Biomedical subjects
Publications and source records attributed to Byeang Hyean Kim.
We have prepared a small library of amphiphiles, each comprising a polar carbohydrate head group attached through an N-terminal amino acid to a nonpolar pyrene tail group. One of these derivatives is sensitive to the presence of insulin in aqueous media.
Explore the source record for details and available documents.
Pyrene-modified adenosine and uridine bases located in the dangling positions of G,C-alternating oligodeoxynucleotides undergo pi-stacking in their B-DNA duplexes, but not in their Z-DNA duplexes; fluorescence quenching in the former, through photoinduced electron transfer, but not in the latter, allows the state of the B-to-Z-DNA transition to be characterized visually.
[reaction: see text] Fluorescence can be quenched through PET from the fluorophore to neighboring C, T, and G bases, but not to the A moiety. The hairpin stem stability arising from pi-stacking and the PET between the pyrene-labeled 2'-deoxynucleotide units and their neighboring bases are the two main factors that affect the operation of these novel fluorescent oligonucleotides.
[structure: see text] Amino acid-appended biotin hydrogelators are a new class of low-molecular-weight gelators that display remarkable gelation properties in aqueous media, including buffer solutions with variable pH.
Phospholipids and liposomes have been the subjects of considerable attention because of their importance in biological systems. We have efficiently synthesized novel nucleoside-based phospholipids in six-step sequences starting from their corresponding nucleosides. These nucleoside-based phospholipids self-assemble into liposome-like structures in aqueous solutions. We have analyzed the structures of these liposomes by dynamic light scattering, transmission electron microscopy, and confocal microscopy.
Explore the source record for details and available documents.
Pyrene-labeled deoxyuracil and deoxyadenine units are useful unnatural nucleobases. These fluorescent nucleobase analogues allow strong interstrand stacking interactions to compensate for a loss of hydrogen bonding and exhibit a range of different emission intensities when they form duplexes with one another. These findings may provide new insights into the design of new probes and nucleobase analogues for applications in molecular biology. For this purpose, we have prepared an hairpin molecular beacon (MB) that incorporates an excimer unit in its closed state, and have utilized lambda(max) changing to discriminate between match and mismatch. This hairpin configuration is attractive because the synthesis of such an MB is relatively simple and inexpensive because it does not require two distinct processes to prepare the fluorophore and quencher.
Their enhanced cell permeability and their ability to mimic DNA structures make modified oligodeoxyribonucleotides (ODNs) very important substances for increasing our understanding of cell biology and for therapeutic applications. Lithocholic acid is a hydrophobic secondary bile acid that is a substrate of nuclear Pregnane X receptor (PXR). We designed and synthesized novel lithocholic acid-based ODNs (L-ODNs) by using a new phosphoramidite derived from lithocholic acid. By comparing data obtained from circular-dichroism, melting-point, and theoretical studies, we believe that these L-ODNs adopt DNA hairpin structures. Furthermore, L-ODNs have enhanced cellular uptake properties with respect to regular ODNs. To demonstrate their enhanced cell permeabilities, we carried out cellular uptake experiments of L-ODNs in HeLa cells. By attaching fluorescein as a fluorescence label and using confocal microscopy, we observed that the permeability of L-ODNs is much higher than that of natural ODNs.
We have synthesized a new family of pi-conjugated dendrimers that are based on bis(enediynyl)benzene units by using both divergent and convergent approaches. The compounds at all three generations have strong bluish-green fluorescence, especially the third-generation dendrimer, which has the highest extinction coefficient and quantum efficiency in this series. [structure: see text]
We have found that aggregation mode and gelation property of thymidine-based organogelator are affected by the addition of its complementary polynucleotide in organic media.
[structure: see text] We have synthesized a number of calix[4]arene derivatives presenting thiourea functional groups at their upper rims by the condensation of a 1,3-di(p-amino)calix[4]arene with alkyl isothiocyanates. Mono- and dithiourea-substituted calix[4]arenes were prepared selectively in good yields, and homocoupling of the former led to calix[4]arene dimers with a thiourea linker. X-ray crystallography revealed interesting intra- and intermolecular hydrogen bonding patterns. (1)H NMR data and computational studies also provided some insight into the hydrogen bonding patterns.
We inserted a fluorene-labeled deoxyuridine derivative, synthesized using Sonogashira coupling, efficiently into the loop region of a DNA hairpin using phosphoramidite chemistry. This molecular beacon, which features no additional fluorescence quencher, discriminates between perfect and one-base-mismatched base pairing by changes in its fluorescence intensity. The discrimination factor is 14.7 for the recognition of a single (A/C) base mismatch.
We have synthesized low-molecular-weight, triazole ring-appended 2'-deoxyuridine hydrogelators that gelate pure water at a concentration as low as 0.2 wt% and these compounds display different aggregation and network structures as evidenced by their SEM images, FTIR spectra and minimum gel concentrations.
We have synthesized a family of bis-enediynes by two complementary Pd/Cu-catalyzed Sonogashira cross-coupling methods. One is a modified Sonogashira reaction between the TMS-protected tetraalkyne 20 (or 21) and various aromatic bromides to afford bis-enediynes 22a-d and 23a-d bearing different peripheral aryl units. The other, the reaction of bifunctional 1,1-dibromo-1-alkenes with phenylacetylene, afforded a series of bis-enediynes 24-32 bearing various core aryl groups. These chemical modifications to the core and periphery of bis-enediynes induce dramatic changes in absorption and emission spectra. Bis-enediynes 22 and 23 show a large Stokes shift of about 50-110 nm when compared to the less-conjugated bis-enediynes 20 and 21. Absorptions and emissions of bis-enediynes 25, 27-29, and 31 were red-shifted relative to those of enediyne 35. Substantial increases in fluorescence quantum yields are observed as a result of extending the pi-conjugation. The emission wavelength of bis-enediynes was tailored from indigo blue to reddish-orange, suggesting that the color of emission can be tunable by modification of the core and/or peripheral units.
We have synthesized three types of calix[4]arene- nucleoside hybrid efficiently by amide bond formation between the amine functional groups of 1,3-diaminocalix[4]arene and the carboxyl groups of thymidine nucleoside derivatives. X-ray crystallography of a homocoupled calix[4]arene-nucleoside hybrid revealed an interesting hydrogen bonding pattern between thymine bases and the amide linkages. We designed the calix[4]arene-oligonucleotide hybrids (5'-AAAAGATATCAAXTTGATATCTTTT-3', 5'-T12-X-T12-3', and 5'-A12-X-T12-3') to be V-shaped oligodeoxyribonucleotides and synthesized them by using a calix[4]arene-nucleoside hybrid (X) as a key building block. Thermal denaturation experiments, monitored by UV spectroscopy at 260 and 284 nm, and circular dichroism spectra of the calix[4]arene-oligonucleotide hybrids suggest that the modified oligonucleotides indeed adopt V-shaped conformations, making them suitable for use as building blocks in the construction of programmed oligonucleotide nanostructures
We report on a synthesis of novel thymidine based organogelators and a study of their gelation types in relation to structure and solvent, using various data acquired through FT-IR, SEM images and differential scanning calorimetry.
Two optically active phosphoramidite monomers for modified oligodeoxyribonucleotides were prepared. These monomers were then introduced into dodecanucleotides in the middle of the sequences. The modified dodecanucleotides were characterized by various analytical methods including MALDI-TOF mass spectrometry and Tm values were obtained to appraise the binding affinity, by measuring change in UV absorbance at 260 nm.