1. 10 September, 2004 Advanced Methods

2. 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.

3. End-labeling

7. Site-directed mutagenesis

9. Primer Extension

10. Filter Binding

11. Gel Mobility Shift

12. DNAse Footprinting

13. DMS Footprinting

14. Microarray Hybridization http://www.dnai.org/d/index.html Suggested Background reading: http://www.ncbi.nlm.nih.gov/About/primer/microarrays.html