Artículo
Family-specific degenerate primer design: a tool to design consensus degenerated oligonucleotides
Iserte, Javier Alonso
; Stephan, Betina Inés
; Goñi, Sandra Elizabeth
; Borio, Cristina Silvia
; Ghiringhelli, Pablo Daniel
; Lozano, Mario Enrique
Fecha de publicación:
01/2013
Editorial:
Hindawi Publishing Corporation
Revista:
Biotechnology Research International
ISSN:
2090-3138
Idioma:
Inglés
Tipo de recurso:
Artículo publicado
Clasificación temática:
Resumen
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 ( nucleotides), Baculovirus ( to bp), Lactobacillus sp. ( to bp), and Pseudomonas sp. ( to bp). 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.
Palabras clave:
Primer Design
,
Degenerate Oligonucleotides
,
Polymerase Chain Reaction
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Citación
Iserte, Javier Alonso; Stephan, Betina Inés; Goñi, Sandra Elizabeth; Borio, Cristina Silvia; Ghiringhelli, Pablo Daniel; et al.; Family-specific degenerate primer design: a tool to design consensus degenerated oligonucleotides; Hindawi Publishing Corporation; Biotechnology Research International; 2013; 1-2013; 1-9; 383646
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