Re: Cytosine appears lighter in colour than other nucletide bases under UV?

Alex, 
I thought of several different answers to your question. 

1.  The most obvious one: If you used single stranded DNA, it simply may 
not have contained many cytosine nucleotides. However, I assume that you 
asked your question because you were working with double stranded DNA and 
expected equimolar amounts of C and G nucleotides.

2.  The acidic conditions probably led to increased deamination of 
cytosine and its conversion to uracil. That could explain the lower amount 
of C on your chromatogram.

3.  Cytosine's absorbance maximum is around 270 nm at very alkaline pH and 
even higher at acidic pH. I assume that you detected your bases with a 
short wave (around 255 nm) UV lamp. Since the absorbance maxima of the 
other bases are closer to the wavelength of your UV lamp, the extinction 
coefficient of cytosine at that wavelength was probably lower than that of 
the other nucleotides.

Hope this helps.

S. Heinhorst