Biomedical subjects

B S Choi

Publications and source records attributed to B S Choi.

At least 37 records · Page 2Linked to original sources

PubMed1998

Proton exchange kinetics in [d(ACGTATACGT)]2-echinomycin and [d(ACGTTAACGT)]2-echinomycin complexes.

Based on imino proton exchange catalysis, base-pair lifetimes and apparent dissociation constants are reported on the complexes formed by bisintercalation of echinomycin at the CpG steps of the d(ACGTATACGT)2 and d(ACGTTAACGT)2 duplexes. The lifetimes of the four central A x T base pairs between two echinomycin binding sites are much shorter than in the free duplexes. The destabilization of base pairs adjacent to the binding sites is propagated one additional base pair away from the binding site.

Base Composition↗

PubMed1998

Antimicrobial activity and conformation of gaegurin-6 amide and its analogs.

A function of the intra-disulfide bridge located at the C-terminal of Rana peptides has not been extensively studied. To investigate the function of the disulfide bridge related to the activity and the structure, we chose Gaegurin-6, isolated from Rana rugosa as a model peptide and synthesized linear analogs. The reduction of the disulfide bridge resulted in the complete loss of antimicrobial activity while replacements of cysteines by serines retained antimicrobial activity. Circular dichroism spectra from a titration of the peptides in sodium dodecyl sulfate indicated that the disulfide bridge of Gaegurin-6 might stabilize the induction of an alpha helical structure in lipid membranes and the alpha helical forming propensity of the peptides correlated with antimicrobial activity.

Amino Acid Sequence↗

PubMed1998

Life-threatening carboplatin hypersensitivity during conditioning for autologous PBSC transplantation: successful rechallenge after desensitization.

Carboplatin hypersensitivity has rarely been reported in patients receiving repeated cycles of therapy, but has not been reported in transplant settings. We report a case of carboplatin hypersensitivity during conditioning for autologous PBSC transplantation. The patient suddenly developed chest tightness, hemoptysis, hypoxia and hypotension, resulting in a transient myocardial ischemia. The pathophysiologic mechanism for the event seemed to be non-immune-mediated direct histamine release given the lack of prior exposure to platinum. Contrary to advice not to continue further treatment with carboplatin by some authors, we successfully desensitized the patient and subsequently gave more carboplatin as a part of conditioning. Awareness of carboplatin as one of the causes of hypersensitivity may help avoid further problems either by substitution or desensitization, along with premedications.

Antineoplastic Agents↗

PubMed1996

Secondary structure of the panhandle RNA of influenza virus A studied by NMR spectroscopy.

The double-stranded panhandle structure of the influenza virus RNA is important for replication, transcription and packaging into the virion of the virion RNA. The solution structure of a 34 nt RNA which contains the conserved panhandle sequences has been investigated by one- and two-dimensional NMR spectroscopy. The partially complementary 5'- and 3'-ends of the RNA form a double helical structure which is, on average, close to A-form. The stem contains bulges at nucleotides A10, A12 and C26. In between these bulges, C11 and G25 form a Watson-Crick base pair. The structural features of the panhandle provide a framework for the explanation of mutational analysis and for a better understanding of RNA-polymerase interactions.

Influenza A virus↗

PubMed1996

Unusually stable helical kink in the antimicrobial peptide--a derivative of gaegurin.

The structure of an active analog of the antibacterial peptide gaegurin was investigated by CD and NMR spectroscopy. The NOE connectivities showed that 21 out of 24 residues formed an a-helix despite the presence of a central proline. CD and NMR analysis indicates that the helix is in fast equilibrium with random coil. From chemical shift analysis of the amide protons, the distances of hydrogen bonding in the helix were calculated, and manifested obvious periodicity which implied a kink in the middle of the helix. 1D amide proton exchange experiments provided further evidence of an exceptionally stable kink. It is inferred that this kink is important not only to the function of the peptide but also to the early stage of the folding as a nucleation site.

