UNIT 10.20 Enzymatic Amplification of DNA by PCR: Standard Procedures and Optimization

  1. Martha F. Kramer,
  2. Donald M. Coen

Published Online: 1 MAY 2001

DOI: 10.1002/0471142735.im1020s24

Current Protocols in Immunology

Current Protocols in Immunology

How to Cite

Kramer, M. F. and Coen, D. M. 2001. Enzymatic Amplification of DNA by PCR: Standard Procedures and Optimization. Current Protocols in Immunology. 24:VII:10.20:10.20.1–10.20.10.

Author Information

  1. Harvard Medical School, Boston, Massachusetts

Publication History

  1. Published Online: 1 MAY 2001
  2. Published Print: DEC 1997


This unit describes a method for amplifying DNA enzymatically by the polymerase chain reaction (PCR) and for optimizing this reaction for the sequence and primer set of interest. Important variables that can influence the outcome of PCR include the MgCl2 concentration and the cycling temperatures. Additives that promote polymerase stability and processivity or increase hybridization stringency, and strategies that reduce nonspecific primer-template interactions, especially prior to the critical first cycle, can greatly improve sensitivity, specificity, and yield. This protocol is designed to optimize the reaction components and conditions in one or two stages. The first stage determines the optimal MgCl2 concentration and screens several enhancing additives. To further improve specificity, sensitivity and yield, the second stage compares methods for optimizing initial specific hybridization to prevent polymerization of misprimed sequences prior to thermal cycling. For initial inhibition of polymerase activity, temperature (i.e., cooling reagents), physical separation (“hot start” method), and reversible antibody binding are compared.