A New Program for the Analysis of Nucleic Acid Structure: Implications for Nucleic Acid Structure Interpretation

Structure of the CAP-DNA Complex at 2.5 Å Resolution: A Complete Picture of the Protein-DNA Interface

“…The primary kinks exhibit roll angles of 52°and 35°and twist angles of 17°and 12° (Babcock & Olson, 1993;Figure 3(c)). The DNA deformation in each primary kink is remarkably localized, with all DNA deformation occurring at a single nucleotide pairnucleotide pair step and with the flanking nucleotide pairs exhibiting the standard B-DNA geometry (Figure 3(c)).…”

“…The primary kinks result in Table 1. Distances and angles Babcock & Olson, 1993). Illustrations in this and subsequent Figures were prepared using MOLSCRIPT (Kraulis, 1991).…”

Solution conformation of the (+)-trans-anti-[BPh]dA adduct opposite dT in a DNA duplex: Intercalation of the covalently attached benzo[c]phenanthrene to the 5'-side of the adduct site without disruption of the modified base pair

“…The dC5*dG18 and [BPh]dA6*dT17 base pairs which flank the intercalation site adopt Watson-Crick pairing alignments. We note that the [BPh] dA6-dT 17 pair is propeller-twisted by 15°[ computed using the approach of Babcock and Olson (1993)] with the minor groove edge of [BPh]dA6 tipped toward the flanking dC7-dG16 base pair. The intercalation site is wedge-shaped at the dC5-[BPh]dA6 step, while the dTl7 and dG18 bases are parallel to each other at the dT17-dG18 step.…”

The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids

“…The derivative information ( Table 2 b) is calculated from the atomic coordinates and includes chemical bond lengths and angles, torsion angles, virtual bond lengths and angles involving phosphorus atoms, and base morphology parameters calculated according to various algorithms (8)(9)(10)(11)(12).…”

“…for those structures that contain only one strand of the double helix in the asymmetric unit. Other structural features, for which there is demonstrated algorithmic sensitivity, are calculated using existing programs (8)(9)(10)(11)(12) minimally modified to facilitate the automated processing of all of the structures in the database.…”