Anti-Infective Agents↗

PubMed1996

The solution structure of a psoralen cross-linked DNA duplex by NMR and relaxation matrix refinement.

The three dimensional structure of the DNA oligomer d(5'GGGTACCC-3')2 cross-linked with 4'-aminomethyl-4, 5', 8-trimethylpsoralen(AMT) has been determined by two-dimensional NMR and a relaxation matrix refinement method. NMR data and structural calculation establish that the cross-linking of the psoralen in the B-DNA duplex retains Watson-Crick type hydrogen bonding throughout the duplex, although the thymine residue which is cross-linked with psoralen forms a weaker hydrogen bond. The psoralen cross-linking in DNA duplex induces significant change of the local DNA structure, but has no important effect on overall DNA helix. Our observation places an upper limit of 10 degrees on overall DNA bending by psoralen cross-linking, which is consistent with the result of HMT-octamer cross link [Spielmann, H. P., Dwyer, T. J., Sastry, S. S., Hearst, J. E., and Wemmer, D. E., (1965) Proc. Natl. Acad. Sci. USA 92, 2345-2349] and gel electrophoretic study [Haran, T. E. and Crothers, D. E. (1988) Biochemistry 27, 6967-6971].

Base Sequence↗

PubMed1996

NMR structural studies of DNA decamer duplex containing the Dewar photoproduct of thymidylyl(3'-- >5')thymidine. Conformational changes of the oligonucleotide duplex by photoconversion of a (6-4) adduct to its Dewar valence isomer.

The single-stranded deoxynucleotide decamer containing a site-specific Dewar valence isomer of the (6-4) adduct of thymidylyl (3'-->5')-thymidine was generated by direct photolysis of d(CGCATTACGC) with UV-B and UV-C irradiation. The conformation of the Dewar-photomodified deoxyoligonucleotide duplex, (C1-G2-C3-A4-T5[DW]T6-A7-C8-G9-C10) . (G11-C12-G13-T14-A15-A16-T17-G18+ ++-C19-G20), has been studied by one- and two-dimensional NMR spectroscopy. While the eight of the ten complementary nucleotides form Watson-Crick-type hydrogen bonding, the 5'-TpT-3' bases of the Dewar lesion show no evidence of complementary hydrogen bonding formation to each other. The Dewar covalent linkage for the adjacent pyrimidine base leads to unusual base stacking, which is different from that of normal B-DNA. Unusual NOEs indicate that the formation of a Dewar photoproduct in the B-DNA duplex is likely to alter its local and global structures. Also, detailed NMR data show that the base pairing and stacking of the Dewar-photoproduct-containing decamer duplex differ from that of the (6-4)-adduct-containing decamer duplex, suggesting that isomerization of the (6-4) adduct to its Dewar form induces a substantial change in the structure of the oligonucleotide duplex.

Base Composition↗

PubMed1995

The solution structure of DNA duplex-decamer containing the (6-4) photoproduct of thymidylyl(3'-->5')thymidine by NMR and relaxation matrix refinement.

The DNA duplex-decamer containing a site-specific (6-4) photoadduct of thymidylyl(3'-->5')thymidine was generated by direct photolytic ultraviolet C irradiation of d(CGCATTACGC). The three-dimensional structure of the duplex (6-4) decamer, d(CGCAT[6-4]TACGC).d(GCGTAATGCG), has been determined by two-dimensional NMR spectroscopy and a relaxation matrix refinement method. NMR data and structural calculations established that the formation of the (6-4) adduct in the B-DNA duplex retains Watson-Crick-type hydrogen bonding throughout the duplex except at the 3'-side of the (6-4) lesion where the T-->C transition mutation is predominantly targeted [LeClerc, J. E., Borden, A. & Lawrence, C. W. (1991) Proc. Natl Acad. Sci. USA 88, 9685-9689], but leads to a 44 degrees bending in the overall DNA helix. Perpendicular base orientation of the (6-4) lesion provides a structural basis where potential hydrogen bonding at the 3' sides of the (6-4) adduct with substituted nucleotide is improbable during replication under stringent conditions.

