Hi, I´m using this method for detection one of phytopathogenic bacteria. Now I´m testing new primers (without loop primers):
reaction:
20 ul reaction with 2 ul 10x Isothermal Buffer (Optigene), 25mM MgSO4 change (3 - 5mM), 1.4 mM dNTP mix , 40uM of each FIP and BIP, 5 uM of each F3 and B3, and 8U GspSSD2.0 Polymerase (Optigene), 3,2 ul template DNA, and molecular grade water.
I´ve had problem with contamination of negativ control (water). Now is good, but I have a problem with specifity and with some eror with preparation reactions.
On two pictures is same reaction which is prepare with same procedure.
from left: Xv - bacteria, which will detect, Xe,Ps,Ea - will no detect, NC - negative control, M - marker
change concetration of MgSO4 (from left 5mM, 4mM, 3 mM)
Why I have got different results? (big mistake in preparation, beacause it is prepare to small amout reaction? bad designed primers? badly concetration MgSO4? Will I add betain?
If anyone has faced the same problems and or know the cause and solution, I would really appreciate some help. Please email me at [email protected]. Thanks!