Solution Structure of a DNA Decamer Containing the Antiviral Drug Ganciclovir: Combined Use of NMR, Restrained Molecular Dynamics, and Full Relaxation Matrix Refinement

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• 作者：Matthew Foti ; Stephen Marshalko ; Eric Schurter ; Surat Kumar ; G. Peter Beardsley ; and Barry I. Schweitzer
• 刊名：Biochemistry
• 出版年：1997
• 出版时间：May 6, 1997
• 年：1997
• 卷：36
• 期：18
• 页码：5336 - 5345
• 全文大小：230K
• 年卷期：v.36,no.18(May 6, 1997)
• ISSN：1520-4995

文摘

The nucleoside analog9-[(1,3-dihydroxy-2-propoxy)methyl]guanine (ganciclovir,DHPG) isan antiviral drug that is used in the treatment of a variety of herpesviruses in immunocompromisedpatients and in a gene therapy protocol that has shown promisingactivity for the treatment of cancer. Toprobe the structural effects of ganciclovir when incorporated into DNA,we determined and compared thesolution structure of a modified ganciclovir-containing decamer duplex[d(CTG)(ganciclovir)d(ATCCAG)]₂and a control duplex d[(CTGGATCCAG)]₂ using nuclearmagnetic resonance techniques. ¹H and³¹Presonances in both duplexes were assigned using a combination of 2-D¹H and ³¹P NMR experiments.Proton-proton distances determined from NOESY data and dihedralangles determined from DQF-COSYdata were used in restrained molecular dynamics simulations startingfrom canonical A- and B-form DNAmodels. Both the control and ganciclovir sets of simulationsconverged to B-type structures. Thesestructures were subjected to full relaxation matrix refinement toproduce final structures that were inexcellent agreement with the observed NOE intensities. Examinationof the final ganciclovir-containingstructures reveals that the base of the ganciclovir residue is hydrogenbonded to its complementary dCand is stacked in the helix; in fact, the base of ganciclovir exhibitsincreased stacking with the 5' baserelative to the control. Interestingly, some of the mostsignificant distortions in the structures occur 3' tothe lesion site, including a noticeable kink in the sugar-phosphatebackbone at this position. Furtherexamination reveals that the backbone conformation, sugar pucker, andglycosidic torsion angle of theresidue 3' to the lesion site all indicate an A-type conformation atthis position. A possible correlationof these structural findings with results obtained from earlierbiochemical studies will be discussed.