The existence of synonymous codon biases across all taxonomic groups is a long standing problem in biology. While codon bias seems to be adequately explained by the maintenance of translation efficiency and accuracy in some organisms, there is still no adequate explanation of why codon biases universally track the intergenic gc content, as these regions of the genome would not be under selection pressures affecting translation. One part of the story may come from the triplet nature of codon in which each third position defines the minor groove width and thus affects the basic structure of the DNA by altering the intrinsic flexibility. In addition, this intrinsic flexibility, which is also GC dependent, play a major role on defining the phosphate linkages of the backbone conformation as well as participating with other binding molecules. Packaging such a type of information within the DNA sequence seems to be essential especially when observing such a variation of codon bias among organism. The potential existence of this form of 'architectural' information in the genome might also predict that evolutionary processes at the synonymous sites are not simply an accident, but it might indicate a fundamental connection between the biophysical aspects of DNA and usage of codons. In this thesis, I present a broad taxonomical analysis of the mutational impacts on the intrinsic flexibility of DNA among 26 prokaryotic genomes and investigate its relationship to entropy based codon bias gc content and protein conservation . I conclude that codon bias appears universally connected to the intrinsic flexibility of the genome especially for genomes with extreme GC contents. In all genomes, genes under strong purifying selection at the level of the protein appear to have constraints in the mutational impacts on DNA flexibility. This may reflect a fundamental limitation in ability of DNA to multiplex information at the levels of protein and nuclear architecture.

Publication Date


Document Type


Student Type


Degree Name

Bioinformatics (MS)

Department, Program, or Center

Thomas H. Gosnell School of Life Sciences (COS)


Gregory Babbitt

Advisor/Committee Member

Gary Skuse

Advisor/Committee Member

Feng Cui


Physical copy available through RIT's The Wallace Library at QH447 .A52 2013


RIT – Main Campus

Plan Codes