Phosphorus Chemical Shifts in a Nucleic Acid Backbone from
Combined Molecular Dynamics and Density Functional Calculations

J 2010

Phosphorus Chemical Shifts in a Nucleic Acid Backbone from Combined Molecular Dynamics and Density Functional Calculations

PŘECECHTĚLOVÁ, Jana, Petr NOVÁK, Markéta MUNZAROVÁ, Martin KAUPP, Vladimír SKLENÁŘ et. al.

Základní údaje

Originální název

Phosphorus Chemical Shifts in a Nucleic Acid Backbone from Combined Molecular Dynamics and Density Functional Calculations

Autoři

PŘECECHTĚLOVÁ, Jana (203 Česká republika, domácí), Petr NOVÁK (203 Česká republika, domácí), Markéta MUNZAROVÁ (203 Česká republika, domácí), Martin KAUPP (276 Německo) a Vladimír SKLENÁŘ (203 Česká republika, garant, domácí)

Vydání

The Journal of the American Chemical Society, Washington, D.C. American Chemical Society, 2010, 0002-7863

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Česká republika

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 9.023

Kód RIV

RIV/00216224:14310/10:00040633

Organizační jednotka

Přírodovědecká fakulta

UT WoS

000285080400022

Klíčová slova anglicky

MD DFT nucleic acids NMR phosphorus

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 10. 3. 2011 13:02, prof. RNDr. Vladimír Sklenář, DrSc.

Anotace

V originále

A comprehensive quantum chemical analysis of the influence of backbone torsion angles on 31P chemical shifts in DNAs has been carried out. An extensive DFT study employed snapshots obtained from the molecular dynamics simulation of [d(CGCGAATTCGCG)]2 to construct geometries of a hydrated dimethyl phosphate, which was used as a model for the phosphodiester linkage. Our calculations provided differences of 2.1 +/- 0.3 and 1.6 +/- 0.3 ppm between the BI and BII chemical shifts in two B-DNA residues of interest, which is in a very good agreement with the difference of 1.6 ppm inferred from experimental data. A more negative 31P chemical shift for a residue in pure BI conformation compared to residues in mixed BI/BII conformation states is provided by DFT, in agreement with the NMR experiment. Statistical analysis of the MD/DFT data revealed a large dispersion of chemical shifts in both BI and BII regions of DNA structures. 31P chemical shift ranges within 3.5 +/- 0.8 ppm in the BI region and within 4.5 +/- 1.5 ppm in the BII region. While the 31P chemical shift becomes more negative with increasing alpha in BI-DNA, it has the opposite trend in BII-DNA when both alpha and zeta increase simultaneously. The 31P chemical shift is dominated by the torsion angles alpha and zeta, while an implicit treatment of beta and epsilon is sufficient. The presence of an explicit solvent leads to a damping and a 2-3 ppm upfield shift of the torsion angle dependences.

Návaznosti

IAA500040903, projekt VaV

Název: Biofyzika a bioinformatika genomových fragmentů DNA velice bohatých na guanin a adenin

Investor: Akademie věd ČR, Biofyzika a bioinformatika genomových fragmentů DNA velice bohatých na guanin a adenin

LC06030, projekt VaV

Název: Biomolekulární centrum

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Biomolekulární centrum

MSM0021622413, záměr

Název: Proteiny v metabolismu a při interakci organismů s prostředím

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Proteiny v metabolismu a při interakci organismů s prostředím

Citovat

PŘECECHTĚLOVÁ, Jana, Petr NOVÁK, Markéta MUNZAROVÁ, Martin KAUPP a Vladimír SKLENÁŘ. Phosphorus Chemical Shifts in a Nucleic Acid Backbone from Combined Molecular Dynamics and Density Functional Calculations. The Journal of the American Chemical Society. Washington, D.C.: American Chemical Society, 2010, roč. 132, č. 48, s. 17139–17148. ISSN 0002-7863.

@article{910251,
   author = {Přecechtělová, Jana and Novák, Petr and Munzarová, Markéta and Kaupp, Martin and Sklenář, Vladimír},
   article_location = {Washington, D.C.},
   article_number = {48},
   keywords = {MD DFT nucleic acids NMR phosphorus},
   language = {eng},
   issn = {0002-7863},
   journal = {The Journal of the American Chemical Society},
   title = {Phosphorus Chemical Shifts in a Nucleic Acid Backbone from Combined Molecular Dynamics and Density Functional Calculations},
   url = {http://pubs.acs.org/doi/abs/10.1021/ja104564g},
   volume = {132},
   year = {2010}
}

TY  - JOUR
ID  - 910251
AU  - Přecechtělová, Jana - Novák, Petr - Munzarová, Markéta - Kaupp, Martin - Sklenář, Vladimír
PY  - 2010
TI  - Phosphorus Chemical Shifts in a Nucleic Acid Backbone from Combined Molecular Dynamics and Density Functional Calculations
JF  - The Journal of the American Chemical Society
VL  - 132
IS  - 48
SP  - 17139–17148
EP  - 17139–17148
PB  - American Chemical Society
SN  - 00027863
KW  - MD DFT nucleic acids NMR phosphorus
UR  - http://pubs.acs.org/doi/abs/10.1021/ja104564g
N2  - A comprehensive quantum chemical analysis of the influence of backbone torsion angles on 31P chemical shifts in DNAs has been carried out. An extensive DFT study employed snapshots obtained from the molecular dynamics simulation of [d(CGCGAATTCGCG)]2 to construct geometries of a hydrated dimethyl phosphate, which was used as a model for the phosphodiester linkage. Our calculations provided differences of 2.1 +/- 0.3 and 1.6 +/- 0.3 ppm between the BI and BII chemical shifts in two B-DNA residues of interest, which is in a very good agreement with the difference of 1.6 ppm inferred from experimental data. A more negative 31P chemical shift for a residue in pure BI conformation compared to residues in mixed BI/BII conformation states is provided by DFT, in agreement with the NMR experiment. Statistical analysis of the MD/DFT data revealed a large dispersion of chemical shifts in both BI and BII regions of DNA structures. 31P chemical shift ranges within 3.5 +/- 0.8 ppm in the BI region and within 4.5 +/- 1.5 ppm in the BII region. While the 31P chemical shift becomes more negative with increasing alpha in BI-DNA, it has the opposite trend in BII-DNA when both alpha and zeta increase simultaneously. The 31P chemical shift is dominated by the torsion angles alpha and zeta, while an implicit treatment of beta and epsilon is sufficient. The presence of an explicit solvent leads to a damping and a 2-3 ppm upfield shift of the torsion angle dependences.
ER  -

PŘECECHTĚLOVÁ, Jana, Petr NOVÁK, Markéta MUNZAROVÁ, Martin KAUPP a Vladimír SKLENÁŘ. Phosphorus Chemical Shifts in a Nucleic Acid Backbone from Combined Molecular Dynamics and Density Functional Calculations. \textit{The Journal of the American Chemical Society}. Washington, D.C.: American Chemical Society, 2010, roč.~132, č.~48, s.~17139–17148. ISSN~0002-7863.

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