User:Qzou3/Primer walking

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3: Primer walking, also called "Chromosome walking" is a technique used to clone a gene (e.g., disease gene) from its known closest markers (e.g., known gene) and hence is used in moderate modifications in cloning and sequencing projects in plants, fungi, and animals. 2 :This technique, also known as “directed sequencing” utilizes a series of Sanger sequencing reactions to either confirm the reference sequence of a known plasmid or PCR product based on the reference sequence (sequence confirmation service), or to determine the unknown sequence (sequence discovery service) of a full plasmid or PCR product by designing primers to sequence overlapping sections.

Article body
Primer walking is a method to determine the sequence of DNA up to the 1.3–7.0 kb range whereas chromosome walking is used to produce the clones of already known sequences of the gene. Chromosome walking is a technique used to clone a gene (e.g., disease gene) from its known closest markers (e.g., known gene) and hence is used in moderate modifications in cloning and sequencing projects in plants, fungi, and animals. In other words, it is used to identify, isolate, and clone a particular sequence present in close vicinity of the gene to be mapped. Libraries of large fragments, mainly bacterial artificial chromosome libraries, are mostly used in genomic projects. To identify the desired colony and to select a particular clone the library is screened first with a desired probe. After screening, the clone is overlapped with the probe and overlapping fragments are mapped. These fragments are then used as a new probe (short DNA fragments obtained from the 3′ or 5′ ends of clones) to identify other clones. A library approximately consists of 96 clones and each clone contains a different insert. Probe one identifies λ1 and λ2 as it overlaps them. Probe two derived from λ2 clones is used to identify λ3, and so on. Orientation of the clones is determined by restriction mapping of the clones. Thus, new chromosomal regions present in the vicinity of a gene could be identified. Protocol for chromosomal walking of DNA is described in Fig. Chromosomal Walking of DNA. Since chromosomal walking is very tedious, chromosome landing is preferred for gene identification. This approach requires the identification of the marker that is tightly linked to mutant locus.

3: The overall process is as follows:


 * 1) A primer that matches the beginning of the DNA to sequence is used to synthesize a short DNA strand adjacent to the unknown sequence, starting with the primer (see PCR).
 * 2) The new short DNA strand is sequenced using the chain termination method.
 * 3) The end of the sequenced strand is used as a primer for the next part of the long DNA sequence, hence the term "walking".

'''The method can be used to sequence entire chromosomes (hence "chromosome walking"). Primer walking was also the basis for the development of shotgun sequencing, which uses random primers instead of specifically chosen ones.'''