Designing a New Class of Bases for Nucleic Acid Quadruplexes
and Quadruplex-Active Ligands

J 2015

Designing a New Class of Bases for Nucleic Acid Quadruplexes and Quadruplex-Active Ligands

BAZZI, Sophia, Jan NOVOTNÝ, Yevgen YURENKO a Radek MAREK

Základní údaje

Originální název

Designing a New Class of Bases for Nucleic Acid Quadruplexes and Quadruplex-Active Ligands

Autoři

BAZZI, Sophia (364 Írán, domácí), Jan NOVOTNÝ (203 Česká republika, domácí), Yevgen YURENKO (804 Ukrajina, domácí) a Radek MAREK (203 Česká republika, garant, domácí)

Vydání

Chemistry - A European Journal, Weinheim, Wiley-VCH, 2015, 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.201500743

Impakt faktor

Impact factor: 5.771

Kód RIV

RIV/00216224:14740/15:00082881

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1002/chem.201500743

UT WoS

000356795000020

Klíčová slova anglicky

Density functional calculations; DNA; G-quadruplexes; ligand design; nucleobases

Štítky

OA, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 29. 3. 2016 14:49, Mgr. Eva Špillingová

Anotace

V originále

A new class of quadruplex nucleobases, derived from 3-deazaguanine, has been designed for various applications as smart quadruplex ligands as well as quadruplex-based aptamers, receptors, and sensors. An efficient strategy for modifying the guanine quadruplex core has been developed and tested by using quantum chemistry methods. Several potential guanine derivatives modified at the 3- or 8-position or both are analyzed, and the results compared to reference systems containing natural guanine. Analysis of the formation energies (BLYP-D3(BJ)/def2-TZVPP level of theory, in combination with the COSMO model for water) in model systems consisting of two and three stacked tetrads with Na+/K+ ion(s) inside the internal channel indicates that the formation of structures with 3-halo-3-deazaguanine bases leads to a substantial gain in energy, as compared to the corresponding reference guanine complexes. The results cast light on changes in the noncovalent interactions (hydrogen bonding, stacking, and ion coordination) in a quadruplex stem upon modification of the guanine core. In particular, the enhanced stability of the modified quadruplexes was shown to originate mainly from increased pi–pi stacking. Our study suggests the 3-halo-3-deazaguanine skeleton as a potential building unit for quadruplex systems and smart G-quadruplex ligands.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

286154, interní kód MU

Název: SYLICA - Synergies of Life and Material Sciences to Create a New Future (Akronym: SYLICA)

Investor: Evropská unie, SYLICA - Synergies of Life and Material Sciences to Create a New Future, Kapacity

Citovat

BAZZI, Sophia, Jan NOVOTNÝ, Yevgen YURENKO a Radek MAREK. Designing a New Class of Bases for Nucleic Acid Quadruplexes and Quadruplex-Active Ligands. Chemistry - A European Journal. Weinheim: Wiley-VCH, 2015, roč. 21, č. 26, s. 9414-9425. ISSN 0947-6539. Dostupné z: https://dx.doi.org/10.1002/chem.201500743.

@article{1299450,
   author = {Bazzi, Sophia and Novotný, Jan and Yurenko, Yevgen and Marek, Radek},
   article_location = {Weinheim},
   article_number = {26},
   doi = {http://dx.doi.org/10.1002/chem.201500743},
   keywords = {Density functional calculations; DNA; G-quadruplexes; ligand design; nucleobases},
   language = {eng},
   issn = {0947-6539},
   journal = {Chemistry - A European Journal},
   title = {Designing a New Class of Bases for Nucleic Acid Quadruplexes and Quadruplex-Active Ligands},
   url = {http://dx.doi.org/10.1002/chem.201500743},
   volume = {21},
   year = {2015}
}

TY  - JOUR
ID  - 1299450
AU  - Bazzi, Sophia - Novotný, Jan - Yurenko, Yevgen - Marek, Radek
PY  - 2015
TI  - Designing a New Class of Bases for Nucleic Acid Quadruplexes and Quadruplex-Active Ligands
JF  - Chemistry - A European Journal
VL  - 21
IS  - 26
SP  - 9414-9425
EP  - 9414-9425
PB  - Wiley-VCH
SN  - 09476539
KW  - Density functional calculations
KW  - DNA
KW  - G-quadruplexes
KW  - ligand design
KW  - nucleobases
UR  - http://dx.doi.org/10.1002/chem.201500743
L2  - http://dx.doi.org/10.1002/chem.201500743
N2  - A new class of quadruplex nucleobases, derived from 3-deazaguanine, has been designed for various applications as smart quadruplex ligands as well as quadruplex-based aptamers, receptors, and sensors. An efficient strategy for modifying the guanine quadruplex core has been developed and tested by using quantum chemistry methods. Several potential guanine derivatives modified at the 3- or 8-position or both are analyzed, and the results compared to reference systems containing natural guanine. Analysis of the formation energies (BLYP-D3(BJ)/def2-TZVPP level of theory, in combination with the COSMO model for water) in model systems consisting of two and three stacked tetrads with Na+/K+ ion(s) inside the internal channel indicates that the formation of structures with 3-halo-3-deazaguanine bases leads to a substantial gain in energy, as compared to the corresponding reference guanine complexes. The results cast light on changes in the noncovalent interactions (hydrogen bonding, stacking, and ion coordination) in a quadruplex stem upon modification of the guanine core. In particular, the enhanced stability of the modified quadruplexes was shown to originate mainly from increased pi–pi stacking. Our study suggests the 3-halo-3-deazaguanine skeleton as a potential building unit for quadruplex systems and smart G-quadruplex ligands.
ER  -

BAZZI, Sophia, Jan NOVOTNÝ, Yevgen YURENKO a Radek MAREK. Designing a New Class of Bases for Nucleic Acid Quadruplexes and Quadruplex-Active Ligands. \textit{Chemistry - A European Journal}. Weinheim: Wiley-VCH, 2015, roč.~21, č.~26, s.~9414-9425. ISSN~0947-6539. Dostupné z: https://dx.doi.org/10.1002/chem.201500743.

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