This paper describes a new strategy for designing degenerate primers for a given multiple alignment of amino acid sequences. Degenerate primers are useful for amplifying homologous genes. However, when a large collection of sequences is considered, no consensus region may exist in the multiple alignment, making it impossible to design a single pair of primers for the collection. In such cases, ...

The polymerase chain reaction (PCR) is a versatile method to amplify specific DNA with oligonucleotide primers. By designing degenerate PCR primers based on amino acid sequences that are highly conserved among all known gene family members, new members of a multigene family can be identified. The inherent weakness of this approach is that the degenerate primers will amplify previously identifie...

Amplification of a product in PCR with specific primers may be viewed as an artificial Darwinian-type "selection of the fittest". In other selective systems, such as general evolution, immune system and probably brain cortex, the stringency of selection is not absolute but rather degenerate, with selection of many highly fit units, not limited, however, to only the fittest. In PCR also, anneali...

A polygalacturonase-inhibiting protein (pgip) gene from Malus domestica cv Granny Smith apple fruit was cloned by degenerate oligo-primed polymerase chain reaction (PCR) and Inverse PCR. An alignment of the pear and bean PGIP sequences was used to design degenerate PCR primers in highly conserved regions. Degenerate PCR allowed the amplification of a 351bp internal fragment of the pgip gene, te...

The polymerase chain reaction (PCR) is widely used to uncover new information about genes and genomes, but is limited in that it is highly dependent on the use of specific and sensitive primers to yield good results. Primers can target a specific, known sequence, but what is often more interesting is the use of degenerate primers to target unknown sequences. Degenerate primers are designed base...

Almond (Prunus dulcis L.) is one of the most important nut crops in Iran. Most almond cultivars and genotypes are self-incompatible. However, research on S-alleles indicates that it is very efficient in cultivar selection. Selfincompatibility in almond is gametophytic and controlled by a single S-locus with multiple codominant alleles. In this study, compatibility relationships among cultivars,...

AN ITERATIVE BEAM SEARCH ALGORITHM FOR DEGENERATE PRIMER SELECTION by Richard M. Souvenir ADVISOR: Professor W. Zhang December, 2003 Saint Louis, Missouri Single Nucleotide Polymorphism (SNP) Genotyping is an important molecular genetics process in the early stages of producing results that will be useful in the medical field. Due to inherent complexities in DNA manipulation and analysis, many ...

Procedures for using PCR to amplify novel members of gene families from genomic DNA frequently involve the use of degenerate primers. Of key importance is the ability to produce ample quantities of specific PCR product while minimizing or eliminating nonspecific side reactions. Primer design protocols and software are improving, but finding the optimal amplification conditions often involves a ...