Structural Studies of a Stable Parallel-Stranded DNA Duplex Incorporating Isoguanine:Cytosine and Isocytosine:Guanine Basepairs by Nuclear Magnetic Resonance Spectroscopy

Abstract

Isoguanine (2-hydroxyladenine) is a product of oxidative damage to DNA and has been shown to cause mutation. It is also a potent inducer of parallel-stranded DNA duplex structure. The structure of the parallel-stranded DNA duplex (PS-duplex) 5'-d(TiGiCAiCiGiGAiCT) + 5'-d(ACGTGCCTGA), containing the isoguanine (iG) and 5-methyl-isocytosine (iC) bases, has been determined by NMR refinement. All imino protons associated with the iG:C, G:iC, and A:T (except the two terminal A:T) basepairs are observed at 2 degrees C, consistent with the formation of a stable duplex suggested by the earlier Tm measurements [Sugiyama, H., S. Ikeda, and I. Saito. 1996. J. Am. Chem. Soc. 118:9994-9995]. All basepairs are in the reverse Watson-Crick configuration. The structural characteristics of the refined PS-duplex are different from those of B-DNA. The PS duplex has two grooves with similar width (7.0 A) and depth (7.7 A), in contrast to the two distinct grooves (major groove width 11.7 A, depth 8.5 A, and minor groove width 5.7 A, depth 7.5 A) of B-DNA. The resonances of the amino protons of iG and C are clearly resolved and observable, but those of the G and iC are very broad and difficult to observe. Several intercalators with different complexities, including ethidium, daunorubicin, and nogalamycin, have been used to probe the flexibility of the backbone of the (iG, iC)-containing PS-duplex. All of them produce drug-induced UV/vis spectra identical to their respective spectra when bound to B-DNA, suggesting that those drugs bind to the (iG, iC)-containing PS-duplex using similar intercalation processes. The results may be useful in the design of intercalator-conjugated oligonucleotides for antisense applications. The study presented in this paper augments our understanding of a growing number of parallel-stranded DNA structures, including the G-quartet, the i-motif, and the unusual homo basepaired parallel-stranded double helix. Their possible relevance is discussed.

Error‐Prone Translesion DNA Synthesis byEscherichia coli DNA Polymerase IV (DinB) on Templates Containing 1,2‐dihydro‐2‐oxoadenine

“…All imino protons associated with the 2-oxodA:dC basepairs are consistent with the formation of a stable duplex suggested by T m measurements [18]. 2-oxodA might form stable reverse Watson-Crick basepair with the normal dC [41]. However, the base pairing would not be present in the active site of a DNA polymerase, as the sugar-triphosphate moiety could not fit properly in the active site.…”

Stacking Effects on Local Structure in RNA: Changes in the Structure of Tandem GA Pairs when Flanking GC Pairs Are Replaced by isoG−isoC Pairs

“…Similar observations of amino protons of iG and iC in RNA and DNA were reported previously. 27,32 In (GCiGGAiCGCA) 2 , the cross-peaks of iG3 amino-G4H1, iG3H1-G4 amino, iG3H1-G4H1′, iG3H8-G4H8 and typical A-form NOE contacts between C2 and iG3 (Supporting Information Table S1) further indicate formation of Watson-Crick like iGiC base pairs. In (GGiCGAiGCCA) 2 , Watson-Crick like iGiC base pairs are also indicated by cross-peaks of iG6 amino-C7 amino, iG6H1-G2H1, and typical A-form NOE contacts between G2 and iC3 (Supporting Information Table S3).…”

“…[13][14][15][17][18][19] The Watson-Crick like iGiC pair, with the amino and carbonyl groups transposed relative to the Watson-Crick GC pair, provides an expanded alphabet [20][21][22][23][24][25][26] for further understanding interactions that shape nucleic acid structure (Figure 1). 7,[25][26][27][28][29][30][31][32] Here, thermodynamic studies of tandem GA pairs flanked by iGiC pairs are reported along with NMR structures of the RNA duplexes (GCiGGAiCGCA) 2 and (GGiCGAiGCCA) 2 . NMR restrained molecular dynamics and energy minimization of (GCiGGAiCGCA) 2 reveal a conformation of tandem sheared GA pairs closed by Watson-Crick like iGiC pairs.…”

Parallel‐stranded DNA and RNA duplexes – structural features and potential applications

“…Oligonucleotides containing iG and iC formed a highly stable parallel‐stranded structure. As indicated by NMR spectra, all base pairs interacted by reverse Watson–Crick hydrogen bonds and the structure differed from the canonical B‐DNA form .…”