What matter if I increase the temperature to 95°C. So double-strand DNA denatured into two ssDNA, and then I decrease the temperature to room temperature. Are they able to reassociate after denaturation?
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$\begingroup$ I've edited this to remove the use of the word recombine which has a special meaning when talking about DNA. I assume that you meant reassociate. $\endgroup$– Alan BoydNov 19, 2013 at 11:59
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$\begingroup$ In PCR there is always some strand reassociation. This is why the primers are added in excess, to make it much more likely that a DNA strand anneals to a primer than back to its anti-sense strand. $\endgroup$– skymningenNov 19, 2013 at 12:31
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Yes, heating the DNA above 94°C for some length of time will melt, or denature, dsDNA into two ssDNA strands. Upon cooling, the complementary strands will come back to anneal. The degree and completeness of annealing, or association, is dependent on a number of factors including the rate of cooling and structural properties of the DNA itself (%GC content, secondary structure). I would not expect that the majority of ssDNA strands will completely anneal to a single, complementary dsDNA strand. What is more likely is that the DNA mix will look more like spaghetti with one strand partly annealed to two other strands. When performing PCR, the primers are designed to be specific, and added in excess, so that you bias the odds of annealing to favour a primer:ssDNA association. If this weren't the case, we could not possibly have efficient PCR amplification.
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$\begingroup$ Because the DNA is too big, from hundred to thousand bp, it's not ~20bp in length like an oligo primer. In PCR the primer always have length ~20bp and i don't know if a bigger primer like template DNA itself can associate to the template strand. $\endgroup$ Nov 20, 2013 at 1:13
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$\begingroup$ Right, length is also a factor. The smaller the DNA length, the more likely for reassociation to dsDNA, but the probability drops as length increases. $\endgroup$– user560Nov 20, 2013 at 2:38