American Journal of Biochemistry and Biotechnology

Minimum Free Energy Based Evaluation of mRNAs Secondary Structures Constructed by 18 Clinically Significant Exonic Single Nucleotide Polymorphisms (SNPs) and Haplotypes of 5 Missense SNPs of RB1 Gene

Sarder Nasir Uddin, Apurba Majumder, Khandker Khaldun Islam, Sk. Amir Hossain and Palash Kumar Sarker

DOI : 10.3844/ajbbsp.2015.191.199

American Journal of Biochemistry and Biotechnology

Volume 11, Issue 4

Pages 191-199

Abstract

Clinically significant 18 Single Nucleotide Polymorphisms (SNPs) from exon regions of Retinoblastoma gene (RB1) were analyzed to find out the structural variations in mRNAs. Online bioinformatic tools i.e., Vienna RNA, RNAfold were used for secondary structure analysis of mRNAs. Predicted minimum Free Energy Change (MFE) was calculated for mRNAs structures. It has been observed that the average of predicted MFE value from 13 nonsense mutations was higher (0.76 kcal/mol) in comparison to 5 missense mutations. Presumably, 13 nonsense mutations are responsible for Nonsense Mediated mRNA Decay (NMD), therefore, excluded from haplotype analysis. From the statistical analysis all the thermodynamic data obtained from four SNP haplotypes are significant (p≤0.05), followed by three-SNP haplotype data except Ensemble diversity (p≤0.10). Interestingly, MEF of Centroid Secondary Structure is highly significant (p≤0.01) in all the cases (Two-SNP haplotypes, Three-SNP haplotypes and Four-SNP haplotypes).

Copyright

© 2015 Sarder Nasir Uddin, Apurba Majumder, Khandker Khaldun Islam, Sk. Amir Hossain and Palash Kumar Sarker. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.