Difference between revisions of "Problems with PCR using VR/VF2"
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==VR Incorrect Annealing== | ==VR Incorrect Annealing== | ||
[[Image:VR annealing.png|thumb|left|Diagram of potential VR binding sites within B0010]] | [[Image:VR annealing.png|thumb|left|Diagram of potential VR binding sites within B0010]] | ||
| − | VR can potentially bind [[Part:BBa_B0010|B0010]] in three different ways. | + | VR can potentially bind [[Part:BBa_B0010|B0010]] in three different ways. One of the annealing schemes seems particularly likely. Only 3 of the last 13 bases of VR mismatch to B0010. Also, VR's 3' end would anneal the the part tightly due to the two G - C pairs. |
==VF2 Incorrect Annealing== | ==VF2 Incorrect Annealing== | ||
Revision as of 16:23, 21 August 2007
VR and VF2 (Parts G00101 and G00100 respectively) are used to verify the lengths of parts. While using them to PCR potential parts (S03582 and I13033, both composite parts) for the Registry's Assembly Ladder, I noticed that I was consistently getting excess bands. Contamination was ruled out since the bands still appeared in a Colony PCR. Upon inspecting the sequence of the two parts, I found that each contained regions that the primers could bind, resulting in the shorter bands I was consistently seeing. Since S03582 and I13033 are both composite parts, I determined where exactly the primers were binding to see what parts would be affected during PCR with VR and VF2.
VR Incorrect Annealing
VR can potentially bind B0010 in three different ways. One of the annealing schemes seems particularly likely. Only 3 of the last 13 bases of VR mismatch to B0010. Also, VR's 3' end would anneal the the part tightly due to the two G - C pairs.
VF2 Incorrect Annealing
VF2 can bind to R0062 in two different places.
