1ana

From Proteopedia

proteopedia linkproteopedia link

Template:STRUCTURE 1ana

HELIX GEOMETRY AND HYDRATION IN AN A-DNA TETRAMER. IC-C-G-G

Overview

The DNA oligomer of sequence IC-C-G-G has been synthesized, and its X-ray crystal structure solved at a resolution of 2.0 A, using anomalous scattering from iodines in phase analysis: 48 cycles of Jack-Levitt restrained least-squares refinement resulted in a residual error of 19.9% over all data, or 16.5% for two-sigma data. Two double-helical tetramers stack in the crystal to form a continuous octamer, except for the two missing phosphate connections across the center. The octamer has a mean helix rotation of 33.7 degrees (10.7 base-pairs per turn), rise of 2.87 A, mean inclination angle of base-pairs of 14 degrees, and mean base-pair propeller twist of +16.3 degrees. Local variations in both helix rotation and base plane roll angles, including those across the center of the octamer, are as predicted from base sequence by sum functions sigma 1 and sigma 2. The three known DNA octamers: IC-C-G-G/IC-C-G-G, G-G-T-A-T-A-C-C and G-G-C-C-G-G-C-C, make up a graded series in this order, with monotonically changing structural parameters. An exhaustive comparison of torsion angle correlations among the known A helices confirms some structural expectations and reveals some new features. 86 water molecules have been located per double-helical IC-C-G-G tetramer (the asymmetric unit), of which 451/2 per tetramer lie within a first hydrogen-bonded shell of hydration. No ordered water structure is observed comparable to the minor groove spine of hydration in B-DNA.

About this Structure

The following page contains interesting information on the relation of 1ANA with [DNA]. Full crystallographic information is available from OCA.

Reference

Helix geometry and hydration in an A-DNA tetramer: IC-C-G-G., Conner BN, Yoon C, Dickerson JL, Dickerson RE, J Mol Biol. 1984 Apr 25;174(4):663-95. PMID:6726797 Page seeded by OCA on Fri May 2 10:28:35 2008