Inhibition of methanogenesis by interaction of aluminium ion with co-factor, F-420, in Methanosarcina barkeri.

Methane emission was inhibited by aluminium ion in paddy fields. Addition of Al3+ (20 mM) to the culture medium containing cells of pure Methanosarcina barkeri, inhibited methanogenesis. Methanogenic co-factor, F-420, was isolated and purified from Methanosarcina barkeri MS. Spectrophotometric and spectrofluorometric analysis of interaction between co-factor, F-420, and Al3+ revealed that they formed a complex compound that might have blocked methanogenesis.

Sequence-based structural signatures of genome evolution.

Among the multitude of methods available for the study of origin and evolution of various life forms on Earth, the phylogenetic approach, i.e. the delineation of natural genetic relatedness amongst different groups of organisms, has been of particular interest to evolutionary biologists. An approach towards analysing phylogeny is the comparison of genome sequences of extant organisms by a variety of computational techniques. These studies rely mostly on the similarity or dissimilarity in global character of the genome in terms of sequence, without any consideration to its structure. In this work, we report a potentially new methodology towards elucidation of molecular phylogeny. The approach considers a structural parameter of the genome, namely its flexibility, and uses it to compare the small subunit ribosomal ribonucleic acid (SSU rRNA) gene from a cross-section of species. We find that the flexibility pattern of the genome is strikingly similar in organisms that are closer in evolutionary distance than the ones that are separated. This method of comparison thus might be utilised in constructing phylogenetic trees from flexibility patterns derived from nucleotide sequence.

Nucleosomal positioning and genetic divergence study based on DNA flexibility map.

Based on worm like chain model, DNA structural parameters--tilt, roll and rise, derived from crystallographic database have been used to determine the flexibility of DNA that regulates the nucleosomal translational positioning. Theoretically derived data has been compared to the experimental values available in loshikhes and Trifonov's database. The methodology has been extended to determine the flexibility of 18S rRNA genome in eukarya, where yeast shows a distinct difference when compared with mammals like human, mouse and rabbit.

Sequence directed flexibility of DNA and the role of cross-strand hydrogen bonds.

Persistence length and torsional rigidity for different B-DNA sequences have been calculated by analysing crystal structure database. The values of these parameters for mixed sequence DNA are in good agreement with those estimated by others. Persistence lengths for the homopolymeric sequences, namely poly(dA).poly(dT) and poly(dG).poly(dC), are significantly large compared to those of others as expected from the inability of these sequences to form nucleosome under normal conditions. The heteropolymeric sequences poly(dA-dC).poly(dG-dT) and poly(dG-dC).poly(dG-dC), on the other hand, have smaller persistence lengths. This implies larger flexibility of the d(AC).d(GT), d(CA).d(TG), d(GC).d(GC) and d(CG).d(CG) doublets, some of which constitute the genetic disease forming triplet repeats d(CTG).d(CAG) and d(CGG).d(CCG). Thus it is expected that these triplet repeat sequences are also flexible and wrap around the histone octamer efficiently. Persistence length calculations also indicate larger flexibility for these triplet repeat sequences. Furthermore, our computations reveal that the rigidity of a given DNA sequence is controlled by its ability to form cross-strand bifurcated hydrogen bonds between the successive base pairs. Molecular orbital calculations suggest that these hydrogen bonds are generally extended with bond lengths around 3A.

Denaturation of supercoiled DNA: a Monte Carlo study.

A theoretical investigation of the denaturation characteristics of a supercoiled DNA has been presented employing a Metropolis Monte Carlo algorithm to examine the overall melting profiles of a supercoiled plasmid as the temperature is varied. We show that in contrast to a previously presented algorithm, this much simpler method is sufficient to explain almost all the overall denaturation characteristics and it also correctly calculates the detailed denaturation probabilities of each base pair at various degrees of supercoiling. We also present for the first time a theoretical investigation of the alkaline denaturation of a supercoiled plasmid. Although one can qualitatively reproduce the denaturation profiles using the present Monte Carlo algorithm, the agreement with experiment is not as good as in the case of thermal denaturation. The possible sources of discrepancy between theory and experiment have been discussed.

Multiple fragment ligation on glass surface: a novel approach.

Binding of DNA to pure silicon dioxide involving formation of hydrogen bonds by disruption of the hydration shell of DNA using chaotropic agents can be easily reversed with water or buffers of low ionic strength. When powdered glass was used instead of pure silicon dioxide the binding of DNA to glass was less easily reversed. DNA bound to glass permits digestion by restriction enzyme, ligation and transformation. The method opens up the possibility of enhancing transformation efficiency especially for DNA digests containing more than two pieces.

Denatured supercoiled DNA--structural and biological activity.

Supercoiled DNA on treatment with NaOH followed by neutralization produces a condensed structure (form Id). This structure does not split into topoisomers when run on long gel in presence of intercalating agents and the migration of this form does not change appreciably in presence or absence of ethidium bromide. Relaxation of form Id by topoisomerase I from pea chloroplast is facilitated more than form I. Single-stranded binding (SSB) protein binds more to form Id as evidenced from gel retardation study. Hydroxyl radical nicking is facilitated in this form. Compared to form I, this form produces half the number of transformants, but adsorption and penetration remain almost same in both the forms. Post-transformational growth using 32P labelled form I and form Id showed greater amount of degradation in form Id.

Biochemical activities of denatured covalently closed circular duplex DNA.

Covalently closed circular duplex DNA when exposed to high alkaline pH followed by neutralization yields a collapsed state structure (form I(d)) that can undergo transition to form I and was susceptible to S1 nuclease. Form I(d), in spite of its compact structure, admits specific cleavage by restriction enzymes over its entire genome. When used in a semi-in vitro replication complex, form I(d) gave significantly better template activity, and undergoes better primer extension in in vitro using Klenow. Thus form I(d) having a compact shape can behave as a better substrate in a few key enzymatic reactions.

Methanog: a specialized database on methanogenic bacteria.

A specialized, interdisciplinary database on various types of related information on methanogenic bacteria is described. Derived from other sequence databases etc., this database collects information from many sources, including unpublished work from research laboratories working in this field, and makes them accessible from a single source, to interested scientists, free of cost. It is presently held in eight 48 T.P.I. floppy disks and can be run on any IBM PC under DOS 3.0 or above, making this database of particular interest to researchers with limited resources and on-line search/access facilities.

A test of the bay-region mechanism in carcinogenesis for monomethyl benz[a]anthracenes in a self-consistent-field molecular orbital theory.

The relative carcinogenic activity of the isomeric monomethyl derivatives of benz[a]anthracene has been studied on the basis of their bay-region reactivity, and the subsequent ease of carbonium ion formation, as obtained from a suitable 'self-consistent-field' molecular orbital theory for the mobile pi-electrons. The predicted order of carcinogenic activity of these molecules is compared with the available experimental data.

Melting transition of covalently closed DNA with supercoil-induced cruciforms.

The melting curve for covalently closed supercoiled DNA has been studied by assuming the existence of cruciforms as significant structural perturbations in the pre-melting region. The statistical mechanical treatment used incorporates these cruciform structures through an appropriate sequence generating function. The variation of the effective hydrogen bond energy with temperature is taken into account by an empirical procedure. The results obtained are in close agreement with the corresponding experimental data in TEA solution where the effect of heterogeneity of the base pairs is minimized.

Growth and reactivation of single stranded DNA phage phiX174 in E. coli undergoing "thymineless death".

The thymine requirement of the E. coli strain HF 4704 (uvr A-, rec A+) is thermosensitive i.e. these cells require for their growth 2 microng thymine per ml at 37 degrees C but not at 30 degrees C. Such cells when starved for thymine for 3 h at 37 degrees C are capable of sustaining growth of single stranded DNA phage phiX174 without any diminution of burst size under nonpermissive conditions. Thymine starved HF 4704 cells also reactivate UV-irradiated phiX174 by about 3fold. To test if the thymine necessary for phage growth under "thymineless" conditions was supplied by host DNA degradation products, the transfer of 32P label from the host DNA to mature progeny phages was measured by means of sucrose density gradient analysis. It was found that only about 0.7% of 32P of the host DNA was transferred to the progeny phages growing in normal cells whereas the corresponding value was 7.8% in the case of thymine starved cells.