F) Nucleic Acids and Derivatives

4) Single stranded DNA with a stacking ligand
(minimized with Quanta/CHARMm)

Anmar Ali, Martin Gasiorek, Hans-Jörg Schneider, Angew. Chem., (1998), 110, Nr. 21, 3183-3186
Angew. Chem.Int. Ed., (1998), 37, No. 21, 3016-3019

Exercise: A) Identify the binding mode,
B) How long are the distances between the nitrogen atoms of the guest compound and the next phosphorus atoms
C) Check where there are possible conformational distortions upon complex formation (induced fit).

Without a Stacking Ligand

With a Stacking Ligand
  Coloured Guest Compound
Wireframe  Wireframe 
Ball&Sticks  Ball&Sticks 
Spacefill  Spacefill 
label atoms labels off  label atoms labels off 
Zoom Reset  Zoom Reset 
White Black Yellow Background  White Black Yellow Background 

Answer