Base Sequence↗

PubMed1995

Structures of revertant signal sequences of Escherichia coli ribose binding protein.

Recently we reported (Yi et al., 1994) that the alpha-helical content of the signal peptide of Escherichia coli ribose binding protein, when determined by circular dichroism (CD) and two-dimensional NMR in trifluoroethanol/water solvent, is higher than that of its nonfunctional mutant signal peptide. In the present investigation, the structures of the signal peptides of two revertant ribose binding proteins in the same solvent were also determined with CD and two-dimensional 1H NMR spectroscopy. According to the CD results, both of these revertant signal peptides showed an intermediate helicity between those of wild-type and mutant signal peptides, the helical content of the revertant peptide with higher recovery of the translocation capability being higher. On the other hand, the alpha-helix regions of the wild-type and the revertant peptides as determined by NMR were shown to be the same. This discrepancy may be due to the difference in stability between identical alpha-helical stretches in wild-type and revertant peptides. A good correlation was observed between the helical content of these four ribose binding protein signal peptides in TFE/water as studied by CD and their in vivo translocation activities. It appears, therefore, that both the proper length of the helix and the stability are of functional significance.

Amino Acid Sequence↗

PubMed1995

NMR investigation of echinomycin binding to d(ACGTTAACGT)2: Hoogsteen versus Watson-Crick A.T base pairing between echinomycin binding sites.

The structure of the echinomycin complex with the self-complementary DNA decamer d(ACGTTAACGT)2 has been investigated in solution by proton NMR spectroscopy. Echinomycin binds as a bisintercalator at the CpG steps. An analysis of the intermolecular NOE patterns defined the position and orientation of the bound drug molecule. The terminal A.T base pairs are Hoogsteen base-paired, whereas the central four A.T base pairs are clearly Watson-Crick base-paired. Thus, the presence of the extra A.T base pairs between the binding sites appears to prevent the formation of Hoogsteen base pairs immediately adjacent to the binding site. All four central A.T base pairs are destabilized relative to those in the free DNA. Because there is no evidence for unwinding of the DNA duplex in the complex relative to the free DNA, we conclude that the hypersensitivity to DNA cleavage reagents distal to echinomycin binding sites might be due to the destabilization of DNA structure induced by the drug binding.

Adenine↗

PubMed1995

Proton exchange and basepair kinetics of yeast tRNA(Phe) and tRNA(Asp1).

Nuclear magnetic resonance measurements of proton exchange were performed on yeast tRNA(Phe) and yeast tRNA(Asp), at temperatures from 20 to 45 degrees C, in the presence of various levels of salt, phosphate, added magnesium, and pH. The dynamical changes of the tRNA molecule were interpreted, with the aid of firmly established assignments and the use of the saturation recovery technique. In tRNA(Phe), the exchange rates in zero magnesium indicated early melting of the acceptor stem, tertiary structure, and D stem. However, in the presence of even low levels of magnesium the D stem remained intact up to high temperature, stabilized by a Mg2+ ion. A similar unfolding sequence was observed in tRNA(Asp). The difference between these two tRNAs was the thermal behavior of the tertiary resonance U8-A14. In tRNA(Phe), this base pair showed sharp rate increases between 32 and 39 degrees C. However, in tRNA(Asp), it remained intact up to 36 degrees C and disappeared at 39 degrees C, even if there was not important kinetic broadening. By measuring the temperature dependence of the exchange rates, we obtained an activation energy of 40-60 kcal/mol for all the imino protons of yeast tRNA(Phe) in zero magnesium. The same activation energy was obtained for tRNA(Phe) with equimolar concentration of magnesium. By investigation of the dependence of the exchange rates of these imino protons on solution conditions, we observed the transition from kop rate limiting in the absence of magnesium to kex rate limiting in the presence of magnesium.

