Family Specific Degenerate Primer Design: A tool to design consensus degenerated oligonucleotides

ISERTE, JAVIER ALONSO; BETINA INÉS STEPHAN; SANDRA ELIZABETH GOÑI; CRISTINA SILVIA BORIO; PABLO DANIEL GHIRINGHELLI; MARIO ENRIQUE LOZANO

Biotechnology Research International

London : SAGE-Hindawi Access to Research

Año: 2013 vol. 2013 p. 1 - 9

2090-3138

Designing degenerate PCR primers for templates of unknown nucleotide sequence may be a very difficult task. In this paper, we present a new method to design degenerate primers, implemented in family-specific degenerate primer design (FAS-DPD) computer software, for which the starting point is a multiple alignment of related amino acids or nucleotide sequences. To assess their efficiency, four different genome collections were used, covering a wide range of genomic lengths: Arenavirus (10 × 104 nucleotides), Baculovirus (0.9 × 105 to 1.8 × 105bp), Lactobacillus sp. (1 × 106 to 2 × 106bp), and Pseudomonas sp. (4 × 106 to 7 × 106bp). In each case, FAS-DPD designed primers were tested computationally to measure specificity. Designed primers for Arenavirus and Baculovirus were tested experimentally. The method presented here is useful for designing degenerate primers on collections of related protein sequences, allowing detection of new family members.