Hello, Shaheer.P Peeralil, you cannot expect the amount of losses as there will be factors like pipetting losses, some amount may be lost when removing the supernatant and many more. In my opinion, if you want to have very less PCR product losses you should go for an enzymatic cleanup like ExoSAP purification. If you just want to increase the concentration, just use a lower amount than 40 µl TE buffer. If you want to increase the PCR yield go for a higher number of PCR cycles. Do you have spin columns with you if you have add your PCR reaction mix along with an equal volume of 96% Ethanol into the centre of the spin column and then centrifuge at a slower speed of 1000g and then at 13000 RPM and make sure everything has passed through the column. After that add pre-warmed nuclease-free water into the centre of the spin column, 40 µl or less and then centrifuge to elute.

You could try precipitating with a co precipitant to maximise the yield. Add glycogen or linear polyacrylamide to ensure that all of the dna comes out of solution rather than staying in suspension as tiny suspended particles. Neither of these are likely to interfere with dna measurement or downstream processes but it just gives you a slightly larger precipitate

Initial concentrations of PCR product is very less.

Try doing PCR using PCR sample as template to increase initial concentration.

After purification dissolve if the half the amount volume of TE.

Overnight precipitation some time leads to loss 1-2hour incubation is sufficient.