DNA can form hydrogen bonds to protein.
In this puzzle, there's a section of DNA on the left and a small protein on the right. Two segments of the protein are shown in yellow, and can be mutated in design mode.
Select Design Mode from the Modes menu. Then click on one of the yellow segments and select a new amino acid. Use the inner blue ring of the mutate wheel to select a hydrophilic.
The help popups suggest a long hydrophilic for one segment, and a shorter, forked hydrophilic for other. Lysine is a long hydrophilic, and asparagine is a forked hydrophilic that's shorter than lysine. Check out the amino acid gallery for all the options.
If you pick the correct amino acids, the puzzle is solved. The shake tool is available, but shouldn't be needed.