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Certain laboratories often need to prepare DNA duplexes for transcription factor binding assays. The DNA is...

Certain laboratories often need to prepare DNA duplexes for transcription factor binding assays. The DNA is purchased as single-stranded polynucleotides and hybridize them to form our duplexes, but this almost always leaves behind some un-renatured, single-stranded DNA, in the solution. How would you go about removing the single-stranded DNA fromour duplexes?

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Answer #1

So, when unnatured, single stranded DNA remains in the solution, then it be removed by the use of enzyme S1 nuclease.

This enzyme is derived from the fungus Aspergillus oryzae and it has an endonuclease activity. It degrades the single stranded DNA from the solution and therefore, we are left with only DNA duplex. The S1 nuclease is ineffective on the double stranded molecule.

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