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Formaldehyde, hybridization, and Northern blots

Joel Huberman camhuber at ubvms.cc.buffalo.edu
Sun Jul 17 09:45:00 EST 1994


Dear Netters,

	To size-fractionate RNA prior to Northern blotting, formaldehyde gels
are frequently used.  Formaldehyde reacts covalently with the bases in single-
stranded nucleic acids, preventing the bases from Watson-Crick base pairing.
By preventing base pairing, formaldehyde prevents formation of secondary struc-
ture, so RNAs run according to their size in the gel.  It seems to me, however,
that the formaldehyde-modified RNA should not be able to hybridize with a probe
after it has been Northern-blotted to a membrane.  Obviously, it does hybri-
dize;  otherwise formaldehyde gels would not be used for Northern blottings.
Thus, the formaldehyde reaction must be reversible.  I would like to know whe-
ther the formaldehyde reaction is fully reversed under standard hybridization
conditions, or is there a possibility that use of a formaldehyde gel leads to
less efficient hybridization than would use of a standard gel or a different
type of denaturing gel, such as a formamide gel?

	If you can help to answer this question, please post your answer to the
news group and also send me e-mail at huberman at acsu.buffalo.edu.  Thanks very
much.

Joel A. Huberman
Dept. of Molecular & Cellular Biology
Roswell Park Cancer Institute
Buffalo, NY  14263
huberman at acsu.buffalo.edu  



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