Skip to Content
Merck
  • Effect of preorganization on the affinity of synthetic DNA binding motifs for nucleotide ligands.

Effect of preorganization on the affinity of synthetic DNA binding motifs for nucleotide ligands.

Organic & biomolecular chemistry (2015-04-23)
S Vollmer, C Richert
ABSTRACT

Triplexes with a gap in the purine strand have been shown to bind adenosine or guanosine derivatives through a combination of Watson-Crick and Hoogsteen base pairing. Rigidifying the binding site should be advantageous for affinity. Here we report that clamps delimiting the binding site have a modest effect on affinity, while bridging the gap of the purine strand can strongly increase affinity for ATP, cAMP, and FAD. The lowest dissociation constants were measured for two-strand triple helical motifs with a propylene bridge or an abasic nucleoside analog, with Kd values as low as 30 nM for cAMP in the latter case. Taken together, our data suggest that improving preorganization through covalent bridges increases the affinity for nucleotide ligands. But, a bulky bridge may also block one of two alternative binding modes for the adenine base. The results may help to design new receptors, switches, or storage motifs for purine-containing ligands.

MATERIALS
Product Number
Brand
Product Description

Sigma-Aldrich
Acetonitrile solution, contains 0.05 % (w/v) ammonium formate, 5 % (v/v) water, 0.1 % (v/v) formic acid, suitable for HPLC
Sigma-Aldrich
Ammonia-14N, 99.99 atom % 14N
Sigma-Aldrich
Ammonium citrate dibasic, puriss., ≥98%
Sigma-Aldrich
Ammonium citrate dibasic, BioXtra, ≥99.0% (T)
Sigma-Aldrich
Acetonitrile solution, contains 0.1 % (v/v) trifluoroacetic acid, suitable for HPLC
Sigma-Aldrich
Acetonitrile solution, contains 0.05 % (v/v) trifluoroacetic acid
Sigma-Aldrich
Acetonitrile solution, contains 0.1 % (v/v) formic acid, suitable for HPLC
Sigma-Aldrich
Ammonia, anhydrous, ≥99.98%
Sigma-Aldrich
Ammonium citrate dibasic, ACS reagent, 98%
Sigma-Aldrich
Adenine, ≥99%
Sigma-Aldrich
Guanosine 3′,5′-cyclic monophosphate, ≥98% (HPLC), powder
Sigma-Aldrich
Adenine, BioReagent, suitable for cell culture
Sigma-Aldrich
Adenine, BioReagent, suitable for plant cell culture, ≥99%
Sigma-Aldrich
Ammonia solution, 0.4 M in THF
Sigma-Aldrich
Ammonia solution, 4 M in methanol
Sigma-Aldrich
Acetonitrile solution, contains 10.0% acetone, 0.05% formic acid, 40.0% 2-propanol
Sigma-Aldrich
Acetonitrile, HPLC Plus, ≥99.9%, poly-coated bottles
Sigma-Aldrich
Acetonitrile, electronic grade, 99.999% trace metals basis
Sigma-Aldrich
Acetonitrile, anhydrous, 99.8%
Sigma-Aldrich
Ethyl alcohol, Pure, 200 proof, anhydrous, ≥99.5%
Sigma-Aldrich
Acetonitrile, ≥99.5%, ACS reagent
Sigma-Aldrich
Ethyl alcohol, Pure, 190 proof, ACS spectrophotometric grade, 95.0%
Supelco
Ethanol standards 10% (v/v), 10 % (v/v) in H2O, analytical standard
Sigma-Aldrich
Adenine hemisulfate salt, ≥99%
Sigma-Aldrich
Guanosine 3′,5′-cyclic monophosphate sodium salt, ≥99% (HPLC), powder