I am conducting 1H NMR experiments on a 700 MHz machine to analyze DNA-chemical binding. The chemical I am using is an intense blue color and I have used a sub-saturation stoichiometry for the concentration of chemical. When I performed the NMR I got the expected chemical shifts but the intensity of the peak was greatly reduced (0.005 for DNA only to 0.0005 upon chemical addition). Does the color of the chemical have any effect on the peaks, and is it as significant as the peak shift? If so, what could be the corrective measure?
The strong blue color makes me wonder whether your reagent might be paramagnetic, i.e. a radical, or a Cobalt or Copper complex?
Hi
If you can rule out equipment set-up (matching/tuning, 90 degree pulse) and simple dilution error, I would think it is more likely that you are getting precipitation of some DNA (changing concentration) or aggregation which broadens line widths to an extent you loose the signal. Be wary of comparing intensities as only areas are proportional to concentration.
I can't think of any reason why the colour of the dye would influence peak intensity. NMR signals are in the radio frequency range. It is more likely that you are diluting the sample, have precipitation or change in solubility or mobility or that your receiver gain has changed due to detection of (stronger) signals from the dye or solvent. You could try a titration experiment where you use lower concentrations of your dye, look for changes in linewidth at half height and look for signals from your dye.
Thank you for your reply. I am going to perform the titration experiment and will revert if my results are better.
Just a thought, but with titrations it can be helpful to have an trustworthy internal reference.
The strong blue color makes me wonder whether your reagent might be paramagnetic, i.e. a radical, or a Cobalt or Copper complex?
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