I am designing a huge multiplex hybridization assay for infectious agents. I am using certain online tools like oligo properties calculators. One of the parameters they calculate for a multiplex assay is the free energy values for interactions between different oligos. I understand that the more a value tends towards negative the more spontaneous their interaction is. However the assay is carried out at higher temperatures (PCR annealing -55-60 and hybridization -60-65 degree c) . What i wanted to know is that is there a simple way of drawing a cutoff free energy value for a assay to avoid non-specific interactions? Also is it based on the size of the oligos or does it depend only on the interaction of strings of complimentary bases?
Find an algorithm to relate the number of carbon and hydrogen atoms in the oligos with its free energy.
The free energy of individual nucleotides is available and that of an oligo can be calculated through various algorithms..i wanted to know about the free energy of different oligo interactions..thanks anyways :)
If they can catabolize amino acids with hydrogenates separately then we can test if oligos in isolation are more exp than in chain
Wow I didnt get most of that..can you explain how that works? Or suggest some reading material? and this is a for a detection system..so I can also test different oligo (primers and probes) interactions of the oligos I've designed and deduce the effects of specific free energy values of interactions with the results I get in the wet lab right?
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