Triplex DNA

Nielsen P.E., Egholm M., Buchardt O. Evidence for (PNA)2/DNA triplex structure upon binding of PNA to dsDNA by strand displacement. J. Md. Recognit. 1994 7 165-170. 

Earlier studies using thermal denaturation analysis and spectrophotomet-ric titration with TxA T and CxC-C" containing DNA triplexes showed that coralyne binds strongly to these triplexes by intercalation and does not exhibit a significant sequence-selectivity [222]. In a later study by Morau Allen et al. [217], employing DNase footprinting, thermal denaturation analysis, UV-visible spectrophotometric titrations, circular dichroism and NMR spectroscopy, showed that coralyne is fully intercalated into TxA T triplex DNA whereas in C GxC triplex, it is partially intercalated due to electrostatic repulsion between the cationic alkaloid and the protonated cytosine [217]. Kepler et al. [223] demonstrated that coralyne intercalated to parallel triplex DNA but did not intercalate to antiparallel triplex DNA. Recently Hud and coworkers [219,224] demonstrated that duplex poly(dA) poly(dT) is trans-... 

Fig. 9.2 Part of a quantitative- /NN HNN-COSY spectrum of a 1.5 mM uniformly 13C/15N-labeled intramolecular DNA triplex. This triplex consists of five Hoogsteen-Watson-Crick T A-T and three Hoogsteen C+ G-C base triplets. The spectral region corresponds to the 10 imino resonances of the Hoogsteen-Watson-Crick T A-T triplets. The data matrix consisted of 250 (q) X1024 (i2) data points (where n refers to complex points) with acquisition times of 45 ms (tn) and 85 ms...

Figure 11.5. Structures of Hoechst 33258, neomycin, and conjugates NHl and NH2. 11.4. DNA TRIPLEX...

Previous work has suggested that aminoglycoside specificity may occur in nucleic acid forms that display features characteristic of an A-type conformation (RNA triplex, DNA-RNA hybrid duplex,RNA duplex, DNA triplex, A-form DNA duplex, and DNA tetraplex ), rather than in naturally occurring RNA. However, conflicting results have been reported regarding the conformation of the triplex and of the Watson-Crick duplex within these triplexes. Both... 

Nymphaea caerulea, for seven natural anthocyanins stabilizing a DNA triplex, etc. Sequential analysis of the oligosaccharide structures of the flavonol tamarixetin-7-O-rutino-side has been performed by ID multistep-relayed COSY-ROESY experiments. Selective excitation was performed by Gaussian-shaped soft pulses. 

Shafer, RH (1998) Stability and structure of model DNA triplexes and quadruplexes and their interactions with small ligands. Prog. Nucleic Acid Bes. Mol. Biol. 59, 55-94. 

Camerini-Otero, R. D and P. Hsieh, Parallel DNA triplexes, homologous recombination and other homology-dependent DNA interaction. Cell 73 217-224, 1993. 

Figure 5.2 PNA binding to duplex DNA target generated [PNA]2/DNA triplex and single-stranded D-loop structure.

Demidov et al., 1994 Hanvey et al., 1992 Knudsen and Nielsen, 1996 Nielsen et al., 1991). The [PNA]2/ DNA triplex structure stabilizes both the bound PNAs and the single stranded D-loop at the PNA binding site (Nielsen et al., 1991 Lohse and Nielsen, 1999). 

Ganesh, Krishna N., Synthetic Control of DNA Triplex Structure Through Chemical Modifications, 3, 263. 

The structures of the bases of these DNA triplexes were studied, by means of B3LYP/6-31+G calculations, in terms of their interaction energies and electron densities for the different hydrogen bonds established. This is one of the interactions that determines the structure and dynamics of nucleic acid molecules, and some of them, 219 and 220, are represented in the below structure [182], A good agreement was found with the experimental results. The trends observed for the interaction energies are consistent with those observed by experimental and/or by... 

Synthetic oligonucleotides are being developed to target defined sites on DNA sequences or genes (double-strand DNA triplex approach) or messenger RNA (antisense approach) so that the production of disease-related proteins is blocked. These oligonucleotides offer prospects of treatment for cancers and viruses without harming healthy tissues.8,9... 

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