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Kim, Byeang Hyean,Chung, Yong Jun,Kim, Do Hyung,Choi, Kwan Yong 한국응용약물학회 1994 Biomolecules & Therapeutics(구 응용약물학회지) Vol.2 No.2
Human immunodeficiency virus type 1 (HIV-1) protease is essential for the replication of the virus and it is therefore an attractive target for antiviral drugs of HIV-1. Several dipeptide isosteres containing 2-isoxazoline or α-hydroxy ketomethylene have been synthesized and their inhibitory effects on the HIV-1 protease examined. The enzymatically active HIV-1 protease was purified to homogeniety from E. coli transformed with a recombinant plasmid (pMAL-pro) containing the entire gene encoding the protease. The purified protease had the substrate specificity with Km value of 9.8 μM when an undecapeptide His-Lys-Ala-Arg-Val-Leu-(p-nitro)Phe-Glu-Ala-Nle-Ser-amide was used as a substrate, and the products from the substrate after specific cleavage by HIV-1 protease were analyzed by HPLC. The synthetic compounds containing dipeptide isosteres showed specific inhibitory effects while a dipeptide isostere containing an isoxazoline ring inhibited the HIV-1 protease competitively with Ki value of 500 μM. Even if the inhibition effects of HIV-1 protease were not very high, these novel dipeptide isosteres can be used as key structural moieties for developing specific inhibitors of HIV-1 protease.
Kim, Ki Tae,Kim, Hyun Woo,Moon, Dohyun,Rhee, Young Min,Kim, Byeang Hyean The Royal Society of Chemistry 2013 Organic & biomolecular chemistry Vol.11 No.34
<P>With the goal of developing a fluorescent nucleoside sensitive to its environment, in this study we synthesized <B><SUP>DNS</SUP>C</B>, a novel modified 2′-deoxycytidine bearing a 5-(dimethylamino)naphthalene-1-sulfonyl (dansyl) moiety at the N4 position, and tested its properties in monomeric and oligomeric states. <B><SUP>DNS</SUP>C</B> undergoes intramolecular photoinduced electron transfer between its dansyl and cytosine units, resulting in remarkable changes in fluorescence that depend on the choice of solvent. In addition, the fluorescence behavior and thermal stability of oligonucleotides containing <B><SUP>DNS</SUP>C</B> are dependent on the nature of the flanking and neighboring bases. Notably, <B><SUP>DNS</SUP>C</B> exhibits fluorescence enhancement only in fully matched duplex DNA containing a GGG triad sequence. The environmental sensitivity of <B><SUP>DNS</SUP>C</B> can be exploited as a fluorescence tool for monitoring the interactions of DNA with other biomolecules, including DNA, RNA, and proteins.</P> <P>Graphic Abstract</P><P>An environmentally sensitive fluorescent nucleoside (<B><SUP>DNS</SUP>C</B>), modified 2′-deoxycytidine bearing 5-(dimethylamino)naphthalene-1-sulfonyl (dansyl) at the N4 position, has been synthesized and exhibits fluorescence enhancement only in fully matched duplex DNA containing a GGG triad sequence. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=c3ob41222a'> </P>
Quencher-free molecular beacons as probes for oligonucleotides containing CAG repeat sequences
Kim, Ki Tae,Veedu, Rakesh N.,Seo, Young Jun,Kim, Byeang Hyean The Royal Society of Chemistry 2014 Chemical communications Vol.50 No.13
<P>We have identified quencher-free molecular beacons that allow the sensitive probing of CAG repeat oligonucleotides, including mRNA fragments of trinucleotide repeat diseases, with significant increases in fluorescence intensity mediated by disruption of the stacking of their <B><SUP>Py</SUP>U</B> units.</P> <P>Graphic Abstract</P><P>Quencher-free molecular beacons allow the sensitive probing of DNA and RNA CAG repeat oligonucleotides with significant increases in fluorescence intensity of 16- and 43.5-fold, respectively. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=c3cc48853e'> </P>
Kim, Ki Tae,Heo, Wooseok,Joo, Taiha,Kim, Byeang Hyean The Royal Society of Chemistry 2015 Organic & Biomolecular Chemistry Vol.13 No.31
<P>In this study, we found a <SUP><B>Py</B></SUP><B>A</B>-modified adenine cluster (A-cluster), a minimum fluorescent unit for significant emission wavelength changes, and investigated its photophysical and structural properties. The basic A-cluster unit was an adenine-pentad duplex containing stacked <SUP><B>Py</B></SUP><B>A</B> pairs in the center aligned in an antiparallel manner. Spectral analysis of the A-cluster revealed remarkable reddish fluorescence with a large Stokes shift (∼195 nm) and a long life-time constant (31 ns), originated from exciton states formed by <SUP><B>Py</B></SUP><B>A</B> pairs and neighboring adenines. Structurally, the exciton state of the A-cluster exhibited unusually high stability, relative to that of other five-mismatched duplexes, as a result of stabilization through strong stacking interactions (zipper-like structure) of the mismatched A–A and <SUP><B>Py</B></SUP><B>A</B> pairs, rather than through traditional Watson–Crick base pairing. These spectral and structural properties of the A-clusters were specific to the adenine bases and highly disturbed by introducing other bases (T, G, and especially C) or an abasic site into the A-cluster, whereas they were enhanced through synergistic effects in systems containing multiple A-clusters. As a minimum unit for these unique properties, finally, the A-cluster was exploited as a fluorescent probing system for specific nucleic acid sequences, such as miR-21, accompanying distinct fluorescence color changes from blue to red. These findings indicated the potential utility of the A-cluster as a part of fluorescent probes exhibiting clear signaling upon micro-environmental changes.</P> <P>Graphic Abstract</P><P>A <SUP><B>Py</B></SUP><B>A</B>-modified adenine cluster, exhibiting a large Stokes shift based on interstrand stacking interactions of adenines, was investigated and exploited as signaling parts of fluorescent DNA probes. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=c5ob01159k'> </P>
Kim, Ki Tae,Kim, Byeang Hyean The Royal Society of Chemistry 2013 Chemical communications Vol.49 No.17
<P>A 6-mer oligonucleotide containing a fluorescent <B><SUP>Bod</SUP>U</B> moiety has been used as a novel fluorescent probe for the 3′-overhang of telomeric DNA based on competition between non-fluorescent tetramolecular and fluorescent (3+1) intermolecular G-quadruplexes.</P> <P>Graphic Abstract</P><P>A 6-mer oligonucleotide containing a fluorescent <B><SUP>Bod</SUP>U</B> moiety is used as a fluorescence probe for the 3′-overhang of telomeric DNA based on competition between non-fluorescent self-assembled tetramolecular and fluorescent (3+1) intermolecular G-quadruplexes. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=c3cc37504h'> </P>
An insulin-sensing sugar-based fluorescent hydrogel
Bhuniya, Sankarprasad,Kim, Byeang Hyean Royal Society of Chemistry 2006 Chemical communications Vol.2006 No.17
<P>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.</P> <P>Graphic Abstract</P><P>A small library of amphiphiles consisting of a polar carbohydrate “headgroup” attached to the N-termini of amino acids, which is linked with a nonpolar pyrene tail group have been prepared and it is found that one of them has insulin sensitivity in aqueous media. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=b516632b'> </P>
Recovery of the Formation and Function of Oxidized G-Quadruplexes by a Pyrene-Modified Guanine Tract
Takahashi, Shuntaro,Kim, Ki Tae,Podbevš,ek, Peter,Plavec, Janez,Kim, Byeang Hyean,Sugimoto, Naoki American Chemical Society 2018 JOURNAL OF THE AMERICAN CHEMICAL SOCIETY - Vol.140 No.17
<P>Oxidation is one of the frequent causes of DNA damage, especially to guanine bases. Guanine bases in the G-quadruplex (G4) are sensitive to damage by oxidation, resulting in transformation to 8-oxo-7,8-dihydroguanine (8-oxoG). Because the formation of G4 represses the expression of some cancer-related genes, the presence of 8-oxoG in a G4 sequence might affect G4 formation and induce cancer progression. Thus, oxidized-G4 formation must be controlled using a chemical approach. In the present study, we investigated the effect of introduction of 8-oxoG into a G4 sequence on the formation and function of the G4 structure. The 8-oxoG-containing G4 derived from the promoter region of the human vascular endothelial growth factor (<I>VEGF</I>) gene differed topologically from unoxidized G4. The oxidized <I>VEGF</I> G4 did not act as a replication block and was not stabilized by the G4-binding protein nucleolin. To recover G4 function, we developed an oligonucleotide consisting of a pyrene-modified guanine tract that replaces the oxidized guanine tract and forms stable intermolecular G4s with the other intact guanine tracts. When this oligonucleotide was used, the oxidized G4 stalled replication and was stabilized by nucleolin as with the unmodified G4. This strategy generally enables recovery of the function of any oxidized G4s and therefore has potential for cancer therapy.</P> [FIG OMISSION]</BR>
Park, Yoojin,Kim, Ki Tae,Kim, Byeang Hyean The Royal Society of Chemistry 2016 Chemical communications Vol.52 No.86
<P>We have developed a simple and sensitive system for detecting AGG trinucleotide repeats through the formation of intermolecular G-quadruplexes using a fluorescent oligonucleotide. The fluorescence signal increased rapidly and dramatically by 44.7-fold with respect to the low background signal in the presence of RNA agg repeats and by 35.0-fold in the presence of DNA AGG repeats.</P>