Weak Supramolecular Interactions Governing Parallel and
Antiparallel DNA Quadruplexes: Insights from Large-Scale
Quantum Mechanics Analysis of Experimentally Derived Models

J 2017

Weak Supramolecular Interactions Governing Parallel and Antiparallel DNA Quadruplexes: Insights from Large-Scale Quantum Mechanics Analysis of Experimentally Derived Models

YURENKO, Yevgen; Jan NOVOTNÝ a Radek MAREK

Základní údaje

Originální název

Weak Supramolecular Interactions Governing Parallel and Antiparallel DNA Quadruplexes: Insights from Large-Scale Quantum Mechanics Analysis of Experimentally Derived Models

Autoři

YURENKO, Yevgen; Jan NOVOTNÝ a Radek MAREK

Vydání

Chemistry - A European Journal, Weinheim, Wiley, 2017, 0947-6539

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Německo

Utajení

není předmětem státního či obchodního tajemství

Odkazy

DOI: 10.1002/chem.201700236

Impakt faktor

Impact factor: 5.160

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14740/17:00096192

Organizační jednotka

Středoevropský technologický institut

Klíčová slova anglicky

G-quadruplex; supramolecular; hydrogen bonding; stacking

Štítky

N-15 NMR, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 19. 2. 2018 08:37, prof. RNDr. Radek Marek, Ph.D.

Anotace

V originále

The topology and energetics of guanine (G) quadruplexes is governed by supramolecular interactions within their strands. In this work, an extensive quantum mechanical (QM) study has been performed to analyze supramolecular interactions that shape the stems of (4+0) parallel (P) and (2+2) antiparallel (AP) quadruplex systems. The large-scale (~400 atoms) models of P and AP were constructed from high-quality experimental structures. The results provide evidence that each of the P and AP structures is shaped by a distinct network of supramolecular interactions. Analysis of electron topological characteristics of hydrogen bonds in P and AP systems indicates that the P model benefits from stronger intratetrad hydrogen bonding. For intertetrad stacking interactions, both noncovalent interaction plot and energy decomposition analysis approaches suggest that the stem of the P quadruplex benefits more from stacking than that of the AP stem; the difference in energetic stabilization for the two topologies is about 10 %. Stronger hydrogen-bonding and stacking interactions in the stem of the P quadruplex, relative to those in the AP system, can be an important indicator to explain the experimental observations that guanine-rich oligonucleotides tend to form all-parallel stems with an all-anti orientation of nucleobases. However, in addition to intrinsic stabilization, partial desolvation effects, which affect the energetics and dynamics of the G-quadruplex folding process, call for further investigations.

Návaznosti

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CEITEC 2020

Přiložené soubory

CEJ17_23_5573.pdf

Požádat o autorskou verzi souboru

Citovat

YURENKO, Yevgen; Jan NOVOTNÝ a Radek MAREK. Weak Supramolecular Interactions Governing Parallel and Antiparallel DNA Quadruplexes: Insights from Large-Scale Quantum Mechanics Analysis of Experimentally Derived Models. Chemistry - A European Journal. Weinheim: Wiley, 2017, roč. 23, č. 23, s. 5573-5584. ISSN 0947-6539. Dostupné z: https://doi.org/10.1002/chem.201700236.

@article{1373307,
   author = {Yurenko, Yevgen and Novotný, Jan and Marek, Radek},
   article_location = {Weinheim},
   article_number = {23},
   doi = {https://doi.org/10.1002/chem.201700236},
   keywords = {G-quadruplex; supramolecular; hydrogen bonding; stacking},
   language = {eng},
   issn = {0947-6539},
   journal = {Chemistry - A European Journal},
   title = {Weak Supramolecular Interactions Governing Parallel and Antiparallel DNA Quadruplexes: Insights from Large-Scale Quantum Mechanics Analysis of Experimentally Derived Models},
   url = {http://dx.doi.org/10.1002/chem.201700236},
   volume = {23},
   year = {2017}
}

TY  - JOUR
ID  - 1373307
AU  - Yurenko, Yevgen - Novotný, Jan - Marek, Radek
PY  - 2017
TI  - Weak Supramolecular Interactions Governing Parallel and Antiparallel DNA Quadruplexes: Insights from Large-Scale Quantum Mechanics Analysis of Experimentally Derived Models
JF  - Chemistry - A European Journal
VL  - 23
IS  - 23
SP  - 5573-5584
EP  - 5573-5584
PB  - Wiley
SN  - 09476539
KW  - G-quadruplex
KW  - supramolecular
KW  - hydrogen bonding
KW  - stacking
UR  - http://dx.doi.org/10.1002/chem.201700236
L2  - http://dx.doi.org/10.1002/chem.201700236
N2  - The topology and energetics of guanine (G) quadruplexes is governed by supramolecular interactions within their strands. In this work, an extensive quantum mechanical (QM) study has been performed to analyze supramolecular interactions that shape the stems of (4+0) parallel (P) and (2+2) antiparallel (AP) quadruplex systems. The large-scale (~400 atoms) models of P and AP were constructed from high-quality experimental structures. The results provide evidence that each of the P and AP structures is shaped by a distinct network of supramolecular interactions. Analysis of electron topological characteristics of hydrogen bonds in P and AP systems indicates that the P model benefits from stronger intratetrad hydrogen bonding. For intertetrad stacking interactions, both noncovalent interaction plot and energy decomposition analysis approaches suggest that the stem of the P quadruplex benefits more from stacking than that of the AP stem; the difference in energetic stabilization for the two topologies is about 10 %. Stronger hydrogen-bonding and stacking interactions in the stem of the P quadruplex, relative to those in the AP system, can be an important indicator to explain the experimental observations that guanine-rich oligonucleotides tend to form all-parallel stems with an all-anti orientation of nucleobases. However, in addition to intrinsic stabilization, partial desolvation effects, which affect the energetics and dynamics of the G-quadruplex folding process, call for further investigations.
ER  -

YURENKO, Yevgen; Jan NOVOTNÝ a Radek MAREK. Weak Supramolecular Interactions Governing Parallel and Antiparallel DNA Quadruplexes: Insights from Large-Scale Quantum Mechanics Analysis of Experimentally Derived Models. \textit{Chemistry - A European Journal}. Weinheim: Wiley, 2017, roč.~23, č.~23, s.~5573-5584. ISSN~0947-6539. Dostupné z: https://doi.org/10.1002/chem.201700236.

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