Journal of
Bioinformatics and Sequence Analysis

  • Abbreviation: J. Bioinform. Seq. Anal.
  • Language: English
  • ISSN: 2141-2464
  • DOI: 10.5897/JBSA
  • Start Year: 2009
  • Published Articles: 42

Full Length Research Paper

Primer designing for PreS region of hepatitis B virus from the most conserved patches of hepatitis B virus genome

Naaz Abbas
  • Naaz Abbas
  • Food and Biotechnology Research Center, PCSIR Laboratories complex Lahore 54600, Pakistan.
  • Google Scholar
Mohammad Ajmal
  • Mohammad Ajmal
  • Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
  • Google Scholar
Talat Afroze
  • Talat Afroze
  • Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
  • Google Scholar


  •  Received: 21 December 2011
  •  Accepted: 08 May 2014
  •  Published: 30 January 2015

Abstract

The most conserved regions for 15 hepatitis B virus complete genome of different subtypes were aligned using PCGENE software CLUSTAL to design a new pair of primer that can bind to each subtype of hepatitis B virus (HBV), to amplify PreS region of HBV genome. A pair of primer from these conserved patches was selected using software PRIMER and named as Nhepf1 and Nhepr1. Nhepf1, forward primer bound 2362-2385 nucleotides and Nhepr1, reverse primer bound 260-283 nucleotide amplify 1.12 Kb region of HBV genome that contain PreS sequence. The pair of primer was optimized for PCR. Nhepf1 and Nhepr1 annealed well at 50°C to subtype adw2 (American), adr4 (Japanese) and Pakistanian patient derived HBV DNA without any nonspecific bands. The results were found to be highly reproducible with greater accuracy.
 
Key words: Hepatitis B virus (HBV) genome, HBV conserved region, polymerase chains reaction (PCR) primers, primer designing.