X-ray Structure Characterization of the Selective Recognition of AT Base Pair Sequences.

The rational design of small molecules that target specific DNA sequences is a promising strategy to modulate gene expression. This report focuses on a diamidinobenzimidazole compound, whose selective binding to the minor groove of AT DNA sequences holds broad significance in the molecular recognition of AT-rich human promoter sequences. The objective of this study is to provide a more detailed and systematized understanding, at an atomic level, of the molecular recognition mechanism of different AT-specific sequences by a rationally designed minor groove binder. The specialized method of X-ray crystallography was utilized to investigate how the sequence-dependent recognition properties in general, A-tract, and alternating AT sequences affect the binding of diamidinobenzimidazole in the DNA minor groove. While general and A-tract AT sequences give a narrower minor groove, the alternating AT sequences intrinsically have a wider minor groove which typically constricts upon binding. A strong and direct hydrogen bond between the N-H of the benzimidazole and an H-bond acceptor atom in the minor groove is essential for DNA recognition in all sequences described. In addition, the diamidine compound specifically utilizes an interfacial water molecule for its DNA binding. DNA complexes of AATT and AAAAAA recognition sites show that the diamidine compound can bind in two possible orientations with a preference for water-assisted hydrogen bonding at either cationic end. The complex structures of AAATTT, ATAT, ATATAT, and AAAA are bound in a singular orientation. Analysis of the helical parameters shows a minor groove expansion of about 1 Å across all the nonalternating DNA complexes. The results from this systematic approach will convey a greater understanding of the specific recognition of a diverse array of AT-rich sequences by small molecules and more insight into the design of small molecules with enhanced specificity to AT and mixed DNA sequences.

A Single-Entity Method for Actively Controlled Nucleation and High-Quality Protein Crystal Synthesis.

Lack of controls and understanding in nucleation, which proceeds crystal growth and other phase transitions, has been a bottleneck challenge in chemistry, materials, biology, and other fields. The exemplary needs for better methods for biomacromolecule crystallization include (1) synthesizing crystals for high-resolution structure determinations in fundamental research and (2) tuning the crystal habit and thus the corresponding properties in materials and pharmaceutical applications. Herein, a deterministic method is established capable of sustaining the nucleation and growth of a single crystal using the protein lysozyme as a prototype. The supersaturation is localized at the interface between a sample and a precipitant solution, spatially confined by the tip of a single nanopipette. The exchange of matter between the two solutions determines the supersaturation, which is controlled by electrokinetic ion transport driven by an external potential waveform. Nucleation and subsequent crystal growth disrupt the ionic current limited by the nanotip and are detected. The nucleation and growth of individual single crystals are measured in real time. Electroanalytical and optical signatures are elucidated as feedbacks with which active controls in crystal quality and method consistency are achieved: five out of five crystals diffract at a true atomic resolution of up to 1.2 Å. As controls, those synthesized under less optimized conditions diffract poorly. The crystal habits during the growth process are tuned successfully by adjusting the flux. The universal mechanism of nano-transport kinetics, together with the correlations of the diffraction quality and crystal habit with the crystallization control parameters, lay the foundation for the generalization to other materials systems.

Drug design and DNA structural research inspired by the Neidle laboratory: DNA minor groove binding and transcription factor inhibition by thiophene diamidines.

The understanding of sequence-specific DNA minor groove interactions has recently made major steps forward and as a result, the goal of development of compounds that target the minor groove is an active research area. In an effort to develop biologically active minor groove agents, we are preparing and exploring the DNA interactions of diverse diamidine derivatives with a 5'-GAATTC-3' binding site using a powerful array of methods including, biosensor-SPR methods, and X-ray crystallography. The benzimidazole-thiophene module provides an excellent minor groove recognition component. A central thiophene in a benzimidazole-thiophene-phenyl aromatic system provides essentially optimum curvature for matching the shape of the minor groove. Comparison of that structure to one with the benzimidazole replaced with an indole shows that the two structures are very similar, but have some interesting and important differences in electrostatic potential maps, the DNA minor groove binding structure based on x-ray crystallographic analysis, and inhibition of the major groove binding PU.1 transcription factor complex. The binding KD for both compounds is under 10 nM and both form amidine H-bonds to DNA bases. They both have bifurcated H-bonds from the benzimidazole or indole groups to bases at the center of the -AATT- binding site. Analysis of the comparative results provides an excellent understanding of how thiophene compounds recognize the minor groove and can act as transcription factor inhibitors.