• Journal of the Korean Magnetic Resonance Society
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• v.1 no.1
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• pp.31-44
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• 1997

The effect of the binding of CRP to the symmetrically synthetic 22, 28, and 30 bp lac promoter was investigated by 1H NMR. The binding of cAMP*CRP to the 22 bp DNA did not bring about any changes in the chemical shift values, but did cause selective line broadening of imino proton resonances of specific base pairs. However, The binding of cAMP*CRP to the 28 and 30 bp DNA brought about large changes on the imino proton resonances that seems to be induced by DNA bending. We studied also the role of cAMP as an activator of DNA/CRP complex formation by gel mobility shift assay. Gel mobility shift assay revealed that the cAMP*CRP complex was not able to bind to the 22 bp DNA fragment, but was able to bind to the 28 bp DNA fragment of lac promoter region.

• Archives of Pharmacal Research
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• v.8 no.3
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• pp.99-107
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• 1985

The interaction of reduced riboflavin 2', 3', 4', 5'-tetrabutyrate with salicylic acid, aspirin, and salicylamide has been spectroscopically investigated to determine the binding mechanism. Hydrogen-1 and carbon-13 unclear magnetic resonance, infrared, and absoption spectra were measured in chloform-d and chloroform. The association of the reduced riboflavin with salicylic acid derivatives is different from that osidizd one. Salicylic acid and the reduced riboflavin form a cyclic hydrogen bounded complex through the imino (3-N, 5-N) protons and the carbonyl (2-C, 4-C) oxygens of the isolloxazine ring of the latter, and the carboxylic hydroxyl proton and carbonyl oxygen of the former. Aspirin and the reduced riboflavin form a complex by the same mode as salicylic acid. Salicylamide forms a cyclic hydrogen bonded complex with the reduced riboflavin through the imino (3-N, 5-N) protons and the carbonyl (2-C, 4-C) oxygens of the isoalloxazine ring, and the amino proton and the carbonyl oxygen of salic aylmide. It appears that both the oxidized and reduced form of riboflavin are associated with salicylic acid derivatives.

• Bulletin of the Korean Chemical Society
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• v.30 no.10
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• pp.2197-2198
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• 2009

• Bulletin of the Korean Chemical Society
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• v.28 no.12
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• pp.2543-2545
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• 2007

• BMB Reports
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• v.31 no.1
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• pp.89-94
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• 1998

The structures of the self-complementary decamer duplexes, $d(ACGTATACGT)_2$ (TATA-duplex) and $d(ACGTTAACGT)_2$, (TTAA-duplex) has been obtained in solution by proton NMR spectroscopy and restrained molecular dynamics. The duplexes are essentially B-type, with distortions apparent at the TATA and TTAA steps. Theses distortions and their effects on dynamics have been investigated by the measurement of imino proton exchange time of the base-pairs. The unusual opening kinetics of central A T base-pairs could be correlated to the abnormal structural properties of the corresponding sequences.

• Journal of the Korean Magnetic Resonance Society
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• v.17 no.2
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• pp.76-80
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• 2013

The TCP domain is a DNA-binding domain present in plant transcription factors and has a similar structural feature to the bHTH motif of eukaryotic transcription factors. The imino proton exchange study has been performed for the DNA duplex containing the consensus DNA-binding site for the AtTCP11 transcription factor. The first two base pairs in the consensus 5'-GTGGG-3' sequence are relatively very unstable but lead to greater stabilization of the neighboring two G C base pairs. These unique dynamic features of the five base pairs in the consensus DNA sequence might play crucial roles in the effective DNA binding of the AtTCP11 protein.

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 1986.12a
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• pp.505.2-506
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• 1986

L-Azetidine-2-carboxylic acid (A-2-C), a four-membered cyclic imino acid has been identified in certain plants, and the microorganism Actinoplanes ferrugineus. The imino acid A-2-C has a physiological significance as an antgaonist of proline during peptide synthesis. The biosynthetic mechanism for the formation of A-2-C has not been studied in any detail. By using various amino acids such as methionine and S-adenosyl-L-methionine labeled with deuterium or carbon-14, the details of the biosynthetic pathway and a possible mechanism for the formation of L-A-2-C in .4. ferrugineus have been unravelled, Both in vivo and in vitro experimental results suggest the biosynthesis of L-A-2-C is mediated by a confactor containing a carbonyl group, probably pyridoxal Phosphate. S-Adenosyl-L-methionine, which seems to be the direct biosynthetic substrate, has undergone a f-displacement by an ${\alpha}$-amino group of the amino acid portion of the substrate S-adenosyl-L-methionine potentially via a vinylglycine intermediate. The overall stereochemical events at the ${\beta}$-carbon of the substrate have been shown to inversion of configuration. The overall stereochemical events at the -position of the sub- strate have also been shown to occur with inversion of configuration. The ${\beta}$, ${\gamma}$-elimination reaction of the substrate seems to follow a cisoidal-type mechanism and the addition portion of the reaction a transoidal-type mechanism . The assignment of the proton NMR of A-2-C has been deduced by apply- ing NOE difference experiments, Gd(III) line-broadening experiments and 2D-NOESY experiments of regio-and stereospecificially deuterated A-2-C's.

