Design of Novel Bases on Recognition of GC Base Pairs of DNA by Oligonucleotide Directed Triple Helix Formation.
Abstract
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 (G+GC 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-(bis(4-methoxyphenyl)phenylmethyl-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 DNA(pH 7.4).
Document Details
- Document Type
- Technical Report
- Publication Date
- Jun 01, 1991
- Accession Number
- ADA237529
Entities
People
- J. S. Koh
- P. B. Dervan
Organizations
- California Institute of Technology