NOPR Collection:

Energy barriers and rates of tautomeric transitions in DNA bases: Ab initio quantum chemical study

Thu, 01 Dec 2005 00:00:00 GMT

Title: Energy barriers and rates of tautomeric transitions in DNA bases: Ab initio quantum chemical study Authors: Basu, Soumalee; Majumdar, Rabi; Das, Gourab K; Bhattacharyya, Dhananjay Abstract: Tautomeric transitions of DNA bases are proton transfer reactions, which are important in biology. These reactions are involved in spontaneous point mutations of the genetic material. In the present study, intrinsic reaction coordinates (IRC) analyses through ab initio quantum chemical calculations have been carried out for the individual D A bases A, T, G, C and also A:T and G:C base pairs to estimate the kinetic and thermodynamic barriers using MP2/6-31G** method for tautomeric transitions. Relatively higher values of kinetic barriers (about 50-60 kcal/mol) have been observed for the single bases, indicating that tautomeric alterations of isolated single bases are quite unlikely. On the other hand, relatively lower values of the kinetic barriers (about 20-25 kcal/mol) for the DNA base pairs A:T and G:C clearly suggest that the tautomeric shifts are much more favorable in DNA base pairs than in isolated single bases. The unusual base pairing A':C, T':G, C':A or G':T in the daughter DNA molecule, resulting from a parent DNA molecule with tautomeric shifts, is found to be stable enough to result in a mutation. The transition rate constants for the single DNA bases in addition to the base pairs are also calculated by computing the free energy differences between the transition states and the reactants. Page(s): 378-385

Expression of Δ¹-pyrroline-5-carboxylate synthetase gene during drought in rice (Oryza sativa L.)

Thu, 01 Dec 2005 00:00:00 GMT

Title: Expression of Δ¹-pyrroline-5-carboxylate synthetase gene during drought in rice (Oryza sativa L.) Authors: Choudhary, N L; Sairam, R K; Tyagi, A Abstract: The 45-days-old seedlings of drought resistant (N-22, CR143-2-2) and susceptible rice (Oryza sativa L.) genotypes (Panidhan, Pusa-169) were subjected to osmotic stress in PEG-6000 solution of -10 and -16 bar and the relative water content (RWC), proline content, and pyrroline-5-carboxylate synthetase (P5CS) activity and its P5CS expression were studied. A gradual decrease in RWC was observed in tolerant genotypes, whereas the decrease was drastic in susceptible ones. Proline content and P5CS activity increased both in susceptible and tolerant genotypes; the increase was higher in tolerant genotypes. Higher proline levels in tolerant genotypes were due to increased P5CS activity. The EcoRI, BamHI and XbaI restricted DNA of N-22 and Panidhan genotypes were hybridized with Arabidopsis P5CS sequence and a single band (approx 2.4 kb) was observed, however, P5CS expression was more in N-22, as compared to Panidhan. Page(s): 366-370

Production of human single-chain variable fragment (scFv) antibody specific for digoxin by ribosome display

Thu, 01 Dec 2005 00:00:00 GMT

Title: Production of human single-chain variable fragment (scFv) antibody specific for digoxin by ribosome display Authors: Yan, Xiang-Hua; Xu, Zi-Rong Abstract: Ribosome display was applied in vitro to select single-chain variable fragment (scFv) antibody specific for digoxin from a human non-immune naive scFv library. A cell-free system was used to produce stable antibody-ribosome-mRNA (ARM) complexes to provide the linkage of genotype and phenotype, allowing simultaneous selection of a desired antibody together with its encoding mRNA. The mRNA was then recovered and amplified as DNA by reverse transcriptase-polymerase chain reaction (RT-PCR). Repeating the display cycle enriched the selected molecules, enabling rare species to be isolated. In this study, digoxin-binding segments were selected over four cycles of ARM display and the selected DNA was cloned and expressed as a single-chain variable fragment antibody (the best scFv, A3) in Escherichia coli. The affinity (equilibrium dissociation constant Kd) of digoxin was 8.3 × 10⁻⁸ M for A3, which validated construction of the naïve library and the power of ribosome display lending to the evolution of functional characteristics, such as potency of leading candidate antibodies to provide therapeutic antibodies. A3 was purified using affinity chromatography and determined by Western blot. The results indicate that ribosome display technnique can be efficiently used to isolate specific antibody fragments from a naive library. Page(s): 350-357

Lead levels in some biological samples of auto-mechanics in Abeokuta, Nigeria

Thu, 01 Dec 2005 00:00:00 GMT

Title: Lead levels in some biological samples of auto-mechanics in Abeokuta, Nigeria Authors: Babalola, O O; Ojo, L O; Aderemi, M O Abstract: Lead levels were determined in the blood, scalp hair and fingernails of 38, all male auto-mechanics (aged 18-45 years) from Abeokuta, South-western Nigeria. The subjects were classified into four sub-groups based on the period of exposure namely: 1-5, 6-10, 11–15, and >16 years. Thirty-two occupationally unexposed subjects (mainly office workers) served as the control. The weight, height and body mass indexes of all subjects were noted, in addition to other information obtained through structured questionnaire. The mean values of blood lead (BPb), hair lead (HPb) and fingernail lead (NPb) of the occupationally exposed subjects (n=38) were 48.50 ± 9.08 μg/dL, 17.75 ± 5.16 μg/g, and 5.92 ± 3.30 μg/g respectively, while the corresponding mean values for these parameters in the control subjects (n = 32) were 33.65 ± 10.09 μg/dL, 14.30 ± 5.90 g/g and 5.31 ± 2.77 μg/g respectively. The differences in BPb and HPb levels of the two groups were statistically significant (P <0.05 and P <0.01 respectively), while that of NPb was not significant. The levels of lead in the biological samples appeared to have no relationship with the number of years on the job. From these results, it was obvious that the higher levels of lead in the biological samples of test subjects, compared with those of the controls were from environmental sources. Page(s): 401-403