Modulation of pK_a of Brooker’s Merocyanine by DNA Hybridization

Abstract

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.

Optical Chemosensors and Chemodosimeters for Anion Detection Based on Merrifield Resin Functionalized with Brooker’s Merocyanine Derivatives

“…Fluorescence Measurements. Based on the fluorescence of the BM system, 64 the emission of the resins was investigated using the laser scanner confocal microscopy (LSCM) technique. Figure 4 shows fluorescence images for MR, MR2OH, and MR2OTIPS, which were excited at 405 nm (A, D, and G), 488 nm (B, E, and H), and 514 nm (C, F, and I), respectively.…”

Development of Pseudo Base-Pairs on d-Threoninol which Exhibit Various Functions

“…45 We also developed a pseudo base pair of a pH-responsive fluorophore. 46 Brooker's merocyanine (BM; Figure 11A) has different absorption and emission maxima when protonated and deprotonated. 47 Introduction of a molecule into DNA often results in an increase of its pK a due to the anionic microenvironment of DNA.…”

Preparation of supramolecular chromophoric assemblies using a DNA duplex

“…We have prepared several homo and hetero dye clusters in this motif. 73,[77][78][79] In addition, we have also prepared sensitive molecular beacons by the introduction of a pair between a fluorophore and a quencher in the stem region. [80][81][82] The second motif is an interstrand wedge motif (Scheme 2B).…”