Nucleic acid quadruplexes based on 8-halo-9-deazaxanthines:
Energetics and non-covalent interactions in quadruplex stems

J 2014

Nucleic acid quadruplexes based on 8-halo-9-deazaxanthines: Energetics and non-covalent interactions in quadruplex stems

YURENKO, Yevgen, Jan NOVOTNÝ, Mariusz P. MITORAJ, Vladimír SKLENÁŘ, Artur MICHALAK et. al.

Základní údaje

Originální název

Nucleic acid quadruplexes based on 8-halo-9-deazaxanthines: Energetics and non-covalent interactions in quadruplex stems

Autoři

YURENKO, Yevgen (804 Ukrajina, domácí), Jan NOVOTNÝ (203 Česká republika, domácí), Mariusz P. MITORAJ (616 Polsko), Vladimír SKLENÁŘ (203 Česká republika, domácí), Artur MICHALAK (616 Polsko) a Radek MAREK (203 Česká republika, garant, domácí)

Vydání

Journal of Chemical Theory and Computation, Washington D.C. American Chemical Society, 2014, 1549-9618

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

Odkazy

DOI: 10.1021/ct5007554

Impakt faktor

Impact factor: 5.498

Kód RIV

RIV/00216224:14740/14:00076936

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1021/ct5007554

UT WoS

000346324000016

Klíčová slova anglicky

nucleic acid; quadruplex; xanthine; halogen; energy of formation; hydrogen bonding; stacking; ion coordination

Štítky

kontrola MP, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 23. 1. 2015 09:29, Martina Prášilová

Anotace

V originále

Structural and energetic features of artificial DNA quadruplexes consisting of base tetrads and their stacks with Na+/K+ ion(s) inside the central pore and incorporating halogenated derivatives of xanthine: 8-fluoro-9-deazaxanthine (FdaX), 8-chloro-9-deazaxanthine (CldaX), 8-bromo-9-deazaxanthine (BrdaX), or 8-iodo-9-deazaxanthine (IdaX), have been investigated by modern state-of-the-art computational tools. The DNA (or RNA) quadruplex models based on 8-halo-9-deazaxanthines are predicted to be more stable relative to those with natural xanthine due to the increased stabilizing contributions coming from all three main types of weak interactions (H-bonding, stacking, and ion coordination). Methods for analyzing the electron density are used to understand the nature of forces determining the stability of the system and to gain a predictive potential. Quadruplex systems incorporating polarizable halogen atoms (chlorine, bromine, or iodine) benefit significantly from the stabilizing stacking between the individual tetrads due to an increased dispersion contribution as compared to xanthine and guanine, natural references used. Ion coordination induces a significant rearrangement of electron density in the quadruplex stem as visualized by electron deformation density (EDD) and analyzed by ETS-NOCV and Voronoi charges. Na+ induces larger electron polarization from the quadruplex towards the ion, whereas K+ has higher propensity to electron sharing (identified by QTAIM delocalization index). We expect that our results will contribute to the development of novel strategies to further modify and analyze the natural G-quadruplex core.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

EE2.3.20.0042, projekt VaV

Název: Internacionalizace programu Strukturní biologie s důrazem na rozvoj nových směrů výzkumu

Přiložené soubory

JCTC14_10_5353_ct5007554.pdf

Požádat o autorskou verzi souboru

Citovat

YURENKO, Yevgen, Jan NOVOTNÝ, Mariusz P. MITORAJ, Vladimír SKLENÁŘ, Artur MICHALAK a Radek MAREK. Nucleic acid quadruplexes based on 8-halo-9-deazaxanthines: Energetics and non-covalent interactions in quadruplex stems. Journal of Chemical Theory and Computation. Washington D.C.: American Chemical Society, 2014, roč. 10, č. 12, s. 5353-5365. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/ct5007554.

@article{1203516,
   author = {Yurenko, Yevgen and Novotný, Jan and Mitoraj, Mariusz P. and Sklenář, Vladimír and Michalak, Artur and Marek, Radek},
   article_location = {Washington D.C.},
   article_number = {12},
   doi = {http://dx.doi.org/10.1021/ct5007554},
   keywords = {nucleic acid; quadruplex; xanthine; halogen; energy of formation; hydrogen bonding; stacking; ion coordination},
   language = {eng},
   issn = {1549-9618},
   journal = {Journal of Chemical Theory and Computation},
   title = {Nucleic acid quadruplexes based on 8-halo-9-deazaxanthines: Energetics and non-covalent interactions in quadruplex stems},
   url = {http://dx.doi.org/10.1021/ct5007554},
   volume = {10},
   year = {2014}
}

TY  - JOUR
ID  - 1203516
AU  - Yurenko, Yevgen - Novotný, Jan - Mitoraj, Mariusz P. - Sklenář, Vladimír - Michalak, Artur - Marek, Radek
PY  - 2014
TI  - Nucleic acid quadruplexes based on 8-halo-9-deazaxanthines: Energetics and non-covalent interactions in quadruplex stems
JF  - Journal of Chemical Theory and Computation
VL  - 10
IS  - 12
SP  - 5353-5365
EP  - 5353-5365
PB  - American Chemical Society
SN  - 15499618
KW  - nucleic acid
KW  - quadruplex
KW  - xanthine
KW  - halogen
KW  - energy of formation
KW  - hydrogen bonding
KW  - stacking
KW  - ion coordination
UR  - http://dx.doi.org/10.1021/ct5007554
L2  - http://dx.doi.org/10.1021/ct5007554
N2  - Structural and energetic features of artificial DNA quadruplexes consisting of base tetrads and their stacks with Na+/K+ ion(s) inside the central pore and incorporating halogenated derivatives of xanthine: 8-fluoro-9-deazaxanthine (FdaX), 8-chloro-9-deazaxanthine (CldaX), 8-bromo-9-deazaxanthine (BrdaX), or 8-iodo-9-deazaxanthine (IdaX), have been investigated by modern state-of-the-art computational tools. The DNA (or RNA) quadruplex models based on 8-halo-9-deazaxanthines are predicted to be more stable relative to those with natural xanthine due to the increased stabilizing contributions coming from all three main types of weak interactions (H-bonding, stacking, and ion coordination). Methods for analyzing the electron density are used to understand the nature of forces determining the stability of the system and to gain a predictive potential. Quadruplex systems incorporating polarizable halogen atoms (chlorine, bromine, or iodine) benefit significantly from the stabilizing stacking between the individual tetrads due to an increased dispersion contribution as compared to xanthine and guanine, natural references used. Ion coordination induces a significant rearrangement of electron density in the quadruplex stem as visualized by electron deformation density (EDD) and analyzed by ETS-NOCV and Voronoi charges. Na+ induces larger electron polarization from the quadruplex towards the ion, whereas K+ has higher propensity to electron sharing (identified by QTAIM delocalization index). We expect that our results will contribute to the development of novel strategies to further modify and analyze the natural G-quadruplex core.
ER  -

YURENKO, Yevgen, Jan NOVOTNÝ, Mariusz P. MITORAJ, Vladimír SKLENÁŘ, Artur MICHALAK a Radek MAREK. Nucleic acid quadruplexes based on 8-halo-9-deazaxanthines: Energetics and non-covalent interactions in quadruplex stems. \textit{Journal of Chemical Theory and Computation}. Washington D.C.: American Chemical Society, 2014, roč.~10, č.~12, s.~5353-5365. ISSN~1549-9618. Dostupné z: https://dx.doi.org/10.1021/ct5007554.

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