UNIT 25B.2 PCR-Based Subtractive cDNA Cloning

  1. Mukesh Patel,
  2. Hazel Sive

Published Online: 1 AUG 2001

DOI: 10.1002/0471142727.mb25b02s55

Current Protocols in Molecular Biology

Current Protocols in Molecular Biology

How to Cite

Patel, M. and Sive, H. 2001. PCR-Based Subtractive cDNA Cloning. Current Protocols in Molecular Biology. 55:B:25B.2:25B.2.1–25B.2.20.

Author Information

  1. Whitehead Institute for Biomedical Research, Cambridge, Massachusetts

Publication History

  1. Published Online: 1 AUG 2001
  2. Published Print: JUL 2001


Subtractive cloning is a powerful technique that allows isolation and cloning of mRNAs differentially expressed in two cell populations. In the generalized subtraction scheme the cell types to be compared are the [+] or tracer cells and the [-] or driver cells, where mRNAs expressed in the tracer and not the driver are isolated. Briefly, tracer nucleic acid (cDNA or mRNA) from one cell population is allowed to hybridize with an excess of complementary driver nucleic acid from a second cell population to ensure that a high percentage of the tracer forms hybrids. Hybrids that form include sequences common to both cell populations. Hybrids between the tracer and driver, and all driver sequences, are removed in the subtraction step. The unhybridized fraction is enriched for sequences that are preferentially expressed in the tracer cell population. The method described in this unit uses double-stranded cDNA (ds cDNA) as both tracer and driver. Reciprocal subtractions are performed between two cell populations, A and B: that is, genes preferentially expressed in A more than in B are isolated, as are genes expressed preferentially in B more than in A. The method uses the polymerase chain reaction (PCR) to amplify cDNAs after each subtraction to prepare tracer and driver for the next subtraction. The progress of subtraction is monitored by slot blot hybridization. Differentially expressed cDNA sequences are used to construct a subtracted cDNA library.