Hey all! Sorry for the simple question, but how to gradiently merge the colors of the rectangle and the other shape, along its outline? Do I need to cut it or... Sorry again, but any help would be appreciated! 
Based on my scientist wife's explanation about what you might mean in regards to a DNA drawing I came up with the process below:
I recreated your image as live art. Then I used the Pathfinder Divide function to make the overlap into a separate shape. Then I created a gradient with the two colors that you used (sampling them with the eyedropper). Then I applied the gradient to the overlap area and using the gradient tool I finessed the gradient as shown. If this is what you're looking for great. If not please provide a sketch as to what you need.
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