Helpful Links

Probe and Primer Design

(Note: the guidelines for designing primers are applicable to probes.)

www.oligo.net
Features DNAsis, a general DNA/protein analysis software.

http://www-genome.wi.mit.edu/cgi-bin/primer/primer3.cgi
Free oligo design software customized for designing a set of three oligos: primer pair plus hybridization probe. No registration or login/pasword required.

www.biowire.com
Features ‘Jelly Fish’ freeware package for gene analysis and oligonucleotide analysis.

www.molecular-beacons.org
Design of molecular beacons, real-time monitoring, troubleshooting, and list of oligo synthesis companies for custom molecular probe synthesis including reference papers.

http://www.biosearchtechnologies.com
Biosearch Technologies is a company where you can order dual-labeled probes, including molecular beacon probes and accompanying primer pairs.

PCR and Related Methods

http://www1.qiagen.com/literature/
Can download documents on the following topics of interest. Critical factors for successful PCR, Optimization of multiplex PCR, RT-PCR for greater specificity and reproducibility, PCR optimization using buffers and additives, effect of PCR buffer on multiplex PCR, design and use of PCR primers.

http://www.public.iastate.edu/~pedro/research_tools.html
Pedro’s BioMolecular Tools is a collection of links to information and services.

www.info.med.yale.edu/genetics/ward/tavi/Guide.html
Primer concentrations, buffer comparisons, dNTP concentrations, troubleshooting for PCR and Multiplex PCR in a question and solution format.

Calculating Concentrations

www.uct.ac.za/microbiology/pcrconcn.htm
How to calculate primer concentration and nucleotide concentrations.