Mismatched DNA digestion (or cleavage)

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Mismatched DNA digestion (or cleavage)

Post by kwanghyunbaek » Wed Apr 19, 2006 2:35 am

Hi, may I ask a help regarding to digesting smismatched DNA?

I am thinking of doing experient for new microarray experiment (just dreaming). For example, if I have cDNA composed of 10 nucleotides, and only one nucleotide (or more) is not matched with the template, can I get rid of of the nucleotide or the double-stranded DNA?

Ex) AAAAAAAAAA (Template)
........ .........
TTTTATTTTT (my cDNA) (only one nucleotide mismatch)

In this case, hybridization happens, but I should have a perfect match for all nucleotides. The double stranded DNA also give a signal, however, there is a mismatch and the double stranded DNA is not the signal I want. So I have to get rid of the double stranded DNA, probably cleaving the site of T or A or digesting the all double stranded DNA (I was thinking about using Mung bean nuclease, but I was not sure the enzyme can cleave even only one mismatched nucleotide). I do not know about any enzymative, chemical, or any physical method for the cleavage. Does anyone have any idea?

Thank you.

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