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Old 10-02-2017, 02:39 PM   #1
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Default Oligo dT VN

Oligo dT VN is used for anchored cDNA synthesis. But what does "VN" in the end do? Please help. Thanks.
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Old 10-03-2017, 02:59 AM   #2
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Oligo dT length is normally 30nt but transcript poly A tail could be longer. Including VN at 3 end of RT primer enriches for non-poly A region of transcripts and without it RT can be primed in poly A region so cDNA would have A/T homopolymer which in most sequencing applications is undesirable. A side effect of VN inclusion is possible bias in some transcripts conversion to cDNA.
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Old 10-17-2017, 05:34 AM   #3
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'N' is any base, 'V' is either A,C or G. This allows for anchoring at the beginning of the Poly-A tail.
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Old 12-22-2017, 01:14 PM   #4
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Default why VN, why not just V for oligo dT anchor?

Why does almost everyone use 3'-VN as the anchor for oligo dT primers rather than using 3'-V?

The former only has a 1/12 chance of matching a given mRNA, vs. 1/3 for the latter. Plus 1/4 of the former will have T as the N, meaning there's a greater potential for annealing and extension within the polyA tail with VN vs V.

Only reason I can think of is legacy.

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Old 12-22-2017, 04:42 PM   #5
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I have not done any tests. I guess the assumption is that the oligos will make multiple attempts to hybridize and that a two-base anchor is "stronger" than a single base.
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