Nucleotides containing variously modified sugars: energetics,
structure, and mechanical properties

J 2016

Nucleotides containing variously modified sugars: energetics, structure, and mechanical properties

YURENKO, Yevgen, Jan NOVOTNÝ, Tymofii NIKOLAIENKO a Radek MAREK

Základní údaje

Originální název

Nucleotides containing variously modified sugars: energetics, structure, and mechanical properties

Autoři

YURENKO, Yevgen (804 Ukrajina, domácí), Jan NOVOTNÝ (203 Česká republika, domácí), Tymofii NIKOLAIENKO (804 Ukrajina) a Radek MAREK (203 Česká republika, garant, domácí)

Vydání

Physical Chemistry Chemical Physics, Cambridge, Royal Society of Chemistry, 2016, 1463-9076

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

DOI: 10.1039/C5CP05478H

Impakt faktor

Impact factor: 4.123

Kód RIV

RIV/00216224:14740/16:00089180

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1039/C5CP05478H

UT WoS

000369482100029

Klíčová slova anglicky

nucleotides; conformational flexibility; relaxed force constants; torsion angle; fluorine

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 17. 3. 2017 13:44, Mgr. Eva Špillingová

Anotace

V originále

The influence of various sugar residue modifications on intrinsic energetic, conformational, and mechanical properties of 2'-deoxyribonucleotide-5'-monophosphates (dNs) was comprehensively investigated using modern quantum chemical approaches. In total, fourteen sugar modifications, including double bonds and heteroatoms (S and N) inside the sugar ring, as well as fluorination in various positions, were analyzed. Among hundreds of possible conformational states of dNs, only two – AI and BI, corresponding to the most biologically significant forms of a double-helical DNA, were considered for each dN. It was established that the most of the studied modifications tend to strongly stabilize either AI or BI conformation of dNs both in the gas phase and in aqueous solution (modelled by implicit solvent models). Therefore, some of these modifications can be used as a tool for reducing structural polymorphism of nucleic acids in solution as well as for designing oligonucleotides with specific structural features. The evaluation of relaxed force constants (RFC) for glycosidic bonds suggests that the majority of the studied modifications of the sugar residue yield increased strengths of glycosidic bonds in dNs, and can therefore be used for designing modified nucleic acids with an increased resistance to abasic lesions. The most significant reinforcement of the glycosidic bond occurs in dNs containing the CF2 group instead of the O4' oxygen and the fluorine atom at the 2'-alpha-position. The calculation of the RFC and vibrational root-mean-square (VRMS) deviations for conformational degrees of freedom revealed a strong dependence between mechanical properties of dNs and their energetic characteristics. In particular, electronic energies of AI and BI conformers of dNs calculated in vacuo are closely connected with the values of relaxed force constants (RFC) for the delta angle: the higher RFC(delta) values correspond to more energetically favorable conformers.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

ED3.2.00/08.0144, projekt VaV

Název: CERIT Scientific Cloud

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

YURENKO, Yevgen, Jan NOVOTNÝ, Tymofii NIKOLAIENKO a Radek MAREK. Nucleotides containing variously modified sugars: energetics, structure, and mechanical properties. Physical Chemistry Chemical Physics. Cambridge: Royal Society of Chemistry, 2016, roč. 18, č. 3, s. 1615-1628. ISSN 1463-9076. Dostupné z: https://dx.doi.org/10.1039/C5CP05478H.

@article{1317956,
   author = {Yurenko, Yevgen and Novotný, Jan and Nikolaienko, Tymofii and Marek, Radek},
   article_location = {Cambridge},
   article_number = {3},
   doi = {http://dx.doi.org/10.1039/C5CP05478H},
   keywords = {nucleotides; conformational flexibility; relaxed force constants; torsion angle; fluorine},
   language = {eng},
   issn = {1463-9076},
   journal = {Physical Chemistry Chemical Physics},
   title = {Nucleotides containing variously modified sugars: energetics, structure, and mechanical properties},
   url = {http://dx.doi.org/10.1039/C5CP05478H},
   volume = {18},
   year = {2016}
}

TY  - JOUR
ID  - 1317956
AU  - Yurenko, Yevgen - Novotný, Jan - Nikolaienko, Tymofii - Marek, Radek
PY  - 2016
TI  - Nucleotides containing variously modified sugars: energetics, structure, and mechanical properties
JF  - Physical Chemistry Chemical Physics
VL  - 18
IS  - 3
SP  - 1615-1628
EP  - 1615-1628
PB  - Royal Society of Chemistry
SN  - 14639076
KW  - nucleotides
KW  - conformational flexibility
KW  - relaxed force constants
KW  - torsion angle
KW  - fluorine
UR  - http://dx.doi.org/10.1039/C5CP05478H
L2  - http://dx.doi.org/10.1039/C5CP05478H
N2  - The influence of various sugar residue modifications on intrinsic energetic, conformational, and mechanical properties of 2'-deoxyribonucleotide-5'-monophosphates (dNs) was comprehensively investigated using modern quantum chemical approaches. In total, fourteen sugar modifications, including double bonds and heteroatoms (S and N) inside the sugar ring, as well as fluorination in various positions, were analyzed. Among hundreds of possible conformational states of dNs, only two – AI and BI, corresponding to the most biologically significant forms of a double-helical DNA, were considered for each dN. It was established that the most of the studied modifications tend to strongly stabilize either AI or BI conformation of dNs both in the gas phase and in aqueous solution (modelled by implicit solvent models). Therefore, some of these modifications can be used as a tool for reducing structural polymorphism of nucleic acids in solution as well as for designing oligonucleotides with specific structural features. The evaluation of relaxed force constants (RFC) for glycosidic bonds suggests that the majority of the studied modifications of the sugar residue yield increased strengths of glycosidic bonds in dNs, and can therefore be used for designing modified nucleic acids with an increased resistance to abasic lesions. The most significant reinforcement of the glycosidic bond occurs in dNs containing the CF2 group instead of the O4' oxygen and the fluorine atom at the 2'-alpha-position. The calculation of the RFC and vibrational root-mean-square (VRMS) deviations for conformational degrees of freedom revealed a strong dependence between mechanical properties of dNs and their energetic characteristics. In particular, electronic energies of AI and BI conformers of dNs calculated in vacuo are closely connected with the values of relaxed force constants (RFC) for the delta angle: the higher RFC(delta) values correspond to more energetically favorable conformers.
ER  -

YURENKO, Yevgen, Jan NOVOTNÝ, Tymofii NIKOLAIENKO a Radek MAREK. Nucleotides containing variously modified sugars: energetics, structure, and mechanical properties. \textit{Physical Chemistry Chemical Physics}. Cambridge: Royal Society of Chemistry, 2016, roč.~18, č.~3, s.~1615-1628. ISSN~1463-9076. Dostupné z: https://dx.doi.org/10.1039/C5CP05478H.

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