*5.3.8 Single-strand conformation polymorphism (SSCP)*

SSCP was developed to detect gene polymorphism in human DNA and mutations by comparing PCR products [59]. DNA fragments are amplified, followed by denaturation and separation in non-denaturing polyacrylamide gel. Singlestranded DNA is separated on a polyacrylamide gel based on differences in mobility caused by their folded secondary structure. DNA fragments of equal size with no denaturant results into folding and movement, depending on the DNA sequences. Single stranded DNA forms secondary structures which are unique to its nucleotide sequence. This secondary structure hinders the movement of DNA in polyacrylamide gel and hence, the banding pattern is obtained at different position from the fragment of equal size but amplified from genetically different species. The advantage of SSCP over DGGE is that here GC clamp is not required during PCR but has a limitation with that there is high rate of re-annealing of DNA strands after an initial denaturation during electrophoresis which can however be overcome using a phosphorylated primer during PCR [21]. Smalla and her team studied the bacterial diversity of the soils by assessing the DGGE, T-RFLP, and SSCP fingerprints of 16s rRNA gene fragments. Although, the fragments amplified comprised different variable regions and lengths, DGGE, T-RFLP and SSCP analyses led to similar findings: (a) a clustering of fingerprints which correlated with soil physico-chemical properties, (b) little variability between the replicates of the same soil, (c) the patterns of the two brown soils were more similar to each other than to those of the other two soils, and (d) the fingerprints of the different soil types revealed significant differences in a permutation test [60]. SSCP fingerprints were also used in study of microbial diversity in landslide soils; the more detailed profile of fungal diversity was obtained using this method [59].
