Naphthyridine tetramer with a pre-organized structure for 1:1 binding to a CGG/CGG sequence

Abstract

A naphthyridine carbamate dimer (NCD) is a synthetic ligand for DNA containing a CGG/CGG sequence. Although NCD can bind selectively and tightly to a CGG/CGG sequence, the highly cooperative 2:1 binding mode has hampered precise analysis of the binding. We describe herein the synthesis of a series of naphthyridine tetramers consisting of two NCD molecules connected with various linkers to seek a ligand that binds to a CGG/CGG sequence exclusively with a 1:1 stoichiometry. Among the tested ligands, NCTB and Z-NCTS, which have linker moieties with restricted conformational flexibility [biphenyl and (Z)-stilbene linker, respectively], gave the exclusive formation of a 1:1 ligand–CGG/CGG complex. The (Z)-stilbene linker in Z-NCTS was designed to have pre-organized conformation appropriate for the binding and, in fact, resulted in the highest binding affinity. Thermodynamic parameters obtained by isothermal titration calorimetry indicated that the stronger binding of Z-NCTS was attributed to its lower entropic cost. The present study provides not only a novel 1:1 binding ligand, but also valuable feedback for subsequent molecular design of DNA and RNA binding ligands.

A Synthetic Riboswitch that Operates using a Rationally Designed Ligand–RNA Pair

“…This result was in marked contrast with the large DT m value of + 21.4 8C observed for the corresponding DNA duplex. [22] In our related studies, the binding of the ligand to the DNA mismatches was accompanied by helix unwinding and basepair rearrangements at the binding site (Figure 1 b). [21] Such structural changes would be less favorable in RNA, because the A-form RNA duplex is more stable than is a duplex DNA with the same sequence and tolerates the presence of mismatched base pairs.…”

“…The mismatch-binding ligands recognize Watson-Crick surface of DNA bases by forming fully matched hydrogen bonds. [19][20][21][22] Although the ligand-accessible surface of Watson-Crick base pairs is almost identical between DNA and RNA, most of the DNA-mismatch-binding ligands developed by us exhibit a reduced or abolished binding affinity to the corresponding RNA mismatches.…”

“…Z-NCTS consists of two units of a naphthyridine carbamate dimer (NCD) connected by a rigid Z-stilbene linker (Figure 1 a). [22] Z-NCTS binds to the GG mismatch in the d(CGG)/d(CGG) sequence of DNA with an entropically favored 1:1 stoichiometry and strongly stabilizes the resulting double-stranded DNA (Figure 1 b). [22] Four naphthyridine moieties in a single Z-NCTS molecule recognize four guanine bases in the d(CGG)/d(CGG) sequence by forming fully Table S1), indicating its weak binding to the r(CGG)/r(CGG) sequence.…”

“…[22] Z-NCTS binds to the GG mismatch in the d(CGG)/d(CGG) sequence of DNA with an entropically favored 1:1 stoichiometry and strongly stabilizes the resulting double-stranded DNA (Figure 1 b). [22] Four naphthyridine moieties in a single Z-NCTS molecule recognize four guanine bases in the d(CGG)/d(CGG) sequence by forming fully Table S1), indicating its weak binding to the r(CGG)/r(CGG) sequence. This result was in marked contrast with the large DT m value of + 21.4 8C observed for the corresponding DNA duplex.…”

“…[21,22,25] A 26-mer hairpin RNA containing a r(UGG)/r(UGG) site gave a single major peak corresponding to the 5 À ion of the RNA (Figure 2 c, black). In the presence of Z-NCTS, an ion peak corresponding to a 1:1 complex (calcd 1894.5, found 1895.2) appeared, together with the loss of the free RNA ion peak (Figure 2 c, red).…”