10 September, 2004 Advanced Methods. Degenerate Oligonucleotides Short amino acid sequences can be used to create degenerate oligonucleotides. PCR primers.

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Presentation transcript:

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 Suggested Background reading: