Triplex stability

Significant increase in triplex stability can be achieved by using intercalating agents, either by conjugate attachment to the third strand TFO or as a separate adjunct ligand, if binding of this residue can preferentially stabilize a... 

Dextran-g-poly (L-lysine) (Dex-g-PLL) Graft copolymer DNA duplex and triplex stabilization (Maruyama et a ., 1997)... 

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. 

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... 

BNA (also known as LNA) has been used in TFOs in a pyrimidine motif at neutral pH. The binding constant of the BNA TFO was about 20 times larger than that of DNA as a result of a large decrease in the dissociation rate constant. A 3 -amino-2, 4 -BNA nucleotide has been prepared to introduce N3 -P5 phosphoramidate linkages. It is introduced as a dinucleotide unit (61), and in thermal stability studies was shown to exhibit superior duplex and triplex stability compared to either BNA or DNA, and shows enhanced resistance to digestion by SVPDE. These properties have previously been observed for N3 -P5 phosphoramidate linkages in DNA. ... 

LNA has frequently been used to stabilise duplex structures, but in triplex structures the effect is mixed. Partial substitution of a DNA TFO by LNA increases triplex stability, whilst complete substitution leads to destabilisation. Optimal stabilisation was found with substitution every 2-3 nucleotides of the TFO. The incorporation of LNA into a G-quadruplex structure was shown to alter the orientation of the quadruplex from antiparallel to parallel. ... 

In general, the stability of Y RY triplexes containing cytosine residues in the third strand decreases as the pH of the solution is raised from acidic to alkaline values [27, 45, 46]. This is due to a decreased protonation at the N3 of C with increased pH. The triplex stability reaches a maximum around pH 5.8, close to the pAa of the N3 of C. Various approaches have been described to overcome this pH limitation (Figure 14), since any triplex-dependent in vivo applications demand stable triplexes at physiological pH. Since the R RY motif does not involve any charged triad bases, its stability is independent of pH. 

Figure 48 Schematic diagram of triplex stabilization by simultaneous formation of a WC duplex and HG pairing in separate domains. Reproduced by permission from Biochemistry, 34, 65 (1995)...

Isothermal titration calorimetry has been used to examine the effects of modifications to a third strand on triplex stability. Modifications of the phosphate backbone (phosphorothioate and 2 -0-Me) are more detrimental to triplex stability than are base modifications. 

---