The synthesis of N-4-(6-aminopyridin-2-yl)-2 '-deoxycytidine for recognizing the CG base pair at neutral pH by oligodeoxyribonucleotide-directed triple helix formation
Tm. Chin et al., The synthesis of N-4-(6-aminopyridin-2-yl)-2 '-deoxycytidine for recognizing the CG base pair at neutral pH by oligodeoxyribonucleotide-directed triple helix formation, J CHIN CHEM, 46(5), 1999, pp. 751-758
The sequence-specific recognition of double-helical DNA by oligodeoxyribonu
cleotide-directed triple helix (triplex) formation is limited mostly to pur
ine tracts. To interrupt the purine tract in a target sequence, a non-natur
al deoxyribonucleoside N-4-(6-aminopyridin-2-yl)-2'-deoxycytidine (C-p) was
designed to interact with the C base in the CG base pair. The protected ph
osphoramidite synthon of C-p was synthesized in seven steps and then was in
corporated into an oligodeoxyribonucleotide by an automatic DNA synthesizer
. Two 22-mers, designated as C2 and P, with a common sequence of 5'-d-T(m)C
TXT(m)CTTCTGTCTCCAGACAG were synthesized in this study. C-m is 5-methyl-2'-
deoxycytidine and X is either 2'-deoxycytidine (C) or C-p for C2 and P, res
pectively. C2 is able to form a paper clip type tripler with one C . CG mis
matched base triad in slightly acidic conditions but not at the neutral pH.
On the other hand, P forms a stable tripler under both acidic and neutral
conditions. This indicates that C-p is able to form a C-p . CG base triad i
n the tripler. Their physical properties were studied by UV thermal melting
experiments and circular dichorism spectroscopy (CD). The thermal melting
results imply that the C-p . CG base triad is as stable as the C+ . GC tria
d at pH 6.0, and C-p helps the tripler formation preferably at neutral to a
cidic pH. In addition to the hydrogen bonding interaction with the CG base
pair, the hydrophobic interaction of C-p may also play an important role in
stabilizing the triplex formation of oligodeoxyribonucleotides. In the pre
sence of spermine at either pH 5.0 or pH 6.0, the melting temperature of th
e third strand of P was elevated about 30 and 21 degrees C, respectively. T
hus, spermine can enhance the stability of the triple-helical structure.