Diffusivity of DNA and RNA molecules

[Frank]

Dear All,

For DNA/RNA segments of 50-150bp, has anyone know any data showing their diffusivity different in
acquous media?

I'm trying to do hybridization to a microarray. I found RNA hyb. signal is much stronger than DNA
hyb. signal in the static case while the signals are comparable in dynamic case. So I'm guessing
that maybe RNA molecules diffuse faster than DNA molecules. Anyone here has similar experience or
can molecular biologists explain?

Thanks, Frank

 

[Tomhendricks474]

<< I'm trying to do hybridization to a microarray. I >>

What kind of temp range are you using to denature and anneal?

 

[Curtadams]

[email protected] writes:

>For DNA/RNA segments of 50-150bp, has anyone know any data showing their diffusivity different in
>acquous media?

>I'm trying to do hybridization to a microarray. I found RNA hyb. signal is much stronger than DNA
>hyb. signal in the static case while the signals are comparable in dynamic case. So I'm guessing
>that maybe RNA molecules diffuse faster than DNA molecules. Anyone here has similar experience or
>can molecular biologists explain?

Two reasons I can think of:

1) DNA is normally double-stranded and RNA single-stranded. So there's competition from
complementary strands in DNA absent in RNA

2) RNA-DNA double helices are more stable than DNA-DNA. I forget why; I think it's because RNA is
more flexible.

I'd be surprised if diffusion has anything to do with it. I doubt the liquid in hybridization assays
is still enough for diffusion to be limiting. You could test by running the hybridization more
slowly. If diffusion is very relevant, this will markedly increase signal.

Curt Adams ([email protected]) "It is better to be wrong than to be vague" - Freeman Dyson