NMR structure of a parallel-stranded DNA duplex at atomic resolution

Abstract

DNA dodecamers have been designed with two cytosines on each end and intervening A and T stretches, such that the oligomers have fully complementary A:T base pairs when aligned in the parallel orientation. Spectroscopic (UV, CD and IR), NMR and molecular dynamics studies have shown that oligomers having the sequences d(CCATAATTTACC) and d(CCTATTAAATCC) form a parallel-stranded duplex when dissolved at 1:1 stoichiometry in aqueous solution. This is due to the C:C+ clamps on either end and extensive mismatches in the antiparallel orientation. The structure is stable at neutral and acidic pH. At higher temperatures, the duplex melts into single strands in a highly cooperative fashion. All adenine, cytosine and thymine nucleotides adopt the anti conformation with respect to the glycosidic bond. The A:T base pairs form reverse Watson-Crick base pairs. The duplex shows base stacking and NOEs between the base protons T(H6)/A(H8) and the sugar protons (H1'/H2'/H2") of the preceding nucleotide, as has been observed in antiparallel duplexes. However, no NOEs are observed between base protons H2/H6/H8 of sequential nucleotides, though such NOEs are observed between T(CH3) and A(H8). A three-dimensional structure of the parallel-stranded duplex at atomic resolution has been obtained using molecular dynamics simulations under NMR constraints. The simulated structures have torsional angles very similar to those found in B-DNA duplexes, but the base stacking and helicoid parameters are significantly different.

Biophysical studies with parallel stranded oligoduplex

“…The probabilities of loops or bubbles, helical segments, and unzipping ends in melting DNA, folded and unfolded states (found to be unique for each sequence), that were compatible with CD spectra difference for structural characterization of nucleic acids (Mergny et al, 2005), the alternative conformations that coexist in equilibrium and the range of their fluctuations (Mergny et al, 2005) were described for antiparallel-stranded oligoduplexes. The parallel stranded oligoduplexes were studied before with CD spectroscopy and NMR for structural conformation study (Gundry et al, 2003;Ramsing and Jouim, 1988;Parvathy et al, 2002;Robinson and Wang, 1993;Dolinnya et al, 1997;Aboul-ela et al, 1994;Rippe et al, 1989;Allwi and Santa Licia, 1998;Tchurikov et al, 1989;Bhoumik et al, 1995;Otto et al, 1991;Klysik et al, 1991;Rippe et al, 1992;Williamson, 1994;Wang and Patel, 1994). In this study, the thermal denaturation profiles of parallel stranded oligoduplexes during UV-spectroscopy and fluorescence spectroscopy, for the first time, were shown to follow the similar patterns as were described for antiparallel stranded oligoduplexes.…”

“…These structures of presumptive parallel oligoduplexes were not determined with NMR. NMR data as well as CD data of various parallel oligoduplexes (Gundry et al, 2003;Ramsing and Jouim, 1988;Parvathy et al, 2002;Robinson and Wang, 1993;Dolinnya et al, 1997;Aboul-ela et al, 1994;Rippe et al, 1989;Allwi and Santa Lucia, 1998;Tchurikov et al, 1989;Bhoumik et al, 1995;Otto et al, 1991;Klysik et al, 1991;Rippe et al, 1992;Williamson, 1994;Wang and Patel, 1994). had shown that, despite from the usual Watson-Crick base pairing, these right-handed helical parallel stranded conformation generally included reverse Watson-Crick base pairing, Hoogstein G:C + base pair, Donhue G:C …”

Mechanisms of Antisense Transcription Initiation from the 3′ End of the GAL10 Coding Sequence In Vivo

“…In support of this possibility, previous studies have demonstrated and characterized A·G, A·C, and A·A mismatched base pairs (72)(73)(74)(75)(76)(77)(78). Further, the P1 primer may also randomly hybridize to RNAs (including mRNAs, rRNAs, and tRNAs) at 42°C during cDNA synthesis via matched (A·T and G·C) and previously demonstrated mismatched (G·T, G·A, A·C, T·C, G·G, A·A, T·T, and C·C) base pairs (72)(73)(74)(75)(76)(77)(78)(79)(80)(81)(82)(83)(84). Moreover, random primers target RNAs and, hence, have been used to analyze a broad spectrum of RNAs.…”

Transcription and translation in an RNA world

“…While the energy of the latter can be calculated using conventional methods, these do not allow the calculation of the energy of a parallel duplex. Parallel-stranded DNA duplex structures are known from X-ray studies (Rippe & Jovin 1992;Parvathy et al 2002) and although no-one has synthesized an RNA equivalent, there is little to make one suspect that it could not exist. By analogy with the DNA structures, it can be expected that this would be much less stable than the reverse complementary duplex.…”