SSCP (single strand conformation polymorphism) is a technique used to detect single nucleotide polymorphisms (SNPs) by analyzing differences in electrophoretic mobility between single strands of DNA that differ in sequence. SSCP relies on the principle that the mobility of a single-stranded DNA molecule in a non-denaturing gel is dependent on its size and 3D structure, which can be altered by a single nucleotide change. This allows SSCP to discern DNA molecules that differ by a single nucleotide and detect mutations and polymorphisms.

1. SSCP (single strand conformation polymorphism) is a
technique used for the detection of single-nucleotide
polymorphism(SNPs).
SSCP technique is a method capable of identifying most
sequence variations in a single strand of DNA, typically
between 150 and 250 nucleotides in length.
Introduction:-
Single-strand conformation polymorphism(SSCP),
or single-strand chain polymorphism, is defined as
conformational difference of single- stranded nucleotide
sequences of identical length as induced by differences in the
sequences under certain experimental conditions.
This property allows to distinguish the sequences by means
of gel electrophoresis, which separates the
different conformations.
The mobility of double-stranded DNA in gel electrophoresis is
dependent on strand size and length but is relatively
independent of the particular nucleotide sequence.
The mobility of single strands, however, is noticeably affected
by very small changes in sequence, possibly one changed
nucleotide out of several hundred .
Small changes are noticeable because of the relatively
unstable nature of single-stranded DNA; in the absence of a
complementary strand, the single strand may experience intra -
strand base pairing, resulting in loops and folds that give the

2. single strand a unique 3Dstructure, regardless of its
length .
A single nucleotide change could dramatically affect the
strand’s mobility through a gel by altering the intra -strand base
pairing and its resulting 3D conformation.
Single-strand conformation polymorphism analysis takes
advantage of this quality of single-stranded DNA.
First announced in 1989 as a new means of detecting DNA
polymorphisms, or sequence variations, SSCP analysis
offers an inexpensive, convenient, and sensitive method for
determining genetic variation.
Like restriction fragment length
polymorphisms(RFLPs),SSCPs are allelic
variants of inherited, genetic traits that can be used as
genetic markers .
Unlike RFLP analysis, however, SSCP analysis can detect
DNA polymorphisms and mutations at multiple places in DNA
fragments .
As a mutation scanning technique, though, SSCP is more often
used to analyze the polymorphisms at single loci, especially
when used for medical diagnoses.
PRINCIPLE:-
SSCP relies on the principle that the electrophoretic mobility of a
single-stranded DNA molecule in a non-denaturing gel is highly
dependent on its size and structure.
In solution, the single-stranded DNA molecules take on secondary
and tertiary conformations due to base pairing between nucleotides
within individual strands.

3. These conformations depend on the length of the strand, its
sequence, and the location and number of regions of base pairing.
Hence, a mutation at a particular nucleotide position in the primary
sequence can alter the conformation of the molecule.
When separated in a non-denaturing gel matrix (at a temperature of
< 10.C), molecules differing by a single nucleotide can be discerned,
given the changes in their mobility as a consequence of differing
conformations.
The mutation detection rate of SSCP varies depending on
parameters, such as size of the fragment, base composition of the
sequence, electrophoresis temperature and/or gel composition (i.e.,
pore size and cross-linking).
Usually, 50–100% of mutations are detected for amplicons of 100–
200 bp in size. This approach is relatively simple technically and can
be used effectively to visually display different sequence types within
and between amplicons (of B100– 500 bp) and to rapidly screen
hundreds of samples per day.
PROTOCOL:-
SSCP analysis involves the following four steps:
(1) Isolation and purification of DNA.
(2) polymerase chain reaction (PCR) amplification of DNA
sequence of interest;
(3)denaturation of double-stranded PCR products;
(4) cooling of the denatured DNA (single-stranded) to maximize
self-annealing;
(5) detection of mobility difference of the single-stranded DNAs
by electrophoresis.

4. (6) DNA Labelling:-
1.The DNA was labelled radioactively and identified by
autoradiography.
2. An alternative that is somewhat more troublesome but faster and
not radioactive is silver staining. Silver-stained gels can be dried
and preserved.
3.Another possibility is staining with ethidium bromide, as described
by Yap and McGee (1992), although its sensitivity leaves something
to be desired, and some of the weaker bands may be overlooked.
Other dyes, such as SYBR Green I from Molecular Probes, may be
more suitable because of their higher sensitivity.
APPLICATION:-
1.Ensuring that intraspecific variation is adequately
represented in phylogenetic sequencing projects.
2 . s c r e e n i n g l a r g e D N A s a m p l e
f o r mitochondrial DNA sequence variation.
3 . D e v e l o p i n g a n d s c r e e n i n g s e q u e n c e -
v a r i a b l e markers.
4.Getting the most out of microsatellites: length
homoplasy and sequence variation.
5.Investigating complex mixtures of similar lengthequence
s: pseudogenes and multigene families.
6.SSCP is the electrophoretic separation of single-
stranded nucleic acids based on subtle differences in sequence
(often a single base pair) which results in a different secondary
structure and a measurable difference in mobility through a gel.

5. 7.SSCP analysis detects sequence variations(single-
point mutations and other small-scale
c h a n g e s ) t h r o u g h
e l e c t r o p h o r e t i c m o b i l i t y differences. These
variations can potentially cause conformational changes in
the DNA molecules.
8.Under nondenaturing conditions and often reduced
temperature, single-stranded DNA molecules can assume
unique conformations that vary depending on their nucleotide
sequences. These conformational changes can result in
detectable differences in mobility.
9.The difference in shape between two single-
stranded DNA strands with different sequences can cause
them to migrate differently on an electrophoresis gel, even
though the number of nucleotides is the same, which is, in fact,
an application of SSCP.