NMR structure of a gemcitabine-substituted model Okazaki fragment

David Konerding, Thomas L. James, Eric Trump, Ana Maria Soto, Luis A Marky, William H. Gmeiner

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

Gemcitabine (2′-deoxy-2′,2′- difluorodeoxycytidine; dFdCTP is a potent anticancer drug that exerts cytotoxic activity, in part, through incorporation of the nucleoside triphosphate dFdCTP into DNA and perturbations to DNA-mediated processes. The structure of a model Okazaki fragment containing a single dFdC substitution, [GEM], was determined using NMR spectroscopy and restrained molecular dynamics to understand structural distortions that may be induced in replicating DNA resulting from dFdC substitution. The electrostatic surface of [GEM] was also computed to determine how the geminal difluoro group of dFdC perturbs DNA electrostatics. The stability of [GEM] was investigated using temperature-dependent UV spectroscopy. dFdC adopted a C3′-endo conformation in [GEM] and decreased the melting temperature of the duplex by 4.3 °C. dFdC substitution did not decrease helical stacking among adjacent purines in the DNA duplex region. dFdC substitution substantially altered the electrostatic properties of the model Okazaki fragment, with increased electron density in the vicinity of the geminal difluoro group. The results are consistent with dFdC substitution altering the structural, electrostatic, and thermodynamic properties of DNA and interfering in DNA-mediated processes. Interference in DNA-mediated processes due to dFdC substitution likely contributes to the anticancer activity of dFdC.

Original languageEnglish (US)
Pages (from-to)839-846
Number of pages8
JournalBiochemistry
Volume41
Issue number3
DOIs
StatePublished - Jan 22 2002

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gemcitabine
Nuclear magnetic resonance
Air cushion vehicles
Substitution reactions
DNA
Static Electricity
Electrostatics
Purines
Temperature
Okazaki fragments
Molecular Dynamics Simulation
Ultraviolet spectroscopy
Thermodynamics
Nucleosides
Freezing
Nuclear magnetic resonance spectroscopy
Carrier concentration
Melting point
Conformations
Molecular dynamics

ASJC Scopus subject areas

  • Biochemistry

Cite this

Konerding, D., James, T. L., Trump, E., Soto, A. M., Marky, L. A., & Gmeiner, W. H. (2002). NMR structure of a gemcitabine-substituted model Okazaki fragment. Biochemistry, 41(3), 839-846. https://doi.org/10.1021/bi015678l

NMR structure of a gemcitabine-substituted model Okazaki fragment. / Konerding, David; James, Thomas L.; Trump, Eric; Soto, Ana Maria; Marky, Luis A; Gmeiner, William H.

In: Biochemistry, Vol. 41, No. 3, 22.01.2002, p. 839-846.

Research output: Contribution to journalArticle

Konerding, D, James, TL, Trump, E, Soto, AM, Marky, LA & Gmeiner, WH 2002, 'NMR structure of a gemcitabine-substituted model Okazaki fragment', Biochemistry, vol. 41, no. 3, pp. 839-846. https://doi.org/10.1021/bi015678l
Konerding D, James TL, Trump E, Soto AM, Marky LA, Gmeiner WH. NMR structure of a gemcitabine-substituted model Okazaki fragment. Biochemistry. 2002 Jan 22;41(3):839-846. https://doi.org/10.1021/bi015678l
Konerding, David ; James, Thomas L. ; Trump, Eric ; Soto, Ana Maria ; Marky, Luis A ; Gmeiner, William H. / NMR structure of a gemcitabine-substituted model Okazaki fragment. In: Biochemistry. 2002 ; Vol. 41, No. 3. pp. 839-846.
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