Oligonucleotides base pairing

The TlPS-protected 2-deoxyribonolactone was used in the synthesis of the 3- and 4-pyridyl nucleoside phosphoramidites [20a, b]. These nucleosides were used in oligonucleotide base pairing experiments and had as complementary base the 2 -deoxyribosyl-l-(4-(2",6",2"-bypyridyl))pyrimidinone phosphoramidite [20c].Other new C-nucleoside phosphoramidites include the pyrido[l,2-a][l,3,5]triazin-4-one derivatives [21a-c] which were obtained via Heck-type palladium-catalysed reaction between 2-alkyl-9-iodo-pyr-ido[l,2-a][l,3,5]triazin-4-one and a silyl protected furanoglycal. ... 

DNA polymerase enzymes all synthesize DNA by adding deoxynucleotides to the free 3 -OH group of an RNA or DNA primer sequence. The identity of the inserted nucleotide is deterrnined by its abiHty to base-pair with the template nucleic acid. The dependence of synthesis on a primer oligonucleotide means that synthesis of DNA proceeds only in a 5%o V direction if only one primer is available, all newly synthesized DNA sequences begin at the same point. 

Some oligonucleotides adopt an A-form helical stmcture (Fig. 2a) (5). The average stmctural parameters have been found consistent with the fiber diffraction model, but, as for B-form DNA, considerable variation is apparent among iadividual base pairs. 

Primers The primers are short (15-30) oligonucleotide sequences designed to base pair or anneal to complementary sequences that flank the DNA target sequence to be amplified. The primers are added at 0.1-1 qM in the assay. 

Fig. 45. (a) Introduction of M(phen)31 complex into DNA oligomers, (b). Steady-state emission spectra of modified oligonucleotides in 0.01 m sodium phosphate buffer, pH 7.0, 0.1 NaCl. Top Ru(phen)3+-modified 20-mer duplex (solid line), a 1 1 mixture of non-comple-mentary Ru(phen)3+- and Os(phen)g+-modified 20-mers (- -) and a 20-mer duplex containing Ru(phen)g+ and Ps(phen)3+groups on different strands separated by one base pair (---). Bottom 20-mer duplex with 5 -terminal Rufphen) (solid line), and Ru(phen)jf/Os(phen)3 -containing analog (---). Reproduced with permission from Ref. (157). Copyright 1998, American Chemical Society. 

Sowers LC, Fazakerley GV, Eritja R, Kaplan BE (1986) Base pairing and mutagenesis observation of a protonated base pair between 2-aminopurine and cytosine in an oligonucleotide by proton NMR. Proc Natl Acad Sci USA 83 5434-5438... 

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