Triplex nucleic acids

Protoberberine Alkaloid-Triplex Nucleic Acid Interaction. 194... 

Griffith M.C., Risen L.M., Greig M.J., Lesnik E.A., Sprankle K.G., Griffey R.H., Kiely J.S., Eeier S.M. Single and bis peptide nucleic acids as triplex-ing agents binding and stoichiometry. 

Knudsen H., Nielsen P.E. Antisense properties of duplex- and triplex-forming PNAs. Nucleic Acids Res. 1996 24 494—500. 

E Wang, J Eeigon. In S Neidle, ed. Structures of Nucleic Acid Triplexes. New York Oxford University Press, 1999, pp 355-388. 

The formation of three-stranded nucleic acid complexes was first demonstrated over five decades ago [56] but the possible biological role of an extended triplex was expanded by the discovery of the H-DNA structure in natural DNA samples [57-59]. H-DNA is an intermolecular triplex that is generally of the pyrimidine-purine x pyrimidine type ( dot -Watson-Crick pairing and cross Hoogsteen base paring) and can be formed at mirror repeat sequences in supercoiled plasmids [59]. 

Peptide nucleic acids (PNAs with a peptide like backbone) also bind via the major groove (Neilsen, 1999). PNAs form a triplex (Lohse et al, 1999), which then result in the displacement of the non-complementary oligopyrimidine DNA strand. This has been extensively reviewed by Hurley (2002). 

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... 

Optical Spectroscopy General principles and overview, 246, 13 absorption and circular dichroism spectroscopy of nucleic acid duplexes and triplexes, 246, 19 circular dichroism, 246, 34 bioinorganic spectroscopy, 246, 71 magnetic circular dichroism, 246, 110 low-temperature spectroscopy, 246, 131 rapid-scanning ultraviolet/visible spectroscopy applied in stopped-flow studies, 246, 168 transient absorption spectroscopy in the study of processes and dynamics in biology, 246, 201 hole burning spectroscopy and physics of proteins, 246, 226 ultraviolet/visible spectroelectrochemistry of redox proteins, 246, 701 diode array detection in liquid chromatography, 246, 749. 

The tertiary structure of DNA is the structural level that is most relevant to 3-D reality. Traditionally, ODNs in a physiologically relevant aqueous solution are considered to be in a random-coiled ssDNA state or in the form of dsDNA helix in the presence of a complementary DNA, including the case of self-complementarity. The double helix is the dominant tertiary structure for biological DNA that can be in one of the three DNA conformations found in nature, A-DNA, B-DNA, and Z-DNA. The B-conformation described by Watson and Crick (11) is believed to predominate in cells (12). However other types of nucleic acid tertiary structures different from random or classical double-stranded helix forms can also be observed. Among them are triplexes, quadruplexes, and several other nucleic acid structures (13, 14). 

Figure 12.16 Photographs of solutions of (a) polymer 12, (b) 12 + single-stranded DNA, and (c) 12 + double-stranded DNA. (d) Schematic description of the formation of pol)dhio-phene/single-stranded nucleic acid duplex and polythiophene/hybridized nucleic acid triplex forms. Reprinted from Ho et al. (2002). Copyright 2002 Wiley-VCH Verlag GmbH and Co. KGaA.

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. 

Ferdous, A., Watanabe, H., Akaike, T. and Mamyama, A. (1998) Poly( 1-lysine>graft-dextran copolymer amazing effects on triplex stabilization under physiological pH and ionic conditions (in vitro). Nucleic Acids Res., 26, 3949-3954. 

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... 

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