PubMed Health⌕ Search

Biomedical subjects

D Bhattacharyya

Publications and source records attributed to D Bhattacharyya.

17 recordsLinked to original sources
PubMed1992

Groove width and depth of B-DNA structures depend on local variation in slide.

The groove widths of DNA helix, especially minor groove width, are generally believed to be important for recognition of DNA by various types of ligands. It has been postulated earlier that large negative propeller twist, in the AT rich regions compresses the minor groove of duplex DNA. A systematic study has now been carried out by generating models with different values of local doublet and intra-basepair parameters and calculating their minor groove widths. It is found that several local doublet parameters affect the minor groove width but it depends most strongly on the local step parameters roll and slide when each parameter is considered individually. However, a detailed analysis of the various local parameters within the B-DNA family of crystal structures indicates that propeller twist and slide are most strongly correlated with the observed values of minor groove width. The groove depth is also strongly correlated with slide. Thus the local base sequence dependent variations in slide can modify both the groove width and depth and consequently determine the ligand binding properties of DNA.

Base Sequence↗
PubMed1990

Physicochemical studies of human O6-methylguanine-DNA methyltransferase.

O6-Methylguanine-DNA methyltransferase, present in most organisms, removes mutagenic and carcinogenic O6-alkylguanine from DNA by accepting the alkyl group in a stoichiometric reaction. The protein has been partially purified from human placenta. It reacts with second-order rate constants of 2.20 x 10(8) and 0.067 x 10(8) lmol-1 min-1 at 37 degrees C for duplex and single-stranded DNA substrates, respectively. The corresponding value for the alkylated base in synthetic poly(dC, dG, m6dG) is 0.02 x 10(8) l mol-1 min-1. The native protein is monomeric with a molecular mass of 22-24 kDa. Methylation of the protein does not lead to a gross change in its conformation but causes a slight reduction in its isoelectric point of 6.2. Although DNA protects the protein from heat inactivation, both duplex and single-stranded DNAs inhibit its activity in a concentration-dependent manner. The transferase reaction rate is also strongly inhibited by salt with about 20% of the maximum rate observed in physiological ionic strength. This inhibition is nonspecific with respect to the ions of univalent salts.

Animals↗
PubMed1990

Local variability and base sequence effects in DNA crystal structures.

The importance and usefulness of local doublet parameters in understanding sequence dependent effects has been described for A- and B-DNA oligonucleotide crystal structures. Each of the two sets of local parameters described by us in the NUPARM algorithm, namely the local doublet parameters, calculated with reference to the mean z-axis, and the local helical parameters, calculated with reference to the local helix axis, is sufficient to describe the oligonucleotide structures, with the local helical parameters giving a slightly magnified picture of the variations in the structures. The values of local doublet parameters calculated by NUPARM algorithm are similar to those calculated by NEWHELIX90 program, only if the oligonucleotide fragment is not too distorted. The mean values obtained using all the available data for B-DNA crystals are not significantly different from those obtained when a limited data set is used, consisting only of structures with a data resolution of better than 2.4 A and without any bound drug molecule. Thus the variation observed in the oligonucleotide crystals appears to be independent of the quality of their crystallinity. No strong correlation is seen between any pair of local doublet parameters but the local helical parameters are interrelated by geometric relationships. An interesting feature that emerges from this analysis is that the local rise along the z-axis is highly correlated with the difference in the buckle values of the two basepairs in the doublet, as suggested earlier for the dodecamer structures (Bansal and Bhattacharyya, in Structure & Methods: DNA & RNA, Vol. 3 (Eds., R.H. Sarma and M.H. Sarma), pp. 139-153 (1990)). In fact the local rise values become almost constant for both A- and B-forms, if a correction is applied for the buckling of the basepairs. In B-DNA the AA, AT, TA and GA basepair sequences generally have a smaller local rise (3.25 A) compared to the other sequences (3.4 A) and this seems to be an intrinsic feature of basepair stacking interaction and not related to any other local doublet parameter. The roll angles in B-DNA oligonucleotides have small values (less than +/- 8 degrees), while mean local twist varies from 24 degrees to 45 degrees. The CA/TG doublet sequences show two types of preferred geometries, one with positive roll, small positive slide and reduced twist and another with negative roll, large positive slide and increased twist.(ABSTRACT TRUNCATED AT 400 WORDS)

Algorithms↗
PubMed1989

A self-consistent formulation for analysis and generation of non-uniform DNA structures.

A fully self-consistent formulation is described here for the analysis and generation of base-pairs in non-uniform DNA structures, in terms of various local parameters. It is shown that the internal "wedge parameters" are mathematically related to the parameters describing the base-pair orientation with respect to an external helix axis. Hence any one set of three translation and three rotation parameters are necessary and sufficient to completely describe the relative orientation of the base-pairs comprising a step (or doublet). A general procedure is outlined for obtaining an average or global helix axis from the local helix axes for each step. A graphical representation of the local helix axes in the form of a polar plot is also shown and its application for estimating the curvature of oligonucleotide structures is illustrated, with examples of both A and B type structures.

Algorithms↗
PubMed1989

Site-directed mutation of the Escherichia coli ada gene: effects of substitution of methyl acceptor cysteine-321 by histidine in Ada protein.

