Keywords / Key Attributes : Concentration independent local melting, Formation of interior bubble, Validation of annotated origin of replications / promoter sequences, Local minima of stability.
Local pseudo-unimolecular partial melting in polymeric cellular DNA is very much different from bimolecular comprehensive melting of short oligonucleotides in solutions. Several softwares estimate the melting temperature pretty accurately for the latter case and are used routinely for primer designing in PCR. However, the local partial melting in polymeric DNA involves the formation of a short-lived interior bubble constrained by double helical DNA at both the ends and thus (i) the melting-annealing transition becomes concentration independent and (ii) the fraying effect due to dangling ends are ruled out. Based on these features, the current study appropriately modifies the thermodynamic equations for calculation of local melting within polymeric DNA and incorporates them in a web-server (http://www.saha.ac.in/biop/www/db/local/nsdnamelt.html). Applications of the method in validating annotated promoter sequences and origin of replication have also been surveyed.
Reference :
Journal of Bioinformatics and Intelligent Control, 2013, 2 (4), 316-320.
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