Simple ethidium bromide question

Hiranya Roychowdhury hroychow at NMSU.EDU
Wed Aug 27 12:14:45 EST 1997

At 03:57 PM 8/26/97 GMT, Pascal_Bochet wrote:
>I was wondering why is it that in PCR when you look at the products on a 
>agarose gel stained with ethidium bromide, you can see primer dimer if
there is 
>any but you cannot see single stranded primer (if for instance you omit TAQ or 
>dNTP from the reaction.) Is it the size or the fact that it is single stranded 
>? In other terms what does ethidium bromide exactly bind to?
>Thank you for any insight.
>Pascal_Bochet at

EtBr intercalates into the "grooves" of double-stranded nucleic acids. This
is the reason why the rRNA molecules, which have extensive secondary
structures, light up brighter on the gels. Short NA's do not provide such
secondary structures to allow EtBr intercalation.

Dr. Hiranya Sankar Roychowdhury
Plant Genetic Engineering Lab.
New Mexico State University
Las Cruces, NM 88003
Ph. (505) 646-5785
hroychow at

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