pyrimidinones and threoninol

Brooker's merocyanine (BM), which changes its emission and absorption maxima upon protonation, was introduced into oligodeoxyribonucleotide (ODN) via d-threoninol by postsynthetic modification on a CPG (controlled-pore glass) support. The pK(a) of BM in the modified ODN increased from 9.5 to 10.1 upon hybridization. As a result, absorption maxima shifted from 492 to 432 nm at pH 10.0 by the presence of its complementary strand. This spectral shift was sufficiently large so that DNA hybridization could easily be discriminated even by the naked eye; the color of the solution changed from orange to yellow upon hybridization. In addition, the fluorescence emission was strongly quenched upon hybridization, demonstrating that this probe can also detect the target DNA by the fluorescence change. Ratiometric detection of hybridization was also possible by simultaneous excitation of both protonated and deprotonated BMs. Furthermore, we could also modulate its pK(a) by the antiparallel stacking of two BM molecules in the duplex; the pK(a) of BM decreased from 10.1 to 9.7 by the stacking of two BMs in an antiparallel manner. Thus, control of the microenvironment around the BM molecule allowed modulation of its pK(a), which is applicable to the sequence-specific recognition of target DNA.

Topics: Absorption; Amino Alcohols; Base Sequence; Butylene Glycols; DNA; DNA, Single-Stranded; Fluorescence; Fluorescent Dyes; Nucleic Acid Hybridization; Oligodeoxyribonucleotides; Protons; Pyrimidinones