i want to know about real time pcr primer way of designing. i want the programe used for designing real time pcr primers. i want to know hoe to interpret the results. i want to know how to avoid primer dimer.
It's basically the same.You may need to design the primers to amplify a product of an appropriate size for your qPCR system (usually 100-200bp) to get truly quantitative results. Too long and the quantification may be non-linear; you might check this by testing your primer efficiency.
You may also need to design the primers with a suitable TM for your qPCR system. The manufacturer often recommends a TM to test first, but you can adjust the run setting to accommodate different TMs it it proves necessary.
Many researchers use Primer 3 (http://bioinfo.ut.ee/primer3-0.4.0/) to design both qPCR and conventional PCR primers, and online tools for qPCR primer design are also available. I am fond if IDTs qPCR primer design tool (https://www.idtdna.com/scitools/Applications/RealTimePCR/)
It all the same set. Only difference is you are adding a signal dye such as BYBR or similar one to indicate with time the annealing process and signal detection that corresponds to successful amplification.
It's basically the same.You may need to design the primers to amplify a product of an appropriate size for your qPCR system (usually 100-200bp) to get truly quantitative results. Too long and the quantification may be non-linear; you might check this by testing your primer efficiency.
You may also need to design the primers with a suitable TM for your qPCR system. The manufacturer often recommends a TM to test first, but you can adjust the run setting to accommodate different TMs it it proves necessary.
Many researchers use Primer 3 (http://bioinfo.ut.ee/primer3-0.4.0/) to design both qPCR and conventional PCR primers, and online tools for qPCR primer design are also available. I am fond if IDTs qPCR primer design tool (https://www.idtdna.com/scitools/Applications/RealTimePCR/)
Actually, it is the same primer tubes you ordedr from whatever company. Two diferences exist between using them in the two assays. In the real time, use lower primer concentration (2-20 Pico Mole) and for the normal PCR, use 100 PicoMole (the same like what you receive from the company in most cases. Another difference is that do not amplify large amplicons with real time (maximum is 25, bP) because it is more senstive, but in the gel-based one, go for higher, it does not matter.
It is essentially the same for the G+C content and runs of identical nucleotides (especially G). The difference is that you aim to target the exon-intron junction for primer binding for gene expression essays, and the amplicon length should be as short as possible (and never more than 400bp). If you are going to use Taqman chemistry, there are rules for the probe design too and the Tm difference between the primers and probe is important.
Normally Real time-PCR contain a dye that emits fluorescence to trace the annealing process in pcr. Two dye named "reporter dye" and "Quencher dye" attached within a short oligo named probe. Upon breakage of this probe system,1 dye(reporter dye) help to trace the amplification process or detection is based on its emissions. The primers used in RT-PCR are normally allele specific primer or sequence specific primers.
Would you mind to check those attached image and "youTube clip" link to understand the process easily.
It depends on the chemistry of the qPCR that you're going to use.
So, if you're going to use SyBR Green, you can design your primers normally (one forward and reverse) with preference that they don't have so different °Tm (differences no more of 3-5°C) (range 58-70°C, optimum 63) and also the GC% (45-55%, optimum 50%); furthermore, you have to take into account that is preferable that your product is 50-150/350 (no more due to the qPCR). So, depending on the site of your exon of interest, you have to select the sites where you want your primers.
However, if you're going to use Taqman probes for doing the qPCR. Some considerations change, your °Tm has to be 55-60 (optimum 60), and the probe has to have °Tm=68-70 (optimium 70) (always it has to have 10°C greater than the primers).
You can use Primer3 also for designing primers for qPCR (you have to choose the probe option which is between the options of primers forward and reverse and below the chart where you have to introduce the sequence of your gene of interest. "Pick hybridization probe (internal oligo), or use oligo below" There you select the probe and after that you choose the parameters for your primers.
To analyze them you can use primer-blast: http://www.ncbi.nlm.nih.gov/tools/primer-blast/ , in there you introduce the sequence of your gene of interest, your sequences of primers forward and reverse (both) (where it says " Use my own forward primer (5'->3' on plus strand; Use my own reverse primer (5'->3' on minus strand" and in "Primer Pair Specificity Checking Parameters" you remove the check from the option "Enable search for primer pairs specific to the intended PCR template". In that way, you will get the specific site where your primers are annealing in the sequence and the thermodynamic features of each primer (°Tm, 5', 3', GC%, so on).
However, also you can use oligoanalyzer which allow you put your PCR conditions such as concentrions of Na+, Mg++, dNTPs, oligos, °Ta. https://www.idtdna.com/calc/analyzer, in there also you can check if your primers tend to form primers dimer with themselves of with other primers (with the respective primers of other primers if you're doing a multiplex PCR).