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Primer Designing

  • Date Submitted: 12/11/2010 07:58 AM
  • Flesch-Kincaid Score: 45.9 
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          In the last 10 to 15 years the computer has become an essential companion for cell

and molecular biologists. Bioinformatics is an emerging scientific discipline that uses

information technology to organize, analyze, and distribute biological information in

order to answer complex biological questions. Bioinformatics is an interdisciplinary

research area, which may be broadly defined as the interface between biological and

computational sciences. It involves the solution of complex biological problems using

computational tools and systems. It also includes the collection, organization, storage and

retrieval of biological information from databases. Selection of oligonucleotide primers is

useful for polymerase chain reaction (PCR), oligo hybridization and DNA sequencing.

Proper primer design is actually one of the most important factors/steps in successful

DNA sequencing. Various bioinformatics programs are available for selection of primer

pairs from a template sequence. The plethora programs for PCR primer design reflects

the central role of PCR in modem molecular biology. Nevertheless, all these computer

programs are written mainly to assist in the primer design process and are not meant to

replace the eye of the experienced researcher, especially considering the sometimes

erratic nature of PCR experiments. When scheduling important PCR experiments, it is

usually worthwhile to evaluate the predictions of numerous different programs and to use

common sense and laboratory experience to evaluate the suggested primers before

committing to their synthesis.

          A primer is a short synthetic oligonucleotide which is used in many molecular
techniques from PCR to DNA sequencing.  These primers are designed to have a
sequence which is the reverse complement of a region of template or target DNA to
which we wish the primer to anneal.   


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