Oligodeoxynucleotide-mediated mutagenesis of the ada gene of Escherichia coli was used to produce two mutant Ada proteins. In mutant I the methyl acceptor Cys-321 for O6-methylguanine was replaced by histidine; and in mutant II the positions of Cys-321 and His-322 of the wild-type protein were inverted. Neither mutant protein had O6-methylguanine-DNA methyltransferase activity, but both retained the phosphotriester-DNA methyltransferase activity involving methyl group transfer to Cys-69. Under the control of the endogenous promoter, synthesis of mutant I protein was undetectable before or after adaptation treatment with promoter, synthesis of mutant I protein was undetectable before or after adaptation treatment with N-methyl-N'-nitro-N-nitrosoguanidine. This appeared to be due to both inhibition of transcription of the mutant gene and degradation of the synthesized protein. On the other hand, mutant II protein was inducible by N-methyl-N'-nitro-N-nitrosoguanidine, although to a smaller extent than the wild-type protein was, and the phosphotriester-DNA methyltransferase activity appeared to reside in 24- to 30-kilodalton cleavage products. Mutant I protein could be produced under lac promoter control, and its cleavage products, unlike those of mutant II protein, tended to aggregate. These results indicate that (i) Cys-321 cannot be replaced or transposed with the nucleophilic amino acid histidine for O6-methylguanine-DNA methyltransferase function, (ii) single amino acid replacement or transposition at the O6-methylguanine methyl acceptor site can have a profound effect on the in vivo stability and regulatory function of the Ada protein, and (iii) the integrity of the protein may not be absolutely needed for its transcription-activation function.

Amino Acid Sequence↗
PubMed1988

Rapid, large-scale purification and characterization of 'Ada protein' (O6 methylguanine-DNA methyltransferase) of E. coli.

The E. coli Ada protein (O6-methylguanine-DNA methyltransferase) has been purified using a high-level expression vector with a yield of about 3 mg per liter of E. coli culture. The 39-kDa protein has an extinction coefficient (E280 nm (1%)) of 5.3. Its isoelectric point of 7.1 is lower than that predicted from the amino acid content. The homogeneous Ada protein is fully active as a methyl acceptor from O6-methylguanine in DNA. Its reaction with O6-methylguanine in a synthetic DNA has a second-order rate constant of 1.1 x 10(9) M-1 min-1 at O degree C. Both the native form and the protein methylated at Cys-69 are monomeric. The CD spectrum suggests a low alpha-helical content and the radius of gyration of 23 A indicates a compact, globular shape. The middle region of the protein is sensitive to a variety of proteases, including an endogenous activity in E. coli, suggesting that the protein is composed of N-terminal and C-terminal domains connected by a hinge region. E. coli B has a higher level of this protease than does K12.

Circular Dichroism↗
PubMed1988

Effect of polyvalent metal ions on the reactivity of human O6-methylguanine-DNA methyltransferase.

Polyvalent metal ions are highly effective in inhibiting human O6-methylguanine-DNA methyltransferase, the repair protein responsible for the removal of the promutagenic and presumably procarcinogenic adduct, O6-alkylguanine, in DNA. The sulfhydryl group-reacting metal ions (Cd2+, Zn2+, Hg2+, Pb2+) completely inhibited the reaction at concentrations of 100-500 microM while other metal ions (Al3+, Fe3+) required concentrations of 1 mM or greater for significant reduction of the reaction rate. Inhibition by the former group of metals could be reversed by dithiothreitol but not by EDTA, while the opposite was true for the second group. Under conditions of partial inhibition of the initial reaction rate by either Hg2+ or Al3+, the extent of reaction was not significantly affected, indicating reversible binding of these ions.

Cations↗
PubMed1987

Energetics of left and right handed models of DNA.

It has been shown by model building studies that various right handed and left handed models are compatible with X-ray data of B-DNA and C-DNA. These models are also found to be in good agreement with infrared dichroism data. Detailed potential energy calculations have now been carried out for these models, viz., right and left handed B-DNA and right and left handed C-DNA. It is found that base sugar stacking and interactions involving the phosphate groups are the dominant forces for stabilizing a particular structure. For some sequences, viz., A-A, T-A and C-A, left handed stacking is quite favourable in both B and C structures. But intranucleotide interactions make the left B-DNA unfavourable while the left C-DNA structure is more stable, for all the sequences, than the right C-DNA structure, proposed from fibre data. For the hexanucleoside pentaphosphate fragments the same trend is observed, with the right handed B-DNA being the most stable of the four models studied. However, the left C-DNA structure is only marginally higher in energy, particularly if the shielding effect of the counter ions, on the phosphate group is taken into consideration.

Chemical Phenomena↗
PubMed1986

Role of selective pressure by screening organisms in the development of producer mutant isolates of different antibiotic markers.

The phenotypes of producer mutant isolates when obtained after mutagenesis of the spontaneous degenerate Aspergillus versicolor N5 by screening on Trichophyton rubrum and those on A. niger G3Br were found to be markedly different. In respect of phenotypic character anti-T. rubrum producer mutant isolates resembled the parental type more closely (which is specifically active against T. rubrum and generally against dermatophytes) than anti-A. niger mutant isolates. This clearly indicates not only the role of selective pressure of the screening organism in the development of a given producer mutant isolate but also shows the possibility of recovery of a producer type of the lost antibiotic marker.

Anti-Bacterial Agents↗
PubMedDate not supplied

Biochemical evidence for mediatory role of 5-hydroxytryptamine in the uterotonic action of prostaglandin F2oc.

5-Hydroxytryptamine (5-HT) is reported to be involved in endogenous prostaglandin (PG)--modulated as well as exogenous PG-induced pharmacological activities including oxytocic effect of PGE1 PGE2oc Biochemical parameters were undertaken for further studies into the possible role of 5-HT in the uterotonic effect of PGF2oc on isolated oestronised rat uterus. The results substantiate the involvement of endogenous 5-HT in the uterotonic effect of PGF2oc.

Animals↗