Why does ssdna hybridise to a probe on a microarray and not to its original complementary strand?

...and if my amplicon is say 500 bp long, why does it preferentially hybridise to a probe that may be only 60 bp long, and not to its complementary strand of 500bp long? Is it something to do with hybridisation temp?|||ssDNA is single stranded (hence the ss) so there is no complementary probe to hybridise to. Now when you speak of amplicons - I assume then you are using dsDNA in which case you have a different scenario.





Hybridisation is a statistical event really. If the probe molecules spotted on the array are in excess of the DNA hybridised to the chip then a greater majority of the sample DNA will hybridise to the probes on the array than will hybridise to its own complement. That is not to say that there is no hybridisation back to its original complement, just that the proportion hybridised to the probe is higher than the proportion hybridised to the original compliment.





The issue of a 500bp target hybridising to a 60 bp probe is somewhat more complex. Again however it tends to depend on concentrations. One thing to remember is that by hybridising to the probe, it does not mean that the rest of the target molecule is not hybridised to part of its original complement. In order to allow this to happen though, the DNA generally needs to be denatured prior to hybridisation to the array. Usually there is a step at which the sample is put at high temperature for 5-10 minutes and then immediately placed onto the array to ensure that when the targets anneal they have a chance of annealing to the probe molecules on the array.