Comparative structural analysis by [1H,31P]-NMR and restrained molecular dynamics of two DNA hairpins from a strong DNA topoisomerase II cleavage site
| Autor: | Arsia Amir-Aslani, Serge Fermandjian, Elie Lescot, Monique Monnot, Richard G. Maroun, Olivier Mauffret |
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| Přispěvatelé: | Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), École normale supérieure - Cachan (ENS Cachan)-Centre National de la Recherche Scientifique (CNRS) |
| Jazyk: | angličtina |
| Rok vydání: | 1998 |
| Předmět: |
Models
Molecular Magnetic Resonance Spectroscopy Base Pair Mismatch MESH: Catalytic Domain MESH: DNA Topoisomerases Type II MESH: Base Sequence 01 natural sciences Substrate Specificity chemistry.chemical_compound Structural Biology Catalytic Domain 0303 health sciences biology Hydrogen bond MESH: Nucleic Acid Conformation Oligodeoxyribonucleotides Two-dimensional nuclear magnetic resonance spectroscopy Cytosine MESH: Models Molecular Plasmids Protein Binding DNA Bacterial Stereochemistry Molecular Sequence Data Stacking 010402 general chemistry Cleavage (embryo) 03 medical and health sciences MESH: Plasmids MESH: Protein Binding [SDV.BBM]Life Sciences [q-bio]/Biochemistry Molecular Biology MESH: Hydrogen Bonding Molecular Biology 030304 developmental biology MESH: Base Pair Mismatch MESH: Molecular Sequence Data Base Sequence Oligonucleotide MESH: Magnetic Resonance Spectroscopy Topoisomerase Hydrogen Bonding MESH: DNA Bacterial 0104 chemical sciences Crystallography DNA Topoisomerases Type II chemistry biology.protein MESH: Oligodeoxyribonucleotides Nucleic Acid Conformation MESH: Substrate Specificity DNA |
| Zdroj: | Journal of Molecular Biology Journal of Molecular Biology, Elsevier, 1998, 283 (3), pp.643-55. ⟨10.1006/jmbi.1998.2095⟩ |
| ISSN: | 0022-2836 1089-8638 |
| DOI: | 10.1006/jmbi.1998.2095⟩ |
| Popis: | International audience; The structural analysis of two single-stranded DNAs d(AGCTTATCATCGATAAGCT) (ATC-19) and d(AGCTTATCGATGATAAGCT) (GAT-19) was performed by NMR and restrained molecular dynamics. These oligonucleotides reproduce the 15-33 segment of phage pBR322 DNA, which contains a strong cleavage site for topoisomerase II coupled to the antitumor drugs VP-16 and ellipticine. Because of their partial palindromic nature, the two oligonucleotides ATC-19 and GAT-19 may fold back into stable hairpin structures, consisting of a stem of eight base-pairs and a loop of three residues. NMR assignments and conformational parameters were determined from combined 2D NOESY, COSY and 1H-31P spectra. Conformations of ATC-19 and GAT-19 hairpins were calculated using the X-PLOR 3.1 program. Structures were generated through simulated annealing procedures starting from 50 structures with randomized torsion angles. A good convergence was observed for ATC-19 molecules, while no consensus was found for GAT-19. Within the GAT-19 loop, the base stacking was poor and no hydrogen bond could be detected. In contrast, ATC-19 displayed a well-defined three residue loop stabilized by both extensive base stackings and hydrogen bonding between the N3 atom of the adenine ring and the amino group of the cytosine ring. The results confirm our earlier ATC-19 structure obtained by a completely different calculation procedure (JUMNA) and the higher thermal stability of ATC-19 compared to GAT-19. Moreover, due to its mismatched base-pair, the ATC-19 loop may be better described as a single residue loop rather than a three residue loop. Comparison of this loop to those containing sheared purine.purine base-pairs revealed striking resemblances, particularly on the backbone angle combination. Finally, the differences observed between the ATC-19 and GAT-19 structures could help toward understanding the sequential cleavage of DNA strands by topoisomerase II. |
| Databáze: | OpenAIRE |
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