What are the criteria for designing biotinylated probes differ from primer designing?
The design of primers verse probes can both be down fairly easily with the use of the companies design tools (as long as you know the regions you want to target) and most companies will provide you with assistance.
Usually most people prefer probe based methods over primer methods since they work better of degraded samples (i.e. you need enough intact copies of your regions to get amplification). If you have good high molecular weight DNA and little to no degradation both primer and probe methods should be find. If you have degraded samples I would suggest using probe methods. I tend to just go with probe methods so that I can use them on both degraded sample (i.e. environmental DNA) and intact samples (i.e. fresh tissue extracts).
Hope this help and good luck!
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