Design of Novel Bases on Recognition of GC Base Pairs of DNA by Oligonucleotide Directed Triple Helix Formation.
Technical rept. no. 2, 31 May 90-1 Jun 91,
CALIFORNIA INST OF TECH PASADENA DIV OF CHEMISTRY AND CHEMICAL ENGINEERING
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The binding of pyrimidine oligonucleotides containing cytosine at single sites on double helical DNA by triple helix formation is sensitive to pH. An important factor is the required protonation of the cytosine N-3 in the third strand to enable the formation of two Hoogsteen hydrogen bonds GGC triplet. Because oligonucleotide specificity could provide a method for artificial repression of viral and pathogenic diseases, it is desirable to design and synthesize a novel base that could bind GC base pairs strongly and selectively over a wide range of intracellular pH. The novel base, N-1-15-O-bis4-methoxyphenylphenylmethyl-2-deoxy-BETA-D-erythro-pentofuranosyl-4,7-dihydro-3-methyl-7-oxo-1H-pyrazolo-4,3-DLPYRIMI-DINE-5-YL-2-methyl-propanamide P1 was designed, synthesized and incorporated within a pyrimidine oligonucleotide and shown to recognize GC base pairs as selectively and strongly as C. Oligonucleotides containing P1 bases show the same specificity as C but with less pH sensitivity in triple helix formation. P1 does not require protonation in triple helix formation. Such specificity allows binding at a 15 base pairs site in plasmid DNA pH7.8 and a 16 base pairs site in the 3 long terminal repeat LTR of HIV DNApH 7.4.
- Medicine and Medical Research