Hi, I am performing a reaction in which i'm conjugating DNA oligonucleotides to an 8-arm PEG-Maleimide. I want to quantify the reaction efficiency by measuring the amount of nucleic acid remaining after separation using nanodrop, but there's a drastic enhancement in the absorbance after conjugation? Does anyone know how the PEG affects DNA absorbance? I tried normalizing my measurements by subtracting the absorbance of a pure PEG solution, but the values are stil too high.
Thanks in advance.
Conjugating your DNA oligos should not affect their absorbance per se - you would simply be adding the absorbance of your PEG to the absorbance of the oligos. As in, the epsilon of the conjugation product is the epsilon of the oligo plus the epsilon of the PEG.
My suggestion for measuring the conjugation efficiency: Measure the absorbance of a known amount of your 8-arm PEG-Maleimide. Better yet, do so for a dilution series so that you can check for linearity. Do the same for your oligo, and you should be able to use the additive nature of the two absorbances to quantify your product - assuming your purification after the conjugation is good enough.
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