Structural influence of RNA incorporation in DNA: Quantitative nuclear magnetic resonance refinement of d(CG)r(CG)d(CG) and d(CG)r(C)d(TAGCG)

Abstract

RNA and DNA adopt different types of conformations, i.e., A-type with C3'-endo sugar pucker for RNA and B-type with C2'-endo sugar pucker for DNA, respectively. The structural influence of the incorporation of RNA nucleotides into DNA is less understood. In this paper, we present the three-dimensional structures of two RNA-containing oligonucleotides, d(CG)r(CG)d(CG) and d(CG)r(C)d-(TAGCG), as determined by the NMR refinement procedure, and assess the possible structural perturbation of DNA induced by RNA. With a single RNA insertion into an octamer DNA, its overall conformation remains as the canonical B-DNA, except that the sugar pucker of the rC3 residue is C3'-endo (pseudorotation angle P = 3.6 degrees). In contrast, the hybrid hexamer is neither the pure B-DNA nor the pure A-DNA conformation. Instead, we propose a model in which the DNA parts adopt B conformation, whereas the RNA part adopts A conformation, with the overall conformation closer to A-DNA. To ensure an exhaustive search of the conformational space, the model was subjected to 100-ps simulated annealing with slow cooling or 100-ps molecular dynamics with subsequent quenching. Models obtained at different time points of the trajectories were further subjected to the SPEDREF NOE refinement [Robinson & Wang (1992) Biochemistry 31, 3524] and they appeared to arrive at a convergent model (< 0.5 A RMSD for the central four base pairs). The consensus hexamer structure contains a significant discontinuity at the (rG4)p(dC5) step with a base pair tilt angle of 6.7 degrees and roll angle of 11.5 degrees.(ABSTRACT TRUNCATED AT 250 WORDS)

Human chromosomal centromere (AATGG)n sequence forms stable structures with unusual base pairs

“…2A, there is no interruption of the connectivity for sequential assignment and every aromatic proton (H 6 and H s) has crosspeaks to the HZlH z' of its own sugar and the sugar on the 3' side, confirming the helical nature of the backbone. To have a more definitive view of the possible structure, several models (including blunt-ended 6-bp duplexes with type-I or type-II G-A mismatches, or a 5-bp duplex with a 3'-overhang G, all with an overall B or A conformation) were constructed and subjected to NOE-constrained refinement by the procedure SPEDREF [11] and a simulated annealing (SA) procedure using X-PLOR [12,15]. Our results indicated that the most plausibe model is a 6-bp B-DNA duplex with type-I G-A base pairs.…”

“…The deblocked oligonucleotides were purified by Sepharose G-50 column chromatography. Solutions of the DNA oligomers (-5 mM duplex) with 150 mM NaCI and 50 mM 'phosphate buffer (pH 7.0) were prepared in 0.5 mi of I)20 as described earlier [11,12]. NMR spectra were collected on either a GE GN500 or a Varian VXR500 500 MHz spectrometer and the data were processed with FELIX via [13].…”

Unveiling the non-repair face of the Base Excision Repair pathway in RNA processing: A missing link between DNA repair and gene expression?

“…It has been studied how the additional presence of a reactive 2′-hydroxyl group on the sugar ring may: i) alter the DNA physical properties, reducing its elasticity [102,103] and structure in a sequence dependent manner [104][105][106][107][108]; ii) induce DNA replication or transcription arrest making the DNA backbone prone to hydrolysis triggering a persistent genomic instability [103,108,109]. This incorporation occurs quite frequently into the cell [110,111], potentially during every DNA replication reaction [110].…”

Effect of Ribonucleotides Embedded in a DNA Template on HIV-1 Reverse Transcription Kinetics and Fidelity

“…Several studies have reported that an rNMP present in dsDNA does change the structure of the duplex DNA by promoting a shift from a B-form helix to an A-form (14,15,17). To investigate the effect of the rNMP present in our DNA tem- plate, we utilized CD, which has been employed to monitor changes in the structure of DNA (16,33).…”