Non-Watson-Crick base pairing in RNA. Quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family
Result description
Large RNA molecules exhibit an astonishing variability of base-pairing patterns, while many of the RNA base-pairing families have no counterparts in DNA. The cis Watson-Crick/sugar edge (cis WC/SE) RNA base pairing is investigated by ab initio quantum chemical calculations. A detailed structural and energetic characterization of all 13 crystallographically detected members of this family is provided by means of B3LYP/ 6-31G** and RIMP2/aug-cc-pVDZ calculations. Further, a prediction is made for the remaining 3 cis WC/ SE base pairs which are yet to be seen in the experiments. The interaction energy calculations point at the key role of the 2 '-OH group in stabilizing the sugar-base contact and predict all 16 cis WC/SE base-pairing patterns to be nearlyisoenergetic. The perfect correlation of the main geometrical parameters in the gas-phase optimized and X-ray structures shows that the principle of isosteric substitutions in RNA is rooted from the intrinsic structural similarity of the
Keywords
LARGE RIBOSOMAL-SUBUNITNONEMPIRICAL AB-INITIOCATION-PI INTERACTIONSHYDRATED MG2+ CATIONCENTER-DOT-OINTERACTION ENERGIESELECTRON CORRELATIONMOLECULAR-DYNAMICSGUANINE-CYTOSINEMETAL-CATIONS
The result's identifiers
Result code in IS VaVaI
Alternative codes found
RIV/68081707:_____/05:00001188
Result on the web
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DOI - Digital Object Identifier
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Alternative languages
Result language
angličtina
Original language name
Non-Watson-Crick base pairing in RNA. Quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family
Original language description
Large RNA molecules exhibit an astonishing variability of base-pairing patterns, while many of the RNA base-pairing families have no counterparts in DNA. The cis Watson-Crick/sugar edge (cis WC/SE) RNA base pairing is investigated by ab initio quantum chemical calculations. A detailed structural and energetic characterization of all 13 crystallographically detected members of this family is provided by means of B3LYP/ 6-31G** and RIMP2/aug-cc-pVDZ calculations. Further, a prediction is made for the remaining 3 cis WC/ SE base pairs which are yet to be seen in the experiments. The interaction energy calculations point at the key role of the 2 '-OH group in stabilizing the sugar-base contact and predict all 16 cis WC/SE base-pairing patterns to be nearlyisoenergetic. The perfect correlation of the main geometrical parameters in the gas-phase optimized and X-ray structures shows that the principle of isosteric substitutions in RNA is rooted from the intrinsic structural similarity of the
Czech name
Non-Watson-Crick párování bazí v RNA. Kvantově-chemická analýza cis Watson-Crick/sugar edge rodiny párů bazí
Czech description
Non-Watson-Crick párování bazí v RNA. Kvantově-chemická analýza cis Watson-Crick/sugar edge rodiny párů bazí
Classification
Type
Jx - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
CF - Physical chemistry and theoretical chemistry
OECD FORD branch
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Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2005
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
JOURNAL OF PHYSICAL CHEMISTRY A
ISSN
1089-5639
e-ISSN
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Volume of the periodical
109
Issue of the periodical within the volume
10
Country of publishing house
US - UNITED STATES
Number of pages
10
Pages from-to
2292-2301
UT code for WoS article
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EID of the result in the Scopus database
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Result type
Jx - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP
CF - Physical chemistry and theoretical chemistry
Year of implementation
2005