Computational investigation on effect of mutations in PCNA resulting in structural perturbations and inhibition of mismatch repair pathway

Abstract

From bacteria to mammals, DNA mismatch repair (MMR) pathway plays an essential role in eliminating mismatched nucleotides and insertion-deletion mismatches during the process of DNA replication. Among many of the proteins which participate in the mismatch repair process, proliferating cell nuclear antigen (PCNA) remains the principal conductor at the replication fork. The pol30-201 and pol30-204 are the two mutated alleles which encode for C22Y and C81R mutant forms of PCNA proteins. We performed long term molecular dynamics (MD) simulations analysis (0.8 μs) to understand the dynamic behavior and alterations in the structure of wild type and mutated forms of PCNA at the atomic level. We observed changes in the structural characteristics like length, radius, rise per residue of alpha helices in both the mutated forms of PCNA. Apart from it, disfigurement of the charge distribution which effects binding with the dsDNA due to mutant C22Y and other structural perturbations were also seen in regions significant for the formation of a biologically active trimeric form of PCNA due to mutant C81R. Our analysis of native and mutated forms of PCNA provides an insight into the essential structural and functional features required for proper and well-coordinated DNA mismatch repair process and consequences of the mutation leading to an impaired process of MMR. These structural characteristics are fundamental for the MMR process and hence our analysis likely contributes to or presents the novel mechanism involved in the process of MMR.

Communicated by Ramaswamy H. Sarma     

An efficient method for DNA extraction from cyanobacteria isolated from hypersaline and marine environments

Cyanobacteria are ancient organisms surviving on the earth due to their simple nutritional requirements and ability to produce distinct secondary metabolites that can combat detrimental environmental impacts. In order to understand these abilities of cyanobacteria at the molecular level, it is necessary to extract high‐quality genomic DNA. However, the presence of secondary metabolites and exopolysaccharides hinders the DNA extraction from these organisms, especially from hypersaline environments. Here we have developed and compared a new method with two known methods of DNA extraction from environmental isolates. The results clearly indicate that the new optimized method yielded large amount of DNA with high purity. Additionally, the extracted DNA showed reduced degradation and excellent overall quality, which can be used directly for downstream purposes such as PCR and sequencing.     

Assessment of heavy-metal pollution in three different Indian water bodies by combination of multivariate analysis and water pollution indices

Abstract

Water quality is a big concern for the humankind as it is the most important natural resource. However, the non-controlled growth of rural and urban areas in rapidly developed countries such as India is affecting water quality. In this research, we pretend to assess and demonstrate the heavy-metal status of three different water bodies of Indus, Beas and Sutlej Rivers and Harike Wetland. Data on water quality from 2013 to 2017 were analyzed through multivariate statistic techniques (cluster analysis – CA – and principal component analysis – PCA) and compared among them using public water pollution indexes. The results of CA and PCA showed that Sutlej River and Harike Wetland are included in the same group, whereas Beas River formed a separate one. This may be due to the high content of Pb, Cu, and Zn in these water bodies as compared with Beas River. The Pb content of all the water bodies exceeded the limit for EPR, BIS and WHO guidelines for drinking water. The heavy-metal pollution index was also applied to the contents of different heavy metals to find which water body is more polluted, and from their results, it was found that Harike Wetland and Sutlej River are critically polluted with heavy metals.     

Alteration in the acceptor side of photosystem II of chloroplast by high light

The effect of high light on the acceptor side of photosystem II of chloroplasts and core particles of spinach was studied. BothV _max and apparentK _m for DCIP were altered in photoinhibited photosystem II core particles. The double reciprocal plot analysis as a function of actinic light showed increased slope in chloroplasts photoinhibited in the presence of DCMU. Exposure of chloroplasts to high light in the presence of DCMU did not protect the chloroplast against high light induced decrease in F_m, level. Further the high light stress induced decrease inF _m level was not restored by the addition of DCMU. These results suggest that the high light stress induced damage to chloroplast involves alteration in the binding site forQ _B on the DI protein on the acceptor side of photosystem II     

Design,synthesis and ex vivo evaluation of colon-specific azo based prodrugs of anticancer agents

Colon-specific azo based prodrugs of anticancer agents like methotrexate (6), gemcitabine (7) and analogue of oxaliplatin (RTB-4) (8) were synthesized and characterized by modern analytical techniques. The prepared prodrugs were stable in acidic (pH 1.2) and basic (pH 7.4) buffers which showed their stability in upper GIT environment. Further, an assay was performed which demonstrated the presence of azoreductase enzyme in the rat fecal material, rat cecum content and other parts of intestinal content which reduce specifically the azo bond and release the drug. The in vitro cytotoxicity assay was also performed which clearly indicated that these azo based prodrugs are active against human colorectal cancer cell lines (COLO 205, COLO 320 DM and HT-29). The release behavior of prodrugs (10, 11 and 15) was 60–70% after 24 h incubation at 37 °C. Therefore, the synthesized azo linked prodrugs of methotrexate, gemcitabine and RTB-4 are the potential candidates for colon targeted drug delivery system with minimal undesirable side effects.