Exploring the Structure of a DNA Hairpin with the Help of NMR
Spin-spin Coupling Constants: An Experimental and Quantum
Chemical Investigation

J 2002

Exploring the Structure of a DNA Hairpin with the Help of NMR Spin-spin Coupling Constants: An Experimental and Quantum Chemical Investigation

SYCHROVSKÝ, Vladimír, Jaroslav VACEK, Pavel HOBZA, Lukáš ŽÍDEK, Vladimír SKLENÁŘ et. al.

Základní údaje

Originální název

Exploring the Structure of a DNA Hairpin with the Help of NMR Spin-spin Coupling Constants: An Experimental and Quantum Chemical Investigation

Autoři

SYCHROVSKÝ, Vladimír (203 Česká republika), Jaroslav VACEK (203 Česká republika), Pavel HOBZA (203 Česká republika), Lukáš ŽÍDEK (203 Česká republika, domácí), Vladimír SKLENÁŘ (203 Česká republika, garant, domácí) a Dieter CREMER (752 Švédsko)

Vydání

Journal of Physical Chemistry B, USA, The American Chemical Society, 2002, 1089-5639

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

Impakt faktor

Impact factor: 2.765

Kód RIV

RIV/00216224:14310/02:00006454

Organizační jednotka

Přírodovědecká fakulta

UT WoS

000178273500038

Klíčová slova anglicky

NMR; coupling constants; DNA hairpin DFT

Štítky

coupling constants, DNA hairpin DFT, NMR

Změněno: 9. 3. 2015 05:41, prof. Mgr. Lukáš Žídek, Ph.D.

Anotace

V originále

A 13C, 15N-labeled DNA hairpin molecule of the sequence d(GCGAAGC) = d(G1C2G3A4A5G6C7) is investigated by NMR spectroscopy to determine one-bond and two-bond NMR spin-spin coupling constants 1J(X, H) (X= C, N), 1J(C, X) (X= C, N), and 2J(X,H) (X=C,N). Measured J values for the Watson-Crick (WC) base-pairs G1C7, G6C2, the mismatched base-pair G3A5 and the unpaired base A4 were compared with calculated J values to verify sign and magnitude. For the J-calculations, coupled perturbed density functional theory in connection with the B3LYP hybrid functional and basis sets (9s5p1d/5s,1p)[6s,4p,1d/3s,1p] as well as (11s,7p,2d/6s,2p)[7s,6p,2d/4s,2p] was employed to determine diamagnetic spin-orbit, paramagnetic spin-orbit, Fermi contact, and spin-dipolar contributions to the total isotropic coupling constant J. Coupling constants 1J(C,H) and 2J(N,H) turn out to be very sensitive to the position of C and N in the pyrimidine or purine rings and, therefore, can be used for rapid structure determination. Coupling constant 1J(N1,C6) in G of GC clearly reflects the impact of H-bonding by an increase from -6.5 to -10.6 Hz. The direct investigation of H-bonding via the 2J(N,N') coupling constants reveals that these parameters depend on the distance R(N-N'), the bending angle N-H..N', and the degree of planarity at the H-donor group. Different types of H-bonding were identified. H-bonding is weaker in AG and therefore, leads to smaller changes in the J values of the bases A and G upon pairing than in the case of the WC base-pair GC.

Návaznosti

LN00A016, projekt VaV

Název: BIOMOLEKULÁRNÍ CENTRUM

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

Citovat

SYCHROVSKÝ, Vladimír, Jaroslav VACEK, Pavel HOBZA, Lukáš ŽÍDEK, Vladimír SKLENÁŘ a Dieter CREMER. Exploring the Structure of a DNA Hairpin with the Help of NMR Spin-spin Coupling Constants: An Experimental and Quantum Chemical Investigation. Journal of Physical Chemistry B. USA: The American Chemical Society, 2002, roč. 106, č. 29, s. 10242-10250. ISSN 1089-5639.

@article{405487,
   author = {Sychrovský, Vladimír and Vacek, Jaroslav and Hobza, Pavel and Žídek, Lukáš and Sklenář, Vladimír and Cremer, Dieter},
   article_location = {USA},
   article_number = {29},
   keywords = {NMR; coupling constants; DNA hairpin DFT},
   language = {eng},
   issn = {1089-5639},
   journal = {Journal of Physical Chemistry B},
   title = {Exploring the Structure of a DNA Hairpin with the Help of NMR Spin-spin Coupling Constants: An Experimental and Quantum Chemical Investigation},
   volume = {106},
   year = {2002}
}

TY  - JOUR
ID  - 405487
AU  - Sychrovský, Vladimír - Vacek, Jaroslav - Hobza, Pavel - Žídek, Lukáš - Sklenář, Vladimír - Cremer, Dieter
PY  - 2002
TI  - Exploring the Structure of a DNA Hairpin with the Help of NMR Spin-spin Coupling Constants: An Experimental and Quantum Chemical Investigation
JF  - Journal of Physical Chemistry B
VL  - 106
IS  - 29
SP  - 10242
EP  - 10242
PB  - The American Chemical Society
SN  - 10895639
KW  - NMR
KW  - coupling constants
KW  - DNA hairpin DFT
N2  - A 13C, 15N-labeled DNA hairpin molecule of the sequence d(GCGAAGC) = d(G1C2G3A4A5G6C7) is investigated by NMR spectroscopy to determine one-bond and two-bond NMR spin-spin coupling constants 1J(X, H) (X= C, N), 1J(C, X) (X= C, N), and 2J(X,H) (X=C,N). Measured J values for the Watson-Crick (WC) base-pairs G1C7, G6C2, the mismatched base-pair G3A5 and the unpaired base A4 were compared with calculated J values to verify sign and magnitude. For the J-calculations, coupled perturbed density functional theory in connection with the B3LYP hybrid functional and basis sets (9s5p1d/5s,1p)[6s,4p,1d/3s,1p] as well as (11s,7p,2d/6s,2p)[7s,6p,2d/4s,2p] was employed to determine diamagnetic spin-orbit, paramagnetic spin-orbit, Fermi contact, and spin-dipolar contributions to the total isotropic coupling constant J. Coupling constants 1J(C,H) and 2J(N,H) turn out to be very sensitive to the position of C and N in the pyrimidine or purine rings and, therefore, can be used for rapid structure determination. Coupling constant 1J(N1,C6) in G of GC clearly reflects the impact of H-bonding by an increase from -6.5 to -10.6 Hz. The direct investigation of H-bonding via the 2J(N,N') coupling constants reveals that these parameters depend on the distance R(N-N'), the bending angle N-H..N', and the degree of planarity at the H-donor group. Different types of H-bonding were identified. H-bonding is weaker in AG and therefore, leads to smaller changes in the J values of the bases A and G upon pairing than in the case of the WC base-pair GC.
ER  -

SYCHROVSKÝ, Vladimír, Jaroslav VACEK, Pavel HOBZA, Lukáš ŽÍDEK, Vladimír SKLENÁŘ a Dieter CREMER. Exploring the Structure of a DNA Hairpin with the Help of NMR Spin-spin Coupling Constants: An Experimental and Quantum Chemical Investigation. \textit{Journal of Physical Chemistry B}. USA: The American Chemical Society, 2002, roč.~106, č.~29, s.~10242-10250. ISSN~1089-5639.

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