SUNY at Albany
June 19-23, 2001
Interaction of EtBr and NMM-porphyrin with the parallel-stranded DNA formed by 3'-d(GTGTGTGTGG)-pO(CH2CH2O)3p-d(GGTGTGTGTG)-3' oligonucleotide
The GT repeats are abundant in telomeres, microsatellites and regulatory regions of genomes. The formation of quadruplex structure by two self-folded oligonucleotides 3'-d(GT)5-pO(CH2CH2O)3p-d(GT)5-3' have been reported . Conformational diversity of the GT repetitive sequence has been observed earlier , where the substitution of the terminal T for G in d(GT)5 strand led to formation of a novel parallel-stranded (ps) intramolecular double helix with GG and TT bases (hp-GT) . In the present work we continued investigation of the conformational features of the hp-GT ps-DNA. The ps double helix was probed with the intercalator EtBr and porphyrin (NMM) . The DNA duplexes both with parallel (ps-t1)  and antiparallel (aps) strands were used as the references.
The following oligonucleotides were studied:
All experiments were run in 10 mM Na-phosphate buffer, pH 7, 0.1 M NaCl, at 3¼C. The EtBr binding isotherms were obtained by fluorescence emission, which is known to originate from intercalated EtBr molecules with a high quantum yield [2-3]. The parameters of EtBr anticooperative binding to the ps and aps hairpins were determined using a statististical mechanical treatment for binding ligands with exclusion length to a finite lattice . The free energy of EtBr binding was found to be close for the both type duplexes: DG(hp-GT) = (6.6±0.1) kcal/mol; D G (ps-tl) = (6.8±0.1) kcal/mol; D G (dsARB) = (6.4±0.1) kcal/mol. Unlike this, the mean EtBr exclusion length (n) of the two ps duplexes was found to be less than that of the aps duplex dsARB: n (hp-GT) = (2.4±0.1) bp; n(ns-tl) = (2.1±0.1) bp; n(dsARB) = (3.0±0.2) bp. These data imply that the ps DNA conformational flexibility permits a maximal (~50%) extension of the structure upon binding of the intercalator.
The NMM porphyrin ligand is known to be a specific ligand for a DNA tetraplex structure . Its binding to the aps Watson-Crick duplex is negligible. Here we have shown that the ps DNA hp-GT practically does not interact with NMM, similar to the aps double helix.References and Footnotes
Olga F. Borisova and Anna K. Shchyolkina.
Engelhardt Institute of Molecular Biology RASc, Vavilova 32, Moscow, 119991, Russia.