Have anyone used realtime PCR, is that the plate for realtime PCR is one-time using or not ? Otherwise how to clean the plate after reaction to prevent wrong result in next time using ?
A possible solution is to use the DNA ZAP solution, which I know many people used in adjacent labs and were happy with for cleaning their DNA free workbench. The product sheet states
When 500 ng of template DNA is dried down in a PCR tube, it is rendered unamplifiable upon treatment with DNA ZAP solutions. Additional experiments demonstrate that the DNA is degraded down to free nucleotides.
Please note that I'm not promoting any specific product here and you can purchase any similar product/technology for your particular application. Obviously the best recommendation is to use new plates for each reaction but this/or a similar product can be an option too although the risk of DNA contamination in a PCR based reaction should be carefully balanced against simply using fresh plates considering the product itself is not free either.
The product sheet provides instruction for cleaning/treating PCR tubes hence I assume you use the same protocol for plates if you have the plate centrifuges available in your lab. You can get rid of the solutions by tapping the plates on a tissue to get the liquid out of the wells.
One of the claimed virtues of RT-PCR plates is their inability to bind DNA. (See for example the assortment at http://www.fisher.co.uk/product/brand_listing.php/T/Thermo%20Scientific%20ABgene/PCR%20plate ). As such, all you need to do to remove the DNA (genomic, amplified, or primers) is to rinse them. This suggests that rinsing may also work for dNTP.
On the other, many types of RT-PCR plates are made of polycarbonate, which is able to bind protein. I would be concerned about an uneven amount of polymerase sticking to the well. To go around that, you should re-use, in any PCR plate, only those wells that saw polymerase before.
I have no idea whether other molecules bind to the wells, but presumably they fall on the DNA or protein paradigm.
It will cost you only one plates and regents for as little as four reactions to test whether these plates are reusable. In the first run, measure two samples, A and B, for some transcript. Rinse the wells, and measure samples A and B again. If the transcript ratio A/B is the wildly different between first and second attempt, you know you can't reuse them. I would also be concerned if it will take many more cycles to reach the plateau stage at the second attempt. Passing these tests, you may be all set. Failing these tests, you may still be able to use the remaining wells. Let us know.