10 september, 2004 advanced methods. degenerate oligonucleotides short amino acid sequences can be...
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10 September, 2004
Advanced Methods
Degenerate Oligonucleotides• Short amino acid sequences can be used to create degenerate oligonucleotides.
• PCR primers
• Oligonucleotide probes
• Often important to determine the lease degenerate possible probe from a given sequence.
• Example: Arg-Leu-Met-Glu-Trp-Ile-Cys-Pro-Met-Leu– What sequence gives the least degenerate 17-mer primer?– What fold degeneracy does this primer have?– How does this compare with the fold-degeneracy of a probe that simply starts with the first amino acid in the
sequence?
• This example is solved for you on Weaver, page 77.
End-labeling
Site-directed mutagenesis
Primer Extension
Filter Binding
Gel Mobility Shift
DNAse Footprinting
DMS Footprinting
Microarray Hybridization
http://www.dnai.org/d/index.html
Suggested Background reading:http://www.ncbi.nlm.nih.gov/About/primer/microarrays.html
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