Northern hyb

[J Preiss--Seq Anal]

Obviously there are some serious misunderstandings concerning nucleic acid 
denaturation. As was shown approximately 30 years ago, formaldehyde does not 
affect the stability of duplex nucleic acid, (monitored as a change in Tm) 
but, upon reacting with the free amino groups exposed during denaturation, 
obstructs the renaturation process (Stollar and Grossman). This is different 
than the effect of formamide, which affects the Tm of nucleic acid directly. 
(Casey and Davidson) The reaction of an aldehyde with an amino group produces 
a Schiff base adduct, which is very labile at pH greater than 7.0 (less than 
the pH of most nucleic acid electrophoresis buffers). Presumably glyoxal 
behaves comparable to formaldehyde in relation to the amino groups involved in 
base pairing. Glyoxal produces an additional more stable lesion in a reaction 
with guanine bases. (Broude and Budowsky) Thus the standard protocols have 
denaturation of the RNA with mild temperature in the presence of the aldehyde 
reagent of choice followed by electrophoresis through a buffer which will 
either not hydrolyze the stable adduct (for glyoxal treated RNA) or will 
provide an environment conducive to maintaining the Schiff base adduct by 
driving the equilibrium toward adduct formation (for formaldehyde treated 
RNA). The failiure to denature secondary structure will result in 
electrophoretic problems (the sieving properties of equal mass objects depends 
significantly upon the shape of the object) as will the failure to maintain 
the denatured state (changing the physical condition of the RNA during 
electrophoresis). The foregoing is pertinent to any single-stranded nucleic 
acid (for example consider DNA sequencing gel protocols which utilize the 
reaction of urea with exposed carbonyl to obstruct secondary structure of the 
DNA fragments to be resolved). 
        The removal of both Schiff base adducts occurs at pH greater than 7.0. 
The stable guanine adduct is effected by heating to 60C at pH 8.0 (Thomas) 
after the nucleic acid is transferred to the membrane of choice. Failure to 
remove these should interfere with renaturation of the probe with the 
immobilized target nucleic acid (Stollar and Grossman). I do not know of 
anyone who willingly admits to not removing the adducts either during or after 
transfer. 
        I have examined the amount of nucleic acid transferred from a 
formaldehyde gel to S&S NYTRAN by fluid using a vacuum transfer device for 20X 
SSC (classic transfer vehicle), 7.5 mM NaOH (modification of BIO-RAD), 7.5 mM 
NaOH for 1/3 time followed by 0.1 X SSC, and electrotransfer. I find the 
relative amount of nucleic acid transfered to the membrane from gels which had 
the same amount of RNA loaded to be in the ratio of 1:3:5:50 for the above 
methods. 50 is a minimal estimate. 

REFS: 
Stollar and Grossman, (1962) JMB 4, 31-38. 
Casey and Davidson, (1977) Nuc. Acids Res. 4, 1539.
Broude and Budowsky, (1971) BBA 254, 380-388. 
Thomas, (1983) Methods in Enzymology 100, 255-266. 
BIO-RAD - User manual for ZETAPROBE membrane.