Usually the melting cycle of 95 ° C for 15s, 60 ° C for 60s and 95 ° C for 15s is used. In my laboratory, they normally used an annealing temperature of 60ºC, I intend to change it to 61.5ºC and see if it improves the specificity of the primer and melt curve. If I do this, should I change the melt temperature as well? I've heard that the temperature of the melting cycle should never be changed, but in the references they say it should be 5 ° C in relation to the annealing, so I was in doubt.
No, yo don't need to change the melting temperature.
All it does is to make sure that your double-stranded products dissociate into two single-strands to which primers can bind during the next annealing step. 95°C is usually high enough to ensure complete dissociation.*
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*Only in exceptional cases where "GC-clamps" are close to the primer binding sites or within the target sequence, it might happen that a few seconds at 95°C are not sufficient, so that the two strangs ramein attached. As a quasi one-molecular reaction, the re-annealing of not completely separated srands in the following annealing step is very fast, often faster than two-molecule reaction of the primer hybridization, leading to a suboptimal amplification efficiency.
You have to make clear the meaning of melting cycle. It's the high resolution process from double strand DNA (60℃) to single strand DNA (95℃) with the ramp rate 0.2℃/s. So the melting cycle provide the melting curves for your PCR products, not the primers. According to the single viable principal, you dont need to change the melting cycle.
If you mean the melting temperature of your amplified product at the end of the qPCR then you can't change that anyway. It has a certain melting temperature and the melting analysis will tell you where it is and if you have additional by-products that melt at different temperature with additional peaks in your melting curve. For this the whole temperature range will be used.
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