A study of 7-deaza-2'-deoxyguanosine 2'-deoxycytidine base pairing in DNA.

Ganguly M, Wang F, Kaushik M, Stone MP, Marky LA, Gold B
Nucleic Acids Res. 2007 35 (18): 6181-95

PMID: 17855404 · PMCID: PMC2094092 · DOI:10.1093/nar/gkm670

The incorporation of 7-deazaguanine modifications into DNA is frequently used to probe protein recognition of H-bonding information in the major groove of DNA. While it is generally assumed that 7-deazaguanine forms a normal Watson-Crick base pair with cytosine, detailed thermodynamic and structural analyses of this modification have not been reported. The replacement of the 7-N atom on guanine with a C-H, alters the electronic properties of the heterocycle and eliminates a major groove cation-binding site that could affect the organization of salts and water in the major groove. We report herein the characterization of synthetic DNA oligomers containing 7-deazaguanine using a variety of complementary approaches: UV thermal melting, differential scanning calorimetry (DSC), circular dichroism (CD), chemical probing and NMR. The results indicate that the incorporation of a 7-deazaguanine modification has a significant effect on the dynamic structure of the DNA at the flanking residue. This appears to be mediated by changes in hydration and cation organization.

MeSH Terms (15)

Base Pairing Calorimetry, Differential Scanning Cations Circular Dichroism Cytosine Deoxycytidine Deoxyguanosine DNA Hydrogen Bonding Nuclear Magnetic Resonance, Biomolecular Nucleic Acid Conformation Spectrophotometry, Ultraviolet Static Electricity Temperature Water

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