Triplex formation

Lyamichev, V., Frank-Kamenetskii, M., Soyfer, V. Protection against UV-induced pyrimidine dimerization in DNA by triplex formation. Nature, Vol.344, No. 6266, (1990), pp. 568-570, ISSN 1476-4687... 

SCHEME 9.23 An oligodeoxynucleotide-bis(quinone methide) conjugate was designed for cross-linking duplex DNA by initial triplex formation but resulted at best in only monoalkylation of its target. 

Ho et al. were able to verify the a-helical shape of the polymer by circular dichroism (CD) spectra. No structural elements were observed until the formation of the double helical DNA at which point they observed a right-handed a-helix in the polythiophene backbone. Their work demonstrates the power of fluorometric detection as they noted a seven order of magnitude increase in detection sensitivity (20 fM in 200 pi) simply through the use of fluorometric detection as opposed to UV-vis absorption. The polymer in solution has a high fluorescence yield with a maximum at 530 nm (Fig. 11a). Upon formation of the duplex the fluorescence is significantly quenched (Fig. lib), while with the addition of the complementary DNA and triplex formation, the fluorescence intensity is enhanced by a factor of 5 (Fig. 11c). The inherent sensitivity of the spectral shift even allowed distinction between DNA with only one and two mismatched bases (Fig. lOBd, e). 

The association of homopyrimidine homopurine stretches of duplex DNA are known as receptors for triplex formation by major groove association of a TFO. TFO recognition of duplex DNA can be exploited by inducing transcription inhibition, site-directed mutagenesis, or recombination. Another attractive feature... 

The PyPuPu and PyPuPy intermolecular triple-stranded DNA (tsDNA) was determined by capillary electrophoresis (CE) (54). The authors report the determination of tsDNA formed by poly(dT20)(dT20) with poly(dA20)-(dA20), and 16-bp dsDNA with 16-nt triplex formation oligonucleotide... 

Recently, triplex formation was employed to purify plasmids (55). 

Triplex formation with cytosine containing PNAs (or oligonucleotides) requires N3 protonation of cytosine (Scheme 2) and is therefore only efficient at acidic pH (pH <6). However, substituting pseudoisocytosine for cytosine in the Hoogsteen strand of bis-PNAs in triplex recognition gives pH independent binding, because pseudoisocytosine mimics the proto-nated cytosine. The synthesis of pseudoisocytosine is shown in Scheme 5.[25]... 

Gannett, P. M., et al. (2002). Probing triplex formation by EPR spectroscopy using a newly synthesized spin label for oligonucleotides. Nucleic Acids Res. 30, 5328—5337. 

The following paper in the same journal [105 b] deals with the same system, this time studied in acetonitrile solution. Here, a CIP (or an exciplex) is formed, which dissociates to the SSIP (which may be quenched by a ground state amine) or reacts otherwise. No triplex formation is observed in the polar solvent. 

NaraH, Ono A, Matsuda A (1995) Nucleosides and nucleotides. 135. DNA duplex and triplex formation and resistance to nucleolytic degradation of oligodeoxynucleotides containing syn-norspermidine at the 5-position of 2 -deoxyuridine. Bioconjug Chem 6 54—61... 

Barawkar DA, Rajeef KG, Kumar VA, Ganesh KN (1996) Triplex formation at physiological pH by 5-Me-dC-N-4-(spermine) [X] oligodeoxynucleotides non protonation of N3 in X of X G C triad and effect of base mismatch ionic strength on triplex stabilities. Nucleic Acids Res 24 1229-1237... 

Triple-helix formation by G-rich oligonncleotides is supported by Mg + but strongly inhibited by physiological concentrations of certain monovalent cations, especially K+, most likely dne to oligonncleotide self-association in competitive structures such as guanine-quadruplexes. " Variation of the cation enviromnent can differentially promote the assembly of multistranded nncleic acid structural alternatives. For example, by specifically counteracting the induction/stabilization of quadruplex structures by potassium ions, certain divalent ions (i.e. Mn +, Co +, and Ni + but not Mg +) at low millimolar concentrations allow triplex formation in the presence of 150mMK+. In contrast, certain mono- and divalent metal ions can promote the transition from Watson-Crick duplexes to G4 quadruplex structures relatively efficiently K" " > Ca + >... 

A-tract DNA duplexes exhibit high propeller twist and rigidity, which makes A-tract DNA unfavourable for triplex formation. It has been demonstrated that the introduction of a single central GC pair into the duplex significantly enhances the stability of the resulting triplex, as does the introduction of dia-minopurine. In both cases, the stabilisation occurs due to the disruption of the intrinsic properties of A-tract DNA. 

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