Summary: Degenerate PCR & Degenerate Primer. Degenerate PCR is a PCR method that uses degenerate primers to amplify unknown DNA sequences that are related to a known DNA sequence or to amplify a mixture of related sequences in one PCR reaction. Degenerate primers are just a mix of primers with similar sequences. Degenerate PCR is useful for identify new members of a gene family or orthologous genes from different organisms.
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Protocols
- Degenerate PCR (Atle M. Bones Lab, Norwegian University of Science and Technology)
Degenerate PCR is in most respects identical to ordinary PCR, but with one major difference. Instead of using specific PCR primers with a given sequence, you use mixed PCR primers. That is, if you do not know exactly the sequence of the gene you are going to amplify, you insert "wobbles" in the PCR primers where there is more than one possibility. For instance, if you just have a protein motif, you can back-translate the protein motif to the corresponding nucleotide motif. (Protein --> Sequence).
http://boneslab.bio.ntnu.no/degpcrshortguide.htm
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Degenerate PCR
(Michael Koelle)
http://www.dartmouth.edu/~ambros/protocols/other/k...
Added: Tue May 14 2002, Hits: 1853, Reviews: 0 Write review Cached -
Degenerate PCR
(Michael Koelle, at another server)
Detailed guide in degenerate PCR, including primer design, reaction conditioning and product analysis.
http://info.med.yale.edu/mbb/koelle/protocols/prot...
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Degenerate PCR Primer Design
(Molecular Biology Techniques Manual)
For amplification of cognate sequences from different organisms, or for "evolutionary PCR", one may increase the chances of getting product by designing "degenerate" primers: these would in fact be a set of primers which have a number of options at several positions in the sequence so as to allow annealing to and amplification of a variety of related sequences.
http://web.uct.ac.za/microbiology/pcroptim.htm#Deg...
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Degenerate primer design method
(Langdale Lab, Department of Plant Sciences, University of Oxford)
http://dps.plants.ox.ac.uk/langdalelab/protocols/P...
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Guidelines for degenerate-primer design and use
(Qiagen)
http://www1.qiagen.com/resources/info/guidelines_f...
Added: Sun Jul 21 2002, Hits: 5000, Reviews: 0 Write review Cached -
PCR with degenerate primers
(Langdale Lab, Department of Plant Sciences, University of Oxford)
Degenerate PCR is pretty standard, with the main difference being that a higher concentration of primer is used.
http://dps.plants.ox.ac.uk/langdalelab/protocols/P...
Added: Wed Feb 11 2009, Hits: 5853, Reviews: 0 Write review