Research Article Open Access

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 Uddin1, Apurba Majumder2, Khandker Khaldun Islam1, Sk. Amir Hossain1 and Palash Kumar Sarker3
  • 1 Khulna University, Bangladesh
  • 2 University of Jyväskylä, Finland
  • 3 National Institute of Biotechnology, Bangladesh

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).

American Journal of Biochemistry and Biotechnology
Volume 11 No. 4, 2015, 191-199

DOI: https://doi.org/10.3844/ajbbsp.2015.191.199

Submitted On: 27 May 2015 Published On: 21 October 2015

How to Cite: Uddin, S. N., Majumder, A., Islam, K. K., Hossain, S. A. & Sarker, P. K. (2015). 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. American Journal of Biochemistry and Biotechnology, 11(4), 191-199. https://doi.org/10.3844/ajbbsp.2015.191.199

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Keywords

  • RB1 Gene
  • Single Nucleotide Polymorphisms
  • Minimum Free Energy Change
  • Genomics
  • Retinoblastoma