How to pool different biotin labelled oligonucleotide probes for hybridization. What should I consider Tm or Heterodimer? If i consider both then number of pools will increase leading to increased number of reactions??
Depending on the method, the probe may be synthesized using the phosphoramidite method, or it can be generated and labeled by PCR amplification or cloning (both are older methods). In order to increase the in vivo stability of the probe RNA is not used, instead RNA analogues may be used, in particular morpholino- derivatives. Molecular DNA- or RNA-based probes are now routinely used in screening gene libraries, detecting nucleotide sequences with blotting methods, and in other gene technologies, such as nucleic acid and tissue microarrays.
If I understand you correctly, then I suspect you are over thinking things. The critical factor us likely to be your hybridization and wash temperatures? Are you working with a published protocol? I did this year's ago and my memory is rusty, but I was using the work from Travis Glenn's lab in Florida.
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