Non-Watson-Crick base pairing in RNA. Quantum chemical analysis
of the cis Watson-Crick/sugar edge base pair family

J 2005

Non-Watson-Crick base pairing in RNA. Quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family

ŠPONER, Judit E, Naděžda ŠPAČKOVÁ, Petr KULHÁNEK, Jerzy LESZCZYNSKI, Jiří ŠPONER et. al.

Základní údaje

Originální název

Non-Watson-Crick base pairing in RNA. Quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family

Název česky

Non-Watson-Crick párování bazí v RNA. Kvantově-chemická analýza cis Watson-Crick/sugar edge rodiny párů bazí

Autoři

ŠPONER, Judit E (203 Česká republika), Naděžda ŠPAČKOVÁ (203 Česká republika), Petr KULHÁNEK (203 Česká republika), Jerzy LESZCZYNSKI (840 Spojené státy) a Jiří ŠPONER (203 Česká republika, garant)

Vydání

JOURNAL OF PHYSICAL CHEMISTRY A, 2005, 1089-5639

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Impakt faktor

Impact factor: 2.898

Kód RIV

RIV/00216224:14310/05:00013729

Organizační jednotka

Přírodovědecká fakulta

UT WoS

000227630200029

Klíčová slova anglicky

LARGE RIBOSOMAL-SUBUNIT; NONEMPIRICAL AB-INITIO; CATION-PI INTERACTIONS; HYDRATED MG2+ CATION; CENTER-DOT-O; INTERACTION ENERGIES; ELECTRON CORRELATION; MOLECULAR-DYNAMICS; GUANINE-CYTOSINE; METAL-CATIONS

Štítky

CATION-PI INTERACTIONS, CENTER-DOT-O, ELECTRON CORRELATION, GUANINE-CYTOSINE, HYDRATED MG2+ CATION, INTERACTION ENERGIES, LARGE RIBOSOMAL-SUBUNIT, METAL-CATIONS, MOLECULAR-DYNAMICS, NONEMPIRICAL AB-INITIO

Změněno: 30. 5. 2005 08:37, RNDr. Petr Kulhánek, Ph.D.

Anotace

ORIG CZ

V originále

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 nearly isoenergetic. 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 isolated base pairs. The present quantum chemical calculations for the first time analyze base pairs involving the ribose 2 '-OH group and unambiguously correlate the structural information known from experiments with the energetics of interactions. The calculations further show that the relative importance and absolute value of the dispersion energy in the cis WC/SE base pairs are enhanced compared to the standard base pairs. This may by an important factor contributing to the strength of such interactions when RNA folds in its polar environment. The calculations further demonstrate that the Cornell et al. force field commonly used in molecular modeling and simulations provides satisfactory performance for this type of RNA interactions.

Česky

Non-Watson-Crick párování bazí v RNA. Kvantově-chemická analýza cis Watson-Crick/sugar edge rodiny párů bazí

Návaznosti

LN00A016, projekt VaV

Název: BIOMOLEKULÁRNÍ CENTRUM

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Biomolekulární centrum

Citovat

ŠPONER, Judit E, Naděžda ŠPAČKOVÁ, Petr KULHÁNEK, Jerzy LESZCZYNSKI a Jiří ŠPONER. Non-Watson-Crick base pairing in RNA. Quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family. JOURNAL OF PHYSICAL CHEMISTRY A. 2005, roč. 109, č. 10, s. 2292-2301. ISSN 1089-5639.

@article{571039,
   author = {Šponer, Judit E and Špačková, Naděžda and Kulhánek, Petr and Leszczynski, Jerzy and Šponer, Jiří},
   article_number = {10},
   keywords = {LARGE RIBOSOMAL-SUBUNIT; NONEMPIRICAL AB-INITIO; CATION-PI INTERACTIONS; HYDRATED MG2+ CATION; CENTER-DOT-O; INTERACTION ENERGIES; ELECTRON CORRELATION; MOLECULAR-DYNAMICS; GUANINE-CYTOSINE; METAL-CATIONS},
   language = {eng},
   issn = {1089-5639},
   journal = {JOURNAL OF PHYSICAL CHEMISTRY A},
   title = {Non-Watson-Crick base pairing in RNA. Quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family},
   volume = {109},
   year = {2005}
}

TY  - JOUR
ID  - 571039
AU  - Šponer, Judit E - Špačková, Naděžda - Kulhánek, Petr - Leszczynski, Jerzy - Šponer, Jiří
PY  - 2005
TI  - Non-Watson-Crick base pairing in RNA. Quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family
JF  - JOURNAL OF PHYSICAL CHEMISTRY A
VL  - 109
IS  - 10
SP  - 2292-2301
EP  - 2292-2301
SN  - 10895639
KW  - LARGE RIBOSOMAL-SUBUNIT
KW  - NONEMPIRICAL AB-INITIO
KW  - CATION-PI INTERACTIONS
KW  - HYDRATED MG2+ CATION
KW  - CENTER-DOT-O
KW  - INTERACTION ENERGIES
KW  - ELECTRON CORRELATION
KW  - MOLECULAR-DYNAMICS
KW  - GUANINE-CYTOSINE
KW  - METAL-CATIONS
N2  - 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 nearly isoenergetic. 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 isolated base pairs. The present quantum chemical calculations for the first time analyze base pairs involving the ribose 2 '-OH group and unambiguously correlate the structural information known from experiments with the energetics of interactions. The calculations further show that the relative importance and absolute value of the dispersion energy in the cis WC/SE base pairs are enhanced compared to the standard base pairs. This may by an important factor contributing to the strength of such interactions when RNA folds in its polar environment. The calculations further demonstrate that the Cornell et al. force field commonly used in molecular modeling and simulations provides satisfactory performance for this type of RNA interactions.
ER  -

ŠPONER, Judit E, Naděžda ŠPAČKOVÁ, Petr KULHÁNEK, Jerzy LESZCZYNSKI a Jiří ŠPONER. Non-Watson-Crick base pairing in RNA. Quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family. \textit{JOURNAL OF PHYSICAL CHEMISTRY A}. 2005, roč.~109, č.~10, s.~2292-2301. ISSN~1089-5639.

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