Dara E. Gilbert

Multistranded DNA structures.

DNA oligonucleotides can form multistranded helices through either the folding of a single strand or the association of two, three or four strands of DNA. Structures of several new DNA triplexes, G-quartet DNA quadruplexes and I-motif DNA quadruplexes have been reported recently. These structures provide new insights into helix stability and folding, loop conformations and cation interactions.

1H NMR spectroscopy of DNA

Publisher Summary This chapter focuses on the methods used to obtain, process, assign, and analyze the nuclear magnetic resonance (NMR) spectra of DNA oligonucleotides. The utility of these studies for qualitative analysis of DNA structures is also discussed in the chapter. Advances in NMR technology and instrumentation since the mid-1980s have led to a revolution in the use of NMR spectroscopy for the determination of macromolecular structures. Protein structures determined from data obtained by NMR methods are now accepted by both NMR spectroscopists and crystallographers. NMR spectroscopy of DNA oligonucleotides was largely made possible by the advent of convenient DNA synthesis methods at about the same time that two-dimensional NMR was beginning to be applied to the study of proteins. Prior to that, most 1 H NMR spectroscopy of nucleic acids was done on transfer RNA and synthetic RNA polymers. DNA in the milligram quantities needed for 1 H NMR spectroscopy can be conveniently synthesized on commercial DNA synthesizers. The most difficult part of obtaining DNA for NMR samples is purification. Many laboratories use high-performance liquid chromatography with adequate results for purification of DNA samples.

Structural analysis of drug—DNA interactions

Abstract This review summarizes results of solution NMR and X-ray crystallographic structural studies of drug—DNA complexes that have been reported since December, 1989. These include minor-groove-binding drugs, intercalators, and covalent adducts. Comparison of results obtained for the same or similar drugs bound to different DNA sequences, or complexes studied in solution and in the crystal, indicates the importance of sequence and conditions in determining the mode of drug binding. Different structures are sometimes observed in the crystal and in solution, and the mode of drug binding is sometimes different for different sequences. Two important general conclusions can be drawn from these studies. Firstly, large structural changes are often observed in the DNA concomitant with drug binding — these include widening of the minor groove to accommodate drug dimers and the formation of Hoogsteen base pairs. Secondly, many drugs exhibit more than one binding mode, and therefore one should be cautious in drawing conclusions about the biological mode of action of a drug based on results for a single structure.

Solution Structure of the Hrpabc14.4 Subunit of Human RNA Polymerases

The protein hRPABC14.4 is an essential subunit of human RNA polymerases I, II, and III and is required for the transcription of all human nuclear genes. The structure of hRPABC14.4 was determined by nuclear magnetic resonance spectroscopy. The protein fold comprises a highