Wobble base-pairing in codon-anticodon interactions: a theoretical modelling study.

The Crick wobble hypothesis attributes the phenomenon of codon degeneracy to a certain impreciseness of pairing between the third base of the codon and the first base of the anticodon. This theoretical study investigates the pairing properties of some wobble bases, including both, observed and unobserved pairs. Some wobble base-pairs are predicted to follow the Watson-Crick pairs in configuration and pairing facility, while others deviate from this norm. The observed U:V pair is unique in that a pairing configuration may be suggested for it wherein the hydrogen-bonding involves the exocyclic 5-carboxymethoxy group of V. By comparing the theoretical data on the configurations of these pairs with the evidence for their existence/non-existence in nature, some guidelines emerge for differentiating between observed and unobserved base pairs on the basis of the pairing configuration.

Methylene blue binding to DNA with alternating GC base sequence: continuum treatment of salt effects.

Methylene blue (MB), an efficient singlet oxygen generating photoactive dye, binds to DNA and allows photosensitized reactions to be used for sequence-specific cleavage of the DNA backbone. Intercalation and groove binding are possible binding modes of the dye, depending on base sequences and environmental conditions. In a recent modeling study of methylene blue binding to a double stranded DNA decamer with an alternating GC sequence, six structural models for intercalation structures and for minor and major groove binding have been obtained. By estimating the binding energies (including electrostatic reaction field contributions of a salt-free aqueous solvent), symmetric intercalation at the 5'-CpG-3' and 5'-GpC-3' steps was found as the predominant binding mode, followed by a slightly weaker binding of the dye in the minor groove. In this study, the stability of the modeled structures has been analysed as a function of salt concentration. The results of finite difference numerical solutions of the non-linear Poisson-Boltzmann equation show that the stabilizing effect of salt is larger for free DNA than for the modeled MB-DNA complexes. Accordingly, the estimated binding energies decrease with increasing ionic strength. A slightly higher stabilization of the groove binding complexes results in comparable binding energies for symmetric intercalation and minor groove binding at high salt concentration. Both results are in qualitative agreement with experimental data.

Utility of a Mycobacterium tuberculosis GC-rich repetitive sequence in the diagnosis of tuberculous pleural effusion by PCR.

A GC-rich repetitive sequence (GCRS) of Mycobacterium tuberculosis was identified in our laboratory which displayed a high homology with GC-rich sequences of M. tuberculosis and M. bovis. A PCR assay based on the amplification of the proximal 150 bp of GCRS and its detection by non-radioactive hybridization was developed. The accuracy of the GCRS-based PCR assay was evaluated in a clinical setting for the detection of mycobacterial DNA in pleural fluids for the diagnosis of tuberculosis (TB) using clinical criteria and pleural biopsy histology as gold standard. In a blind study, a total of 67 pleural fluid samples (38 tuberculous and 29 nontuberculous) were analysed by PCR and the results were compared with pleural biopsy, Ziehl-Neelsen staining and culture. Mycobacteria could not be detected by either smear or culture techniques in any of the pleural fluids samples. Out of 38 tuberculous pleural effusions, 24 were positive by PCR (63.2% sensitivity). When PCR results were compared with pleural biopsy histology, an increased sensitivity of 73.3% was obtained. Out of the 29 nontuberculous pleural effusions, 2 false positive results were obtained accounting for an overall specificity of 93.1%. The GCRS-based PCR assay thus has a definite role in the diagnosis of tuberculous pleural effusion in contrast to smear and/or culture techniques.

Intra- and interloop interactions in the folded G quartet structure of Oxytricha telomeric sequence.

The antiparallel intramolecular G quartet structure for the 3.5 copy Oxytricha telomeric sequence d(G4T4)3G4 has been established using a combination of spectroscopic and chemical probing methods. In the presence of Na+ ions, this sequence exhibits a circular dichroism spectrum with a positive band at 295 nm and a negative band around 265 nm, characteristic of an antiparallel G quartet structure. Further, we show that d(G4T4)3G4 adopts an antiparallel intramolecular G quartet structure even in K+ unlike d(G4T4G4). KMnO4 probing experiments indicated the existence of intra and interloop interactions in the Na+ induced structure. We have found that K+ not only increases the thermal stability of G quartet structure but also binds to the loop region and disrupts stacking and interloop interactions. Biological consequences of such cation-dependent conformational micro-heterogeneity in the loop region of G quartet structures is also discussed.