Modified guanines as constituents of smart ligands for nucleic
acid quadruplexes

J 2016

Modified guanines as constituents of smart ligands for nucleic acid quadruplexes

DUREC, Matúš, Francesco ZACCARIA, Célia FONSECA GUERRA a Radek MAREK

Základní údaje

Originální název

Modified guanines as constituents of smart ligands for nucleic acid quadruplexes

Autoři

DUREC, Matúš (703 Slovensko, domácí), Francesco ZACCARIA (380 Itálie), Célia FONSECA GUERRA (528 Nizozemské království) a Radek MAREK (203 Česká republika, garant, domácí)

Vydání

Chemistry - A European Journal, Weinheim, Wiley-VCH, 2016, 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.201601608

Impakt faktor

Impact factor: 5.317

Kód RIV

RIV/00216224:14740/16:00089862

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1002/chem.201601608

UT WoS

000382885500029

Klíčová slova anglicky

Density functional calculations; DNA recognition; G-quadruplexes; Nucleobases; pi interactions; stacking; hydrogen-bond cooperativity

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 28. 2. 2017 09:17, prof. RNDr. Radek Marek, Ph.D.

Anotace

V originále

Repetitive guanine-rich nucleic acid sequences play a crucial role in maintaining the genome stability and cell live cycle and represent potential targets for regulatory drugs. Recently, it has been demonstrated that the guanine-based ligands with porphyrin core can be used as markers of G-quadruplex assemblies in the cell tissues. In this contribution we explore the model systems of the guanine-based ligands by methods of density-functional theory (DFT). We calculate the energy of formation for modified guanine tetrads as well as those for the modified tetrads stacked on the top of natural guanine tetrads. We decompose interaction energy to the contributions of hydrogen bonding, stacking, and ion coordination and the twist-rise potential energy scan is performed to find the individual local minima. The energy decomposition analysis reveals the impact of various substituents (F, Cl, Br, I, Me, NMe2) on individual energy terms. In addition, we analyze the cooperative reinforcement in forming the modified tetrads and stacked tetrads as well as the frontier orbitals participating in the hydrogen bonding framework involving HOMO-LUMO gap between the occupied sigma(HOMO) on the proton-accepting C=O and =N- groups and unoccupied sigma(LUMO) on the N-H groups. The investigated systems are demonstrated to have a potential in the ligand development mainly due to the stacking enhancement compared to natural guanine, a reference used.

Návaznosti

ED3.2.00/08.0144, projekt VaV

Název: CERIT Scientific Cloud

LM2010005, projekt VaV

Název: Velká infrastruktura CESNET (Akronym: VI CESNET)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Velká infrastruktura CESNET

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

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

Přiložené soubory

CEJ16_22_10912.pdf

Požádat o autorskou verzi souboru

Citovat

DUREC, Matúš, Francesco ZACCARIA, Célia FONSECA GUERRA a Radek MAREK. Modified guanines as constituents of smart ligands for nucleic acid quadruplexes. Chemistry - A European Journal. Weinheim: Wiley-VCH, 2016, roč. 22, č. 31, s. 10912-10922. ISSN 0947-6539. Dostupné z: https://dx.doi.org/10.1002/chem.201601608.

@article{1344476,
   author = {Durec, Matúš and Zaccaria, Francesco and Fonseca Guerra, Célia and Marek, Radek},
   article_location = {Weinheim},
   article_number = {31},
   doi = {http://dx.doi.org/10.1002/chem.201601608},
   keywords = {Density functional calculations; DNA recognition; G-quadruplexes; Nucleobases; pi interactions; stacking; hydrogen-bond cooperativity},
   language = {eng},
   issn = {0947-6539},
   journal = {Chemistry - A European Journal},
   title = {Modified guanines as constituents of smart ligands for nucleic acid quadruplexes},
   url = {http://dx.doi.org/10.1002/chem.201601608},
   volume = {22},
   year = {2016}
}

TY  - JOUR
ID  - 1344476
AU  - Durec, Matúš - Zaccaria, Francesco - Fonseca Guerra, Célia - Marek, Radek
PY  - 2016
TI  - Modified guanines as constituents of smart ligands for nucleic acid quadruplexes
JF  - Chemistry - A European Journal
VL  - 22
IS  - 31
SP  - 10912-10922
EP  - 10912-10922
PB  - Wiley-VCH
SN  - 09476539
KW  - Density functional calculations
KW  - DNA recognition
KW  - G-quadruplexes
KW  - Nucleobases
KW  - pi interactions
KW  - stacking
KW  - hydrogen-bond cooperativity
UR  - http://dx.doi.org/10.1002/chem.201601608
L2  - http://dx.doi.org/10.1002/chem.201601608
N2  - Repetitive guanine-rich nucleic acid sequences play a crucial role in maintaining the genome stability and cell live cycle and represent potential targets for regulatory drugs. Recently, it has been demonstrated that the guanine-based ligands with porphyrin core can be used as markers of G-quadruplex assemblies in the cell tissues. In this contribution we explore the model systems of the guanine-based ligands by methods of density-functional theory (DFT). We calculate the energy of formation for modified guanine tetrads as well as those for the modified tetrads stacked on the top of natural guanine tetrads. We decompose interaction energy to the contributions of hydrogen bonding, stacking, and ion coordination and the twist-rise potential energy scan is performed to find the individual local minima. The energy decomposition analysis reveals the impact of various substituents (F, Cl, Br, I, Me, NMe2) on individual energy terms. In addition, we analyze the cooperative reinforcement in forming the modified tetrads and stacked tetrads as well as the frontier orbitals participating in the hydrogen bonding framework involving HOMO-LUMO gap between the occupied sigma(HOMO) on the proton-accepting C=O and =N- groups and unoccupied sigma(LUMO) on the N-H groups. The investigated systems are demonstrated to have a potential in the ligand development mainly due to the stacking enhancement compared to natural guanine, a reference used.
ER  -

DUREC, Matúš, Francesco ZACCARIA, Célia FONSECA GUERRA a Radek MAREK. Modified guanines as constituents of smart ligands for nucleic acid quadruplexes. \textit{Chemistry - A European Journal}. Weinheim: Wiley-VCH, 2016, roč.~22, č.~31, s.~10912-10922. ISSN~0947-6539. Dostupné z: https://dx.doi.org/10.1002/chem.201601608.

Podrobný výpis o publikaci