Base Composition↗

PubMed1995

Contrasting structural impacts induced by cis-syn cyclobutane dimer and (6-4) adduct in DNA duplex decamers: implication in mutagenesis and repair activity.

The relative biological importance of cis--syn cyclobutane dimer and pyrimidine(6-4)pyrimidone photoadduct ([6-4] photoadduct) appears to be dependent on the biological species, dipyrimidine sites and local conformational variation induced at the damaged sites. The single-strained deoxynucleotide 10-mers containing the site-specific (6-4) adduct or cis--syn cyclobutane dimer of thymidylyl(3'-->5')-thymidine were generated by direct photolysis of d(CGCATTACGC) with UVC (220-260 nm) irradiation or UVB (260-320 nm) photosensitization. Three-dimensional structures of the duplex cis--syn and (6-4) decamers of d(CGCATTACGC)xd(GCGTAATGCG) were determined by NMR spectroscopy and the relaxation matrix refinement method. The NMR data and structural calculations establish that Watson-Crick base pairing is still intact at the cis--syn dimer site while the hydrogen bonding is absent at the 3'-side of the (6-4) lesion where the T-->C transition mutation is predominantly targeted. Overall conformation of the duplex cis--syn decamer was B-DNA and produced a 9 degree bending in the DNA helix, but a distinctive base orientation of the (6-4) lesion provided a structural basis leading to 44 degree helical bending. The observed local structure and conformational rigidity at the (6-4) adduct of the thymidylyl(3'-5')-thymidine (T-T [6-4]) lesion site suggest the potential absence of hydrogen bonding at the 3' sides of the (6-4) lesion with a substituted nucleotide during replication under SOS conditions. Contrasting structural distortions induced ny the T-T (6-4) adduct with respect to the T-T cis--syn cyclobutane pyrimidine photodimer may explain the large differences in mutation spectrum and repair activities between them.

Base Sequence↗

PubMed1994

Formation of a hairpin structure by telomere 3' overhang.

The telomeres of most eukaryotes contain tandemly-repeated DNA sequences, with a cluster of G residues on one strand. Recent studies showed that the Oxytricha telomeric DNA oligonucleotide, d(G4T4G4), dimerizes to form a quadruplex in the presence of Na+ or K+. We have observed that the oligonucleotide d(G4T4G4) does not dimerize in the presence of Li+ ion at low sample concentrations. In the monomeric state, this molecule forms a simple foldback hairpin structure containing G x G reverse Hoogsteen basepairs in the stem region. This hairpin structure has a thermal stability which is well reconciled with telomere functions in vivo.

Animals↗

PubMed1994

Structures of wild-type and mutant signal sequences of Escherichia coli ribose binding protein.

The structure of a chemically synthesized 25-residue-long functional signal peptide of Escherichia coli ribose binding protein was compared with that of a nonfunctional mutant-signal peptide using circular dichroism and two-dimensional 1H NMR in solvents mimicking the amphiphilic environments. The functional peptide forms an 18-residue-long alpha-helix starting from the NH2-terminal region and reaching to the hydrophobic stretch in a solvent consisting of 10% dimethylsulfoxide, 40% water, and 50% trifluoroethanol (v/v). The nonfunctional mutant peptide, which contains a Pro at position 9 instead of a Leu in the wild-type peptide, does not have any secondary structure in that solvent but forms a 12-residue-long alpha-helix within the hydrophobic stretch in water/trifluoroethanol (50:50, v/v) solvent. It seems that the Pro-9 residue in the nonfunctional peptide disturbs the helix propagation from the hydrophobic stretch to the NH2-terminal region. Because both of these peptides have stable helices within the hydrophobic stretch, it may be concluded that the additional 2 turns of the alpha-helix in the NH2-terminal region of the wild-type signal peptide is important for its function.

