Restriction site variation

More importantly, it is sometimes more informative. A very long nucleotide sequence may be required to provide more information than a restriction site survey. For example, a phylogenetic analysis of 22 taxa from the sunflower family used both restriction site variation in chloroplast DNA and nucleotide sequence variation in the chloroplast-encoded gene rbcL.5 The restriction site survey identified 583 variable sites of which 169 were shared between two or more taxa, whereas the sequence survey found only 109 shared variable positions. Even though the restriction site survey included only 11 enzymes, nearly 3500 nucleotides are included in the variable sequences surveyed, whereas rbcL is only 1428 base pairs (bp) in length. 

The differences in DNA sequence cited above can result in variations of restriction sites and thus in the length of restriction fragments. An inherited difference in the pattern of restriction (eg, a DNA variation occurring in more than 1% of the general population) is known as a restriction fragment length polymorphism,... 

Variations The poly(A) tailing kit (Ambion) produces a mRNA population with varying lengths of poly(A) tails, controlled by altering poly(A) polymerase concentrations and incubation times. An alternate method to incorporate a poly(A) tail is to clone a defined stretch of adenosines/ thymidines into the > UTR of the template pDNA. To allow transcripts to finish on an adenosine, the insert should be followed by a restriction site for an enzyme that cleaves 5 of the last antisense strand thymidine, such as Nsi I. In this way, the poly (A) tail can be incorporated directly into the... 

VNTRs (variable number of tandem repeats). These polymorphisms are the result of varying numbers of minisatellite repeats in a specific region of a chromosome. The repeat units typically range in size from 20 to 70 bases each. The repeat is flanked on both sides by a restriction site, and variation in the number of repeats produces restriction fragments of varying size. 

A. In an RFLP, the presence or absence of a restriction site (aJ produces DMA fragments of varying lengths, reflecting sequence variation. 

Variations may occur in restriction sites so that, for example, a sequence within a gene may be cleaved by a specific restriction enzyme but its allele may not. 

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