• Bulletin of the Korean Chemical Society
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• v.35 no.12
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• pp.3495-3501
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• 2014

A novel crystal, the mono-protonated metformin acetate (1), was obtained and characterized by elemental analysis, IR spectroscopy and X-ray crystallography. It was found that one of the imino group in the metformin cation was protonated along with the proton transfer from the secondary amino group to the other imino group. Its crystal structure was then compared with the previously reported diprotonated metformin oxalate (2). The difference between them is that the mono-protonated metformin cations can be linked by hydrogen bonding to form dimers while the diprotonated metformin cations cannot. Both of them are stabilized by intermolecular hydrogen bonds to assemble a 3-D supermolecular structure. The four potential tautomer of the mono-protonated metformin cation (tautomers 1a, 1b, 1c and 1d) were optimized and their single point energies were calculated by Density Functional Theory (DFT) B3LYP method based on the Polarized Continuum Model (PCM) in water, which shows that the most likely existed tautomer in human cells is the same in the crystal structure. Based on the optimized structure, their Wiberg bond orders, Natural Population Analysis (NPA) atomic charges, molecular electrostatic potential (MEP) maps were calculated to analyze their electronic structures, which were then compared with the corresponding values of the diprotonated metformin cation (cation 2) and the neutral metformin (compound 3). Finally, the possible tautomeric mechanism of the mono-protonated metformin cation was discussed based on the observed phenomena.

• Journal of the Korean Magnetic Resonance Society
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• v.3 no.1
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• pp.60-70
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• 1999

The pyrimidine(6-4) pyrimidone photoproduct [(6-4) adduct] is one of the major photoproducts induced by UV irradiation of DNA and occurs at TpT sites. The (6-4) adduct is highly mutagenic and specific during translesion replication. The marked preference for insertion of A opposite the 5'-T and G opposite the 3--T of the (6-4) adducts leads to a predominantly 3'-T\longrightarrowC transition with 85% replicating error rate. In order to obtain insight into the origin of 3'-T\longrightarrowC transition induced by the (6-4) adduct, we have performed one - and two-dimensional NMR experiment. The 3'-Tof the (6-4) lesion forms the stable hydrogen bonding to the imino proton of an opposed G, which stabilizes the overall helix and diminishes the highly distorted conformation caused by the (6-4) lesion in the (6-4)/AA duplex. We proposed that the greater insertion of a G over an A opposite the 3'-T of the (6-4) lesion These results may account for the greater preference for the insertion of a G over a A opposite the 3'-T of the (6-4) lesion. Thus this insertion leads to the highly specific 3'-T\longrightarrowC multation at the (6-4) lesion site.

• Bulletin of the Korean Chemical Society
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• v.29 no.10
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• pp.1937-1940
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• 2008

The P1 duplex of Tetrahymena group I ribozyme is the important system for studying the conformational changes in folding of ribozyme. The formation of the P1 duplex between IGS and substrate RNA and the catalytic activity of ribozyme require a variety of metal ions such as $Mg^{2+}$ and $Mn^{2+}$. In order to investigate the effect of the $Mg^{2+}$ concentration on the conformation of the P1 duplex, the NMR study was performed as a function of $Mg^{2+}$ concentration. This study revealed that the less stable AU-rich region formed duplex at $50{^{\circ}C}$ under high $Mg^{2+}$ concentration condition but melts out under low $Mg^{2+}$ concentration condition. It was also found that in the active conformation under 10 mM $MgCl_2$ condition, the unstable central G${\cdot}$U wobble pair maintains the significant base pairing up to $50{^{\circ}C}$. This study provides the information of the unique feature of the P1 duplex structure and the roll of $Mg^{2+}$ ion on the formation of the active conformation.