Im hoping to streamline a process which has been established in my lab for some time, but is very time consuming for large numbers of samples. Currently we pellet cells, extract RNA, make cDNA and then do conventional PCR for amplifying a gene of interest, before analysing the products on a gel. I would like to switch to using real-time PCR for this analysis and am hoping to use a cells-cDNA-realtime quick kit to speed up the process. I am then hoping to use the real time to analyse the size of my amplicon - normally we would expect a size of 670bp for the full PCR product, but this varies greatly (reduces) if single or multiple exons are deleted. My questions are:
A) Is a 670bp product too big for conventional SYBR green chemistry based real-time PCR? (And if so, could i solve this by just increasing elongation time etc)
B) I know that melting temperatures can be used to determine amplicon size, but how sensitive is this to changes?