Amino Acid Sequence↗

PubMed1992

NMR study of nitrogen-15-labeled Escherichia coli valine transfer RNA.

1,3-15N-Labeled uracil was synthesized chemically and used to prepare labeled Escherichia coli tRNA(Val) biosynthetically. 500-MHz measurements of 15N and proton chemical shift were obtained, for all uridine and uridine-related bases, by heteronuclear multiple-quantum coherence spectroscopy. All the uracil NH group resonances were assigned and were in agreement with previous proton-only assignments. The temperature dependence of intensities of resonances was used to infer the relative stability of parts of the molecule. The acceptor stem was the least thermally stable structural feature, while the anticodon and T loop were relatively more stable.

Base Sequence↗

PubMed1992

The conformation of glucagon in dilute aqueous solution as studied by 1H NMR.

The structure of monomeric glucagon in dilute aqueous solution was studied by 500 MHz NMR. Hydrogen-deuterium exchange experiments monitored by NMR showed that the backbone amide NHs form intrastrand hydrogen bonds suggesting the existence of some degree of compact structure. The temperature dependent shift of several amide NH resonances supported the above conclusion. The small J coupling constants arising from the interactions between 6 amide NHs and C alpha Hs (less than 6 Hz) imply a helical structure.

Glucagon↗

PubMed1990

Free amino acid turnover in methanogens measured by 15N NMR spectroscopy.

Turnover of the nitrogen moiety from free amino acid pools in two thermophilic methanogens, Methanobacterium thermautotrophicum delta H and Methanococcus thermolithotrophicus SN1, has been monitored with 15N NMR spectroscopy. In cells growing exponentially on 15NH4Cl, glutamate was the major soluble 15N-labeled species in both organisms. When the Mb. thermoautotrophicum cells were harvested, washed, and resuspended into medium containing 14NH4Cl, the resonance for [15N]glutamate decreased with a half-life of 0.5 h. This is considerably faster than the turnover rate for the carbon side chain of glutamate (7 h) obtained when a 13CO2 pulse followed by a 12CO2 chase was incorporated into the 15N/14N-labeling experiment. Such behavior is consistent with recycling of the glutamate carbon skeleton via alpha-ketoglutarate after transamination reactions remove the 15N for biosynthesis of other amino acids, nucleic acids, etc. When the cells were in stationary phase, 15N turnover was considerably slower indicating that transaminase activity had also decreased. Mc. thermolithotrophicus has a much more fragile cell wall and easily lyses. To avoid cell loss in the 15N/14N experiment, 15NH+4 growth followed by 14NH4+ dilution was used. In this organism the glutamate-labeled nitrogen turns over quite rapidly (t1/2 approximately 9 min), at a rate comparable to that for the carbon skeleton (t1/2 approximately 10 min). Beta-Glutamate, the second major carbon and nitrogen pool in this organism, turns over its 15N label very slowly. Therefore, this beta-amino acid does not appear to serve as a nitrogen donor in Mc. thermolithotrophicus.

Amino Acids↗

PubMed1990

Inhibition of DNA excision by DNA polymerase-alpha inhibitor in UV-damaged HeLa cells.

HeLa cells treated with 10 J/m2 of ultraviolet (UV) radiation were examined for inhibition of DNA excision by inhibitors of DNA polymerase-alpha and -beta. DNA repair synthesis and excision were inhibited by aphidicolin, a specific inhibitor of DNA polymerase-alpha. Decreased release of radioactive nucleotides from UV-damaged DNA by the inhibitor indicates that the action of DNA polymerase-alpha activity is closely associated with DNA excision. Dideoxythymidine also inhibited DNA repair synthesis but failed to block the excision, suggesting that polymerization by DNA polymerase-beta might precede removal of damaged DNA.

Antibiotics, Antineoplastic↗