Sequence specificity in triple-helix formation: experimental and theoretical studies of the effect of mismatches on triplex stability.
The specificity of a homopyrimidine oligonucleotide binding to a homopurine-homopyrimidine sequence on double-stranded DNA was investigated by both molecular modeling and thermal dissociation experiments. The presence of a single mismatched triplet at the center of the triplex was shown to destabilize the triple helix, leading to a lower melting temperature and a less favorable energy of interaction. A terminal mismatch was less destabilizing than a central mismatch. The extent of destabilization was shown to be dependent on the nature of the mismatch. Both single base-pair substitution and deletion in the duplex DNA target were investigated. When a homopurine stretch was interrupted by one thymine, guanine was the least destabilizing base on the third strand. However, G in the third strand did not discriminate between a C.G and an A.T base pair. If the stretch of purines was interrupted by a cytosine, the presence of pyrimidines (C or T) in the third strand yielded a less destabilizing effect than purines. This study shows that oligonucleotides forming triple helices can discriminate between duplex DNA sequences that differ by one base pair. It provides a basis for the choice of antigene oligonucleotide sequences targeted to selected sequences on duplex DNA.
Mergny
J L
JL
Laboratoire de Biophysique, INSERM U201, CNRS UA481, Paris, France.
Sun
J S
JS
Rougée
M
M
Montenay-Garestier
T
T
Barcelo
F
F
Chomilier
J
J
Hélène
C
C
D001482:Base Composition; D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D006358:Hot Temperature; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D009690:Nucleic Acid Conformation; D013056:Spectrophotometry, Ultraviolet; D013329:Structure-Activity Relationship
D004247:DNA