Pyrimidine motif

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. ... 

The base modifications discussed so far are mostly concerned with those permissible in the pyrimidine motif (Y RY). In the purine motif (R RY), the permitted triads are A-AT, T AT and G GC, and the following examples illustrate the permissible base modifications in this motif. 

NMR spectroscopy of multiply C-labeled Compound ( samples (obtained by rapid quench experiments with various C-labeled samples of 6,7-dimethyl-8-ribityllumazine) revealed the pentacyclic structure 36 that is clearly an adduct of two 6,7-dimethyl-8-ribityllumazine (9) molecules (Figures 10 and 11). The optical absorption of the compound is well in line with the presence of a lumazine motif and a pyrimidine motif... 

Torigoe, H., Ferdous, A., Watanabe, H., Akaike, T., Maruyama, A. Poly(L-lysine)-graft-dextran copolymer promotes pyrimidine motif triplex DNA formation at physiological pH. J. Biol. Chem. 274, 6161-6167 (1999). doi 10.1074/jbc.274.10.6161... 

Triplex formation, which involves site-specific recognition of duplex DNA by hydrogen bonding between oligonucleotide bases in the 3 end extension and purine bases in the major groove, can occur in two distinct patterns termed the pyrimidine motif and the purine motif [22,40]. In the former motif, pyrimidine... 

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