Potassium Chloride Concentration

Potassium chloride (KCl) is normally used in a PCR amplification at a final concentration of 50mM. To improve the PCR amplification of DNA fragments, especially fragments in the size range 100bp to 1000bp, a KCl concentration of between 70mM and 100mM is sometimes recommended. For the amplification of longer products a lower salt concentration appears to be better. But the PCR amplification of short products works better at higher salt concentrations. This is probably because an increase in salt concentration permits shorter DNA molecules to denature preferentially to longer DNA molecules. Shorter molecules are therefore amplified better at higher salt concentration. It should be remembered however that a salt concentration above 50mM can inhibit the Taq polymerase.

If you are finding unwanted, long, non-specific products an increase in KCl concentration may reduce the appearance of these products. Similarly, to get rid of short, non-specific products you can decrease the KCl concentration to about 35 or 40mM. In either case do not change the MgCl₂ concentration. To improve the yield of a product you can try adjusting the KCl concentration: increase it for a desired product less than 1000bp; lower it for a desired product greater than 1000bp.

Recommended Reading

	Real-Time PCR: Advanced Technologies and Applications Edited by: Nick A. Saunders and Martin A. Lee Provides both the novice and experienced user with an invaluable reference to a wide-range of real-time PCR technologies and applications and supplies detailed technical insights into the underlying principles, methods and practice of real-time PCR. read more ...
	Real-Time PCR in Food Science: Current Technology and Applications Edited by: David Rodríguez-Lázaro An indispensable manual on real-time PCR for scientists in the food industry and for anyone involved in the detection of foodborne pathogens. read more ...
	Quantitative Real-time PCR in Applied Microbiology Edited by: Martin Filion Aimed specifically at microbiologists, this volume describes and explains the most important aspects of current real-time quantitative PCR (qPCR) strategies, instrumentation and software. "useful book ... filled with valuable information" (Doodys) read more ...
	PCR Troubleshooting and Optimization: The Essential Guide Edited by: Suzanne Kennedy and Nick Oswald Control, optimize and troubleshoot PCR, reverse transcriptase PCR, real-time PCR and quantitative PCR. An essential book. "an essential book ... a valuable tool to all those interested in PCR" (Doodys); "an essential guide" Aus. J. Med. Sci. read more ...
	Lab-on-a-Chip Technology (Vol. 2): Biomolecular Separation and Analysis Edited by: Keith E. Herold and Avraham Rasooly Applications in the biomedical and life sciences: biomolecule separation, electrophoresis, chromatography, protein and cell separation, genetic and transcriptome analysis, PCR, cell viability analysis and microorganism capturing. "a comprehensive and felicitous compendium" (Drug Research) read more ...