RFLP - BsaJ1 (Nov/12/2008 )

HI All,

I was reading a journal on PCR-RFLP.In their work, the use BsaJ1. Why must they use BsaJ1 in RFLP?

Hope someone could enlighten me.



Thank you
Dian ben

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You don't HAVE to use BSAJ1. I have done RFLP with enzymes like Cac8I, XbaI, HindIII, and others. The particular study you read just happened to use BSAJ1. If you are assaying for a specific mutation, pick an enzyme that has a recognition sequence that will be altered by the polymorphism.

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You don't HAVE to use BSAJ1. I have done RFLP with enzymes like Cac8I, XbaI, HindIII, and others. The particular study you read just happened to use BSAJ1. If you are assaying for a specific mutation, pick an enzyme that has a recognition sequence that will be altered by the polymorphism.
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Hi there...thank you.But i wonder when is for you to decide to use which enzyme in RFLP? i am new in RFLP...maybe some expalnation.I do read but could not really imagine the application.

Please help

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What you can do to determine which enzyme to use is look at the recognition sequence in relation to your DNA sequence in question. You want an enzyme that either:
1) Cuts the normal sequence at the mutation site but leaves the mutated sequence alone
or
2) Cuts the mutant sequence at the mutation site but leaves the normal sequence alone

There is software that can do this, such as Sequence Analysis or Serial Cloner. I think New England Biolabs even has an online utility to do it. This has a spot to put in your sequence. Put in the normal sequence, record the enzymes and where they cut. Then put in the mutant sequence and record what enzymes cut where. Then find the difference between the two groups and that's the enzyme you need to use!

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