Suppression subtractive hybridization

Methods Mol Biol. 2004:258:107-34. doi: 10.1385/1-59259-751-3:107.


Suppression subtractive hybridization (SSH) is a widely used method for separating DNA molecules that distinguish two closely related DNA samples. Two of the main SSH applications are cDNA subtraction and genomic DNA subtraction. In fact, SSH is one of the most powerful and popular methods for generating subtracted cDNA or genomic DNA libraries. The SSH method is based on a suppression PCR effect and combines normalization and subtraction in a single procedure. The normalization step equalizes the abundance of DNA fragments within the target population, and the subtraction step excludes sequences that are common to the populations being compared. This dramatically increases the probability of obtaining low-abundance differentially expressed cDNA or genomic DNA fragments, and simplifies analysis of the subtracted library. In our hands, the SSH technique has enriched over 1000-fold for rare sequences in a single round of subtractive hybridization.

MeSH terms

  • DNA, Complementary / analysis
  • Gene Expression
  • Genomic Library
  • Humans
  • Nucleic Acid Hybridization / methods*
  • Polymerase Chain Reaction / methods*
  • RNA, Messenger / analysis
  • Subtraction Technique


  • DNA, Complementary
  • RNA, Messenger