Dear Baidya,

As such there should not be any difference. The blood collected in EDTA or Heparin should not matter much while doing PCR. Please check the gDNA (yield) in 0.8%-1% Agarose by running the eluted DNA (2-3uL) per sample. Check whether the DNA content is ok with your Heparin yield.

Somnath.

Thank you Somnath, I have quantified the samples on nanodrop aswell as on agarose gel however the quality and quantity is good, bands are thik and sharp. the problem arising is on the amplification.

Yes, heparin will inhibit PCR. It binds majority od DNA-interacting proteins. IN fact, some DNA pol purification protocols use heaprin-Sepharose affinity columns.

EDTA is much better anticoagulant compared to heparin, especially when there is more than 6-10 hr delay in processing or transporting collected blood samples. Heparin may be a better choice for chromosomal analysis.

Thank you Piotr & nikhil, heparin sepharose can be helpful, and yes EDTA & heparin have different prospects of anlysis, molecular biology and cytogenetics respectively

Heparin inhibits the Taq polymerase. While EDTA chelates Mg2+, you can still supplement this in the amplification mix. If you cannot get around the heparin (eg. have samples already collected), you could still try several folds dilution which may be required anyway for amplification. 

There are more discussion of this same topic at RG, see:

https://www.researchgate.net/post/What_is_the_difference_between_heparin_and_EDTA_tubes_for_blood_collection_and_what_is_the_effect_on_blood

thank you alice and yuan for suggestions

Heparin inhibits by interfering amplification by taq pol.add DMSO to minimize the interference.

Thank You  Brijesh for your suggestion

Dear,

I were used heparin and EDTA blood samples and no troubles has gone with both, by Real Time PCR. I thought your problem is in PCR protocol. Try check it back

specimens with large amounts of DNA tended to exhibit less interference by heparin. The addition of > or = 0.1 to 0.0016 U of heparin per reaction mixture (50 microl) suppressed DNA amplification in a dose-dependent fashion. We therefore concluded that much care should be taken when heparinized blood is used as a PCR material.

As heparin does inhibit PCR, you can use heparinase I or LiCl ethanol precipitation to get rid off heparin. This works.

Heparinase I from Flavobaterium heparinum : 1 U / µg DNA/RNA, 2 h at 25°C. Cleanup of DNA/RNA on column, for example.

LiCl : 1/10 volume of LiCl 8M + 2 vol of EtOH, 10 min on ice. Then centrifugation. Rince with 70% EtOH.

Good luck.

Yes, as it is a general DNA binding protein, thus it will inhibit DNA polymerase.