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.

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.