Restriction enzyme specificity for thymine and DNA - are thymine/uracil and DNA/RNA interchangeable? (Nov/09/2006 )

Hi there,

Two questions:

Are uracial and thymine interchangeable when it comes to RE recognition sites?

Are DNA and dsRNA interchangeable when it comes to RE recognition sites (assuming that dsRNA contains all G and C)?

Or are both these ideas wrong? i.e. the recognition sequence must contain thymine (not uracil) and must be DNA (not RNA). I'm asking because I'm wondering if first strand cDNA (i.e. one strand RNA and one strand DNA) can be digested with restriction enzymes.

Cheers, Rob

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I'm fairly sure it would depend on the restriction enzyme, but my guess is that for most of them, the answer is no.

If restriction enzymes recognized RNA or dsRNA, then mRNA or rRNA (or tRNA) in the cell would be constrained to not contain restriction sites, and this has never been reported to my knowledge,

DNA does not need to be constrained, because DNA can be modified during replication (methylation of bases etc) to prevent restriction digestion.

Also, from a "lock and key" point of view, it stands to reason that the 2' hydroxyl group on RNA would interfere with RE binding at least some, and probably most, of the time, and a similar situation would probably exist regarding T vs. U.

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