NMR study of a heterochiral DNA hairpin:impact of L-enantiomery in the loop.
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.
El Amri
C
C
Department de Biologie et Pharmacologie Structurales, UMR 8532, CNRS, PR2, Institut Gustave-Roussy, 39, rue Camille-Desmoulins, 94805 Villejuif Cedex, France.
Mauffret
O
O
Santamariar
F
F
Tevanian
G
G
Rayner
S
S
Fermandjian
S
S
D020029:Base Pairing; D001483:Base Sequence; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D008433:Mathematics; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D011522:Protons; D013237:Stereoisomerism; D013696:Temperature; D013816:Thermodynamics
D009838:Oligodeoxyribonucleotides; D011522:Protons; D004247:DNA