Tags

Type your tag names separated by a space and hit enter

A-form conformational motifs in ligand-bound DNA structures.
J Mol Biol. 2000 Jul 21; 300(4):819-40.JM

Abstract

Recognition and biochemical processing of DNA requires that proteins and other ligands are able to distinguish their DNA binding sites from other parts of the molecule. In addition to the direct recognition elements embedded in the linear sequence of bases (i.e. hydrogen bonding sites), these molecular agents seemingly sense and/or induce an "indirect" conformational response in the DNA base-pairs that facilitates close intermolecular fitting. As part of an effort to decipher this sequence-dependent structural code, we have analyzed the extent of B-->A conformational conversion at individual base-pair steps in protein and drug-bound DNA crystal complexes. We take advantage of a novel structural parameter, the position of the phosphorus atom in the dimer reference frame, as well as other documented measures of local helical structure, e.g. torsion angles, base-pair step parameters. Our analysis pinpoints ligand-induced conformational changes that are difficult to detect from the global perspective used in other studies of DNA structure. The collective data provide new structural details on the conformational pathway connecting A and B-form DNA and illustrate how both proteins and drugs take advantage of the intrinsic conformational mechanics of the double helix. Significantly, the base-pair steps which exhibit pure A-DNA conformations in the crystal complexes follow the scale of A-forming tendencies exhibited by synthetic oligonucleotides in solution and the known polymorphism of synthetic DNA fibers. Moreover, most crystallographic examples of complete B-to-A deformations occur in complexes of DNA with enzymes that perform cutting or sealing operations at the (O3'-P) phosphodiester linkage. The B-->A transformation selectively exposes sugar-phosphate atoms, such as the 3'-oxygen atom, ordinarily buried within the chain backbone for enzymatic attack. The forced remodeling of DNA to the A-form also provides a mechanism for smoothly bending the double helix, for controlling the widths of the major and minor grooves, and for accessing the minor groove edges of individual base-pairs.

Links

Publisher Full Text

Authors+Show Affiliations

Lu XJ
Department of Chemistry, Wright-Rieman Laboratories, Rutgers, the State University of New Jersey, 610 Taylor Road, Piscataway, NJ, 08854-8087, USA.
Shakked Z
No affiliation info available
Olson WK
No affiliation info available

MeSH

AnimalsBase PairingBase SequenceCisplatinCrystallography, X-RayDNADNA-Binding ProteinsDNA-Directed DNA PolymeraseDeoxyribonucleases, Type II Site-SpecificEndodeoxyribonucleasesHIV Reverse TranscriptaseHumansLigandsModels, MolecularNucleic Acid ConformationProtein ConformationTransposases

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, U.S. Gov't, P.H.S.

Language

eng

PubMed ID

10891271

Citation

Lu, X J., et al. "A-form Conformational Motifs in Ligand-bound DNA Structures." Journal of Molecular Biology, vol. 300, no. 4, 2000, pp. 819-40.
Lu XJ, Shakked Z, Olson WK. A-form conformational motifs in ligand-bound DNA structures. J Mol Biol. 2000;300(4):819-40.
Lu, X. J., Shakked, Z., & Olson, W. K. (2000). A-form conformational motifs in ligand-bound DNA structures. Journal of Molecular Biology, 300(4), 819-40.
Lu XJ, Shakked Z, Olson WK. A-form Conformational Motifs in Ligand-bound DNA Structures. J Mol Biol. 2000 Jul 21;300(4):819-40. PubMed PMID: 10891271.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A-form conformational motifs in ligand-bound DNA structures. AU - Lu,X J, AU - Shakked,Z, AU - Olson,W K, PY - 2000/7/13/pubmed PY - 2000/8/19/medline PY - 2000/7/13/entrez SP - 819 EP - 40 JF - Journal of molecular biology JO - J Mol Biol VL - 300 IS - 4 N2 - Recognition and biochemical processing of DNA requires that proteins and other ligands are able to distinguish their DNA binding sites from other parts of the molecule. In addition to the direct recognition elements embedded in the linear sequence of bases (i.e. hydrogen bonding sites), these molecular agents seemingly sense and/or induce an "indirect" conformational response in the DNA base-pairs that facilitates close intermolecular fitting. As part of an effort to decipher this sequence-dependent structural code, we have analyzed the extent of B-->A conformational conversion at individual base-pair steps in protein and drug-bound DNA crystal complexes. We take advantage of a novel structural parameter, the position of the phosphorus atom in the dimer reference frame, as well as other documented measures of local helical structure, e.g. torsion angles, base-pair step parameters. Our analysis pinpoints ligand-induced conformational changes that are difficult to detect from the global perspective used in other studies of DNA structure. The collective data provide new structural details on the conformational pathway connecting A and B-form DNA and illustrate how both proteins and drugs take advantage of the intrinsic conformational mechanics of the double helix. Significantly, the base-pair steps which exhibit pure A-DNA conformations in the crystal complexes follow the scale of A-forming tendencies exhibited by synthetic oligonucleotides in solution and the known polymorphism of synthetic DNA fibers. Moreover, most crystallographic examples of complete B-to-A deformations occur in complexes of DNA with enzymes that perform cutting or sealing operations at the (O3'-P) phosphodiester linkage. The B-->A transformation selectively exposes sugar-phosphate atoms, such as the 3'-oxygen atom, ordinarily buried within the chain backbone for enzymatic attack. The forced remodeling of DNA to the A-form also provides a mechanism for smoothly bending the double helix, for controlling the widths of the major and minor grooves, and for accessing the minor groove edges of individual base-pairs. SN - 0022-2836 UR - https://www.unboundmedicine.com/medline/citation/10891271/A_form_conformational_motifs_in_ligand_bound_DNA_structures_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0022-2836(00)93690-8 DB - PRIME DP - Unbound Medicine ER -