Probe and Primer Design
(Note: the guidelines for designing primers are applicable to probes.)
Features DNAsis, a general DNA/protein analysis software.
Free oligo design software customized for designing a set of three oligos: primer pair plus hybridization probe. No registration or login/pasword required.
Features 'Jelly Fish' freeware package for gene analysis and oligonucleotide analysis.
Design of molecular beacons, real-time monitoring, troubleshooting, and list of oligo synthesis companies for custom molecular probe synthesis including reference papers.
Biosearch Technologies is a company where you can order dual-labeled probes, including molecular beacon probes and accompanying primer pairs.
PCR and Related Methods
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.
Primer concentrations, buffer comparisons, dNTP concentrations, troubleshooting for PCR and Multiplex PCR in a question and solution format.
How to calculate primer concentration and nucleotide concentrations.