First Structure of a Designed Minor Groove Binding Heterocyclic Cation that Specifically Recognizes Mixed DNA Base Pair Sequences

Abstract

The high-resolution NMR structure of the first heterocyclic, non-amide, organic cation that strongly and selectively recognizes mixed AT/GC bp (bp=base pair) sequences of DNA in a 1:1 complex is described. Compound designs of this type provide essential methods for control of functional, non-genomic DNA sequences and have broad cell uptake capability, based on studies from animals to humans. The high-resolution structural studies described in this report are essential for understanding the molecular basis for the sequence-specific binding as well as for new ideas for additional compound designs for sequence-specific recognition. The molecular features, in this report, explain the mechanism of recognition of both A⋅T and G⋅C bps and are an interesting molecular recognition story. Examination of the experimental structure and the NMR restrained molecular dynamics model suggests that recognition of the G⋅C base pair involves two specific H-bonds. The structure illustrates a wealth of information on different DNA interactions and illustrates an interfacial water molecule that is a key component of the complex.

Bound Compound, Interfacial Water, and Phenyl Ring Rotation Dynamics of a Compound in the DNA Minor Groove

“…With the –AAGATA- sequence only one favored bound form of DB2277 is observed and this allowed determination of the DB2277-DNA complex structure. 7…”

“…7 The three aromatic groups of DB2277 were initially very close to one plane while the amidine groups are twisted about 30° out of the phenyl plane due to a steric clash of protons on the phenyls and amidines. 7…”

“…Up to 1218 frame of the observed nanosecond, the DB2277-AAGATA complex (Figure 2), stays close to the initial low energy conformation which is similar to the published NMR structure of the complex (PDB ID 6AST). 7 In this conformation, N2 of the planar amidine, Am1, points above the plane of the aromatic groups of DB2277 (Figure 2) to facilitate the water-mediated H-bond with O2 of T16 (N2-H--O-H--O-T16). C1 and C2 Ph1 phenyl atoms (Figure 2) project out of the minor groove in this structure.…”

“…5 The formation of a unique 1:1 complex for NMR studies was achieved with a DNA sequence that has a central –AAGATA– binding site. 7…”

Small Sequence‐Sensitive Compounds for Specific Recognition of the G⋅C Base Pair in DNA Minor Groove

“…Specific atom types assigned for DB2692 molecule were adapted from the ff99 force field. Most of the force field parameters for DB2692 molecule were derived from the existing set of bonds, angles and dihedrals for the similar atom types in parm99 and GAFF force fields . Some dihedral angle parameters were obtained from previously reported parametrized data .…”