Yuthana Tantirungrotechai

Photoactive azoimine dyes: 4-(2-Pyridylazo)-N,N-diethylaniline and 4-(2-pyridylazo)-N,N-dimethylaniline: Computational and experimental investigation

4-(2-Pyridylazo)-N,N-dimethylaniline and 4-(2-pyridylazo)-N,N-diethylaniline, two photoactive azoimine dyes, were prepared from the reaction of 2-aminopyridine with N,N-dialkyl-1,4-nitrosoaniline at room temperature. Structural characterizations of these dyes using single crystal X-ray diffraction, (1)H NMR, elemental analysis, mass spectroscopy and IR spectroscopy have been carried out. The X-ray structure indicates a trans configuration around the azo group. The photochemical behavior of these compounds differs from that of 2-phenylazopyridine, the non-dialkylamino substituent compound. The synthesized compounds show emission spectra at room temperature while 2-phenylazopyridine does not. The excitation spectra of these compounds differ from their absorption spectra which can be explained on the basis of the trans to cis photoisomerization which is supported by the TD-PBE0/6-31G(d,p) calculations. Both oxidation of the dialkylamino substituents (-NR(2); R=-CH(3) and -C(2)H(5)) and reduction of -N=N-/-N=N-(-) and -N=N-(-)/-N=N-(2-) were observed in the cyclic voltammogram indicating a π-acidity of both dyes.

Oligonucleotide Hybridization Combined with Competitive Antibody Binding for the Truncation of a High-Affinity Aptamer

Truncation can enhance the affinity of aptamers for their targets by limiting nonessential segments and therefore limiting the molecular degrees of freedom that must be overcome in the binding process. This study demonstrated a truncation protocol relying on competitive antibody binding and the hybridization of complementary oligonucleotides, using platelet derived growth factor BB (PDGF-BB) as the model target. On the basis of the immunoassay results, an initial long aptamer was truncated to a number of sequences with lengths of 36-40 nucleotides (nt). These sequences showed apparent KD values in the picomolar range, with the best case being a 36-nt truncated aptamer with a 150-fold increase in affinity over the full-length aptamer. The observed binding energies correlated well with relative energies calculated by molecular dynamics simulations. The effect of the truncated aptamer on PDGF-BB-stimulated fibroblasts was found to be equivalent to that of the full-length aptamer.

Effect of PDGF-B aptamer on PDGFRβ/PDGF-B interaction: Molecular dynamics study

PDGFRβ/PDGF-B interaction plays a role in angiogenesis, and is mandatory in wound healing and cancer treatment. It has been reported that the PDGF-B aptamer was able to bind to PDGF-B, thus regulating the angiogenesis. However, the binding interaction between the aptamer and the growth factor, including the binding sites, has not been well investigated. This study applied a molecular dynamics (MD) simulation to investigate the aptamer-growth factor interaction in the presence or absence of a receptor (PDGFRβ). Characterization of the structure of an aptamer-growth factor complex revealed binding sites from each section in the complex. Upon the complex formation, PDGF-B and its aptamer exhibited less flexibility in their molecular movement, as indicated by the minimum values of RMSD, RMSF, loop-to-loop distance, and the summation of PCA eigenvalues. Our study of residue pairwise interaction demonstrated that the binding interaction was mainly contributed by electrostatic interaction between the positively-charged amino acid and the negatively-charged phosphate backbone. The role of the PDGF-B aptamer in PDGFRβ/PDGF-B interaction was also investigated. We demonstrated that the stability of the Apt-PDGF-B complex could prevent the presence of a competitor, of PDGFRβ, interrupting the binding process. Because the aptamer was capable of binding with PDGF-B, and blocking the growth factor from the PDGFRβ, it could down regulate the consequent signaling pathway. We provide evidence that the PDGF-BB aptamer is a promising molecule for regulation of angiogenesis. The MD study provides a molecular understanding to modification of the aptamer binding interaction, which could be used in a number of medical applications.