Hello everyone,
I have a question about DNA and RNA hybridization. I read somewhere that DNA:RNA duplex are more stable compared to DNA:DNA duplex. But my question is somewhat related to DNA:RNA hybridization kinetics. If I mix template DNA (250bp long) and DNA as well as RNA oligos (20 nt long) complementary to a part of the template DNA, which oligo (DNA or RNA) will bind to the template DNA first (or have higher affinity towards the template DNA)?
1. DNA > RNA oligos, or
2. RNA > DNA oligos, or
3. DNA ∼ RNA oligos
I presume that it could be temperature dependent. For example, during cDNA synthesis the reaction is incubated at 25°C for 10min (for oligo(dT) binding and extension), while in PCR annealing step minimum temperature of 50°C is considered good (higher is even better).
Any thoughts will be appreciated.
Kind regards,
S.
Hi Sandeep,
You should note, that not only oligo-to-oligo binding makes the deal in the certain type of reaction (PCR, RT, or whatever). In fact, the annealing occurs at a wide range of temperatures (0 - 600C). But the final choice of temperatures is based on the temperature depended activity of polimerases: 40-500C range is good for MuLV (RT), while Taq prefers 55 - 620C.
I understand your point. But my question is more about just temperature based annealing of DNA and RNA to a DNA template, and not polymerisation.
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