Biomedical subjects
Publications and source records attributed to Hiromu Kashida.
By introducing an intercalator through D-threoninol to the 10-23 DNAzyme at the junction between its catalytic loop and the binding arm, the RNA cleavage activity was greatly improved.
For the detection of deletion polymorphisms, two pyrene moieties are tethered to an oligodeoxyribonucleotide (ODN) on both sides of the intervening base; one- and two-base deletions can be selectively detected by the strength of the excimer emission.
An ordered dye cluster of Methyl Reds was formed in double-stranded DNA by hybridizing two complementary DNA-dye conjugates, each involving a Methyl Red moiety on a threoninol linker and a 1,3-propanediol spacer arranged alternately in the middle of the DNA sequence. In the duplex, Methyl Reds from each strand were axially stacked antiparallel to each other, as determined from NMR analysis. This clustering of Methyl Reds induced distinct changes in both UV/Vis and CD spectra. Single-stranded DNA-Methyl Red conjugates on D-threoninol linkers and (1,3-propanediol) spacers exhibited broad absorption spectra with lambda(max) at around 480 nm, and almost no CD was observed at around the absorption maximum of Methyl Red. However, as Methyl Reds were clustered by hybridization, lambda(max) shifted towards shorter wavelengths with respect to its monomeric transition. This hypsochromic shift increased as the number of Methyl Red molecules increased. Furthermore, a positive couplet was also strongly induced here. These dye clusters are H-aggregates, in which molecular excitons are coupled. The positive couplet demonstrates that the clusters on D-threoninol form a right-handed helix. In contrast, the induced CD became much weaker with Methyl Red on L-threoninol, which intrinsically prefers counterclockwise winding. Thus, mutual orientation of the stacked dye molecules was controlled by the chirality of the linker.
We have synthesized azobenzene-tethered DNAs and have successfully photo-regulated various DNA functions. In the present study, we synthesized azobenzenes substituted with methyl group for still more effective photo-regulation of DNA hybridization. In trans-form, mono substituted azobenzene at ortho position stabilized the DNA duplex more efficiently than the other mono-substituted ones. In contrast, melting temperature (T(m)) for 2-methylazobenzene was lower in cis-form. As a result, change of T(m) (DeltaT(m)) induced by trans-cis isomerization became larger than that of unmodified azobenzene. Furthermore, di-substituted azobenzene at both ortho positions exhibited even larger DeltaT(m). Quite interestingly, thermal cis-to-trans isomerization of this azobenzene was about 10-fold slower than that of unmodified one. Thus, introduction of methyl group at 2, 6 positions raised both photo-regulatory activity and thermal stability of cis-form.
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Two diastereomers of a photoresponsive oligodeoxyribonucleotide tethering a trans-azobenzene, based on the chirality of the central carbon of a diol linker, were separated by reversed-phase HPLC. On the basis of 2D NMR analysis, absolute configurations of the diastereomers alpha and beta (tentatively designated from differences in their retention time) were determined as R- and S-forms, respectively. For both diastereomers, their NMR-determined duplex structure showed that trans-azobenzene intercalates between base pairs, because distinct NOEs were observed between the protons of azobenzene and those of the adjacent base pairs, such as with the imino protons and methyl protons of thymine. The melting temperatures of both duplexes were higher than that of the corresponding native duplex, which contained no azobenzene residue, due to the intercalated trans-azobenzene stabilizing the duplex by a stacking interaction. Between these two diastereomers, differences in T(m) were also found: the melting temperature of the R-form duplex (alpha-isomer) was higher than that of the S-form (beta-isomer). On the basis of the NMR-determined structure, this difference was attributed to the fact that the S-form (beta isomer) causes more stress forming the duplex than does the R-form (alpha isomer) due to disturbances of the right-hand helix.
The Naphthyl Red moiety, conjugated to DNA, shows distinct chromism by hybridization with its complementary DNA. Single-stranded DNA involving the Naphthyl Red moiety exhibits an orange color and has lambda(max) at 466 nm at pH 7.0. The absorption maximum is shifted towards 545 nm by the presence of its complementary DNA, and the color of the solution changes from orange to magenta accordingly.
Methyl Red H aggregate of predetermined size is successfully synthesized from the DNA conjugate involving multiple Methyl Red moieties in sequence. In the single stranded state, hypsochromicity monotonically increases with the number of incorporated dyes: the peak maximum of the conjugate involving six Methyl Reds appears at 415 nm, and the shift is as great as 69 nm (3435 cm(-)(1)) with respect to the monomeric transition. This large hypsochromicity accompanied by the narrowing of the band clearly demonstrates that H aggregate is formed in the single strand. H aggregation is further promoted at higher ionic strength. Upon addition of complementary DNA below the T(m), however, this H band disappears and a new peak appears at 448 nm, indicating that aggregated structure is changed by the duplex formation. This spectral change is completely reversible so that the H band at 415 nm appears again above T(m). Thus, aggregated structure can be reversibly controlled by the formation and dissociation of the DNA duplex.
Naphthyl Red moiety, conjugated to DNA, shows distinct chromism by hybridization with its complementary DNA. Single-stranded DNA involving Naphthyl Red moiety exhibits orange color and has lambda max at 466 nm at pH 7.0. Absorption maximum shifts towards 545 nm by the presence of its complementary DNA, and accordingly color of the solution changes from orange to magenta.