Designed Nucleotide Binding Motifs

Gaps in the central strand of oligonucleotide triplexes bind nucleoside phosphates tightly. Watson-Crick and Hoogsteen base pairing as design principle yield motifs with high affinity for nucleoside phosphates with A or G as nucleo-base, including ATP. The second messenger 3',5'-cAMP is bound with nanomolar affinity. A designed DNA motif accommodates seven nucleotides at a time. The design was implemented for both DNA and RNA.