Is a purification step between cDNA generation and library construction necessary?

[kobeho24]

Hi all,
Recently, I was wondering that is it necessary to perform a purification step after cDNA generation and prior to library construction? Because I am gonna do the cDNA generation in a very tiny volume. The library construction can be either ligation-based or tagmentation-based.
Best!
Gary

[Simone78]

Hi all,
Recently, I was wondering that is it necessary to perform a purification step after cDNA generation and prior to library construction? Because I am gonna do the cDNA generation in a very tiny volume. The library construction can be either ligation-based or tagmentation-based.
Best!
Gary

it´s not necessary at all! Just dilute the PCR product to reduce the amount of salt, take an aliquot for ligation/tagmentation and go on. I tried it myself and it works quite well. I never compared the efficiency with a "standard" protocol, though. Based on what I see on the Bioanalyzer (haven´t sequenced any sample yet) I would be surprised to find out that the difference is so dramatic.
good luck!

[Chipper]

No, you can do end repair after the 2nd strand reaction without purification.

[cmbetts]

I believe the main reason you typically see cleanup between 2nd strand and end repair is that the 2nd strand buffer for most systems has ammonium sulphate in it, and the T4 PNK used in end repair is potently inhibited by ammonium. It might work out if the reaction is diluted enough that the ammonium is a nonfactor.
Ex, NEBNext
20 mM Tris-HCl
12 mM (NH4)2SO4
5 mM MgCl2
0.16 mM β-NAD
0.19 mM dNTPs each
pH 7.4 @ 25°C

[nucacidhunter]

I think by cleaning up cDNA uniformity and consistency among samples and batches will be increased. Non-cleaned cDNA would have various amounts of left over oligos and salts which may affect library quality.