1FV8

NMR STUDY OF AN HETEROCHIRAL HAIRPIN

Summary for 1FV8

• Entry DOI: 10.2210/pdb1fv8/pdb
• Descriptor: 5'-D(*TP*AP*TP*CP*AP*(0DT)P*CP*GP*AP*TP*A)-3' (1 entity in total)
• Functional Keywords: hairpin, heterochiral loop, flexibilty, antisense dna, dna
• Total number of polymer chains: 1
• Total formula weight: 3332.21

Authors

El Amri, C.,Mauffret, O.,Santamaria, F.,Rayner, B.,Fermandjian, S. (deposition date: 2000-09-19, release date: 2000-10-11, Last modification date: 2022-02-23)

Primary citation

El Amri, C.,Mauffret, O.,Santamariar, F.,Tevanian, G.,Rayner, B.,Fermandjian, S.
NMR study of a heterochiral DNA hairpin:impact of L-enantiomery in the loop.
J.Biomol.Struct.Dyn., 19:459-470, 2001

PubMed Abstract: We carried out a structural study of the DNA heterochiral strand d (AGCTTATCAT(L)CGATAAGCT), -AT(L)C-, where T(L) (L thymine ) replaces T (natural D-thymine). -AT(L)C- is a structural analog of -ATC- that belongs to a strong topoisomerase II DNA cleavage site and which has been shown to resolve into a hairpin structure with a stem formed by eight Waston-Crick base-pairs and a single residue loop closed by an A.C sheared base-pair. Although - AT(L)C-, like its parent -ATC-, folds into a hairpin structure at low and high DNA concentrations it displays a lower stability (Tm of 56 degrees C versus 58.5 degrees C). Several NMR features in -AT(L)C- account for the disruption of the A.C pairing in the loop and a weakening of the C.G base-pair stability at the stem-loop junction. For instance, the exchange of the loop imino protons with solvent is accelerated compared with the natural oligonucleotide -ATC-. The higher flexibility of the heterochiral loop is confirmed by the results of NMR restrained molecular dynamics. In the calculated final structures of -AT(L)C-, the T10(L) residue moves the A9 and C11 residues away, thus preventing the loop closure through a C.A sheared base-pair and the achievement of a good base-base or sugar-base stacking. Actually, most of the stabilizing interactions present in -ATC- are lost in the heterochiral - AT(L)C- explaining its weaker stability.

PubMed: 11790144

Experimental method

SOLUTION NMR