Calculation of Tm for RNA:RNA duplex

Enrique Castro ecastro at eucmax.sim.ucm.es
Thu Mar 4 09:33:37 EST 1999


Dear everyone

	I am a biochemist, not a molecular biologist. I am about to perform
some in situ hybrydization experiments to localize mRNA for some
neurotransmitter receptors in bain and cell culture. I have cDNA for
these receptors and I can to make full length RNA probes. I have seen
some formulas to calculate the melting temperature, Tm, of DNA:DNA and
DNA:RNA hybrids (for instance in Casey & Davidson 1977). There are also
programs to calculate Tm of primers (DNA:DNA hybrids) for PCR, but I am
not aware of any such program for RNA duplex. I want to manage
temperature (and formamide) during hybridization and post-hybriditation
washes to control binding to partially-homologous sequences.

	Could anybody indicate some program to calculate Tm for RNA:RNA duplex?

	Any tip for information of physical chemistry (thermal stability and
kinetics) of NATURAL RNA:RNA hybrids? (I have searched MEDLINE but
obtained most work on DNA denaturation or new compounds for use as
probes)
	
Thanks a lot

Enrique Castro
-- 
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                               Dept. Bioquimica, Fac. Veterinaria,
UCM     
   Enrique Castro      Ciudad Universitaria. 28040 Madrid. Spain   
                               Tel: 34-91-394 38 90   Fax: 34-91-394 39
09   
                               e-mail:
ecastro at eucmax.sim.ucm.es           
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