J Bacteriol Virol.  2008 Dec;38(4):259-266. 10.4167/jbv.2008.38.4.259.

Development of UPSR Primer Design Program for Efficient Detection of Viruses

• Jang SY
• Yoon HW
• Oh SA
• Lee KM
• Lee CH

• KMID: 1483967
• DOI: http://doi.org/10.4167/jbv.2008.38.4.259

Abstract

PCR is a rapid and sensitive method for detection of viruses from clinical samples and good primers are essential for successful PCR. However, high mutation rate of viral genomes often results in failure in detecting viruses, and there have been attempts to develop primers from multiple viral sequences. Thus, we developed a program called Universal Primers Score Ranking (UPSR) which generates primers from multiple sequences and ranks the quality of primers automatically. The feasibility of the UPSR program was tested using hepatitis B viruses (HBV) isolated from Korean patients. UPSR generated primer candidates with quality score ranks according to two T(m) values. We found that T(m2) values calculated based on the thermodynamics of nearest neighboring bases were better correlated with actual detection rate of HBV from patients' sera. The primer with number 1 rank by T(m2) values detected more samples than any other primers designed by UPSR, commercial primer, or other reference primers suggested by previous literatures. Thus, UPSR proved to be easy and useful to design primers from multiples sequences in detecting viruses.

Keyword

UPSR program; Hepatitis B Virus; PCR

MeSH Terms

Collodion
Genome, Viral
Hepatitis B virus
Humans
Mutation Rate
Polymerase Chain Reaction
Thermodynamics
Collodion

Figure

• 

  Figure 1. Screen capture of the UPSR program. The captured UPSR screen shot shows the quality ranks and scores for primers designed by UPSR.

• 

  Figure 2. Relation between the primer quality ranks and HBV detection rate. Primers with high quality scores according to Tm1 (circle) or Tm2 (triangle) were selected and applied to HBV detection by PCR from 14 HBV sAg(+) serum samples.

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