Triple helices formed at oligopyrimidine*oligopurine sequences with base pair inversions: effect of a triplex-specific ligand on stability and selectivity.
Oligonucleotide-directed triple helix formation is mostly restricted to oligopyrimidine*oligopurine sequences of double helical DNA. An interruption of one or two pyrimidines in the oligopurine target strand leads to a strong triplex destabilisation. We have investigated the effect of nucleotide analogues introduced in the third strand at the site opposite the base pair inversion(s). We show that a 3-nitropyrrole derivative (M) discriminates G*C from C*G, A*T and T*A in the presence of a triplex-specific ligand (a benzo[e]pyridoindole derivative, BePI). N6-methoxy-2,6-diaminopurine (K) binds to an A*T base pair better than a T*A, G*C or C*G base pair. Some discrimination is still observed in the presence of BePI and triplex stability is markedly increased. These findings should help in designing BePI-oligonucleotide conjugates to extend the range of DNA sequences available for triplex formation.
Kukreti
S
S
Laboratoire de Biophysique, Muséum National d'Histoire Naturelle, INSERM U201, CNRS URA481, 43 rue Cuvier, 75231 Paris Cedex 05, France.
Sun
J S
JS
Loakes
D
D
Brown
D M
DM
Nguyen
C H
CH
Bisagni
E
E
Garestier
T
T
Helene
C
C
D007446:Chromosome Inversion; D004247:DNA / Q000737:chemistry* / Q000187:drug effects; D006860:Hydrogen Bonding; D007211:Indoles / Q000494:pharmacology; D008024:Ligands; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides; D011687:Purines; D011725:Pyridines / Q000494:pharmacology; D011743:Pyrimidines
D007211:Indoles; D008024:Ligands; D009841:Oligonucleotides; D011687:Purines; D011725:Pyridines; D011743:Pyrimidines; C051802:triplex DNA; C082732:3-methoxy-7H-8-methyl-11-((3'-amino)propylamino)benzo(e)pyrido(4,3-b)indole; D004247:DNA