalating metal ion is as important as the ionic radius in forming a stable G4 structure. Thus, a delicate balance between these competing noncovalent interactions makes the chair-type antiparallel G4 structure of TBA selective for intercalating metal ions. | - |
dc.language | English | - |
dc.publisher | ROYAL SOC CHEMISTRY | - |
dc.relation.isPartOf | PHYSICAL CHEMISTRY CHEMICAL PHYSICS | - |
dc.title | Charge–Dipole Interactions in G-Quadruplex Thrombin-Binding Aptamer | - |
dc.type | Article | - |
dc.identifier.doi | 10.1039/c8cp03050b | - |
dc.type.rims | ART | - |
dc.identifier.bibliographicCitation | PHYSICAL CHEMISTRY CHEMICAL PHYSICS, v.20, no.32, pp.21068 - 21074 | - |
dc.identifier.wosid | 000447367900032 | - |
dc.citation.endPage | 21074 | - |
dc.citation.number | 32 | - |
dc.citation.startPage | 21068 | - |
dc.citation.title | PHYSICAL CHEMISTRY CHEMICAL PHYSICS | - |
dc.citation.volume | 20 | - |
dc.contributor.affiliatedAuthor | SHIN, SEUNG KOO | - |
dc.identifier.scopusid | 2-s2.0-85051996883 | - |
dc.description.journalClass | 1 | - |
dc.description.journalClass | 1 | - |
dc.type.docType | ARTICLE | - |
dc.subject.keywordPlus | BASE-STACKING | - |
dc.subject.keywordPlus | STRUCTURAL DYNAMICS | - |
dc.subject.keywordPlus | POTENTIAL FUNCTIONS | - |
dc.subject.keywordPlus | MOLECULAR-DYNAMICS | - |
dc.subject.keywordPlus | DNA QUADRUPLEX | - |
dc.subject.keywordPlus | CATION-BINDING | - |
dc.subject.keywordPlus | NUCLEIC-ACIDS | - |
dc.subject.keywordPlus | FORCE-FIELD | - |
dc.subject.keywordPlus | SIMULATIONS | - |
dc.subject.keywordPlus | STABILITY | - |
dc.relation.journalWebOfScienceCategory | Chemistry, Physical | - |
dc.relation.journalWebOfScienceCategory | Physics, Atomic, Molecular & Chemical | - |
dc.description.journalRegisteredClass | scie | - |
dc.description.journalRegisteredClass | scopus | - |
dc.relation.journalResearchArea | Chemistry | - |
dc.relation.journalResearchArea | Physics | - |
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