When digesting with T1 and A, I consistently get a protected fragment 50bp smaller than expected. When digesting with T1 only, I get the exact predicted size in the correct tissues at the correct times. However, every protocol I have run into suggests T1 and A, and I need to have some basis before I continue with my thesis project supporting my T1 only method. I do understand that cutting with T1 only can yield slightly larger fragments, but the additional 50bp seen seems too large, and the resulting band is perfect based on sequence information. Any suggestions or articles would be helpful. Thank you, Brian Lovitt.
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RPA digestion problem
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