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polDNAmelt: Local Melting Within Polymeric DNA—An Improved Method and Its Applications

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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.
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Keywords: CONCENTRATION INDEPENDENT DNA MELTING; FRAYING EFFECT; LOCAL PSEUDO-UNIMOLECULAR PARTIAL MELTING; SHORT-LIVED INTERIOR BUBBLE; TM

Document Type: Short Communication

Publication date: December 1, 2013

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  • Journal of Bioinformatics and Intelligent Control (JBIC) is an international journal that publishes research articles in areas of the bioinformatics and intelligent control. JBIC is aimed to provide an international forum for the exchange of ideas and new scientific and technological findings to disseminate information and promote the transfer of knowledge between professionals in academia and industry. The journal publishes original research papers; review papers; technical reports and notes; short communications focused on emerging new developments in these research areas.
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