1d68

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SOLUTION STRUCTURE OF [D(GCGTATACGC)]2

Overview

The solution structure of the alternating pyrimidine-purine DNA duplex, [d(GCGTATACGC)]2 has been determined using two-dimensional nuclear, magnetic resonance techniques and distance geometry methods. Backbone, distance constraints derived from experimental nuclear Overhauser, enhancement and J-coupling torsion angle constraints were required to, adequately define the conformation of the inter-residue backbone linkages, and to avoid underwinding of the duplex. The distance geometry structures, were further refined by back-calculation of the two-dimensional nuclear, Overhauser enhancement spectra to correct spin-diffusion distance errors., Fifteen final structures for [d(GCGTATACGC)]2 were generated from the, refined experimental distance bounds. These structures all exhibit fully, wound B-form geometry with small penalty values (< 1.5 A) against the, distance bounds and small pair-wise root-mean-square deviation values, (typically 0.6 A to 1.5 A). The final structures exhibit positive, base-pair inclination with respect to the helix axis, a marked alternation, in rise and twist, and are shorter and wider than classical fiber B-form, DNA. The purines were found to adopt a sugar pucker close to the C-2'-endo, conformation while pyrimidine sugars exhibited significantly lower, pseudorotation phase angles in the C-1'-exo to C-2'-endo range. The minor, groove cross-strand steric clashes at pyrimidine-purine steps that would, exist in pure B-DNA are attenuated by an increased rise at these steps, (and an increased roll angle at TpA steps). Concomitantly the backbone, torsion angles of the pyrimidine moieties have larger gamma values, larger, epsilon values, and smaller zeta values than the purines. The structures, generated by distance geometry methods were also compared with those, obtained from restrained molecular dynamics with empirical force-field, potentials. The results indicate that the nuclear magnetic, resonance/distance geometry approach alone is capable of elucidating most, of the salient structural features of double-stranded helical nucleic, acids in solution without resorting to empirical energy potentials and, without using any structural assumptions from crystallographic data.

About this Structure

1D68 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

Reference

Solution structure of [d(GCGTATACGC)]2., Cheng JW, Chou SH, Salazar M, Reid BR, J Mol Biol. 1992 Nov 5;228(1):118-37. PMID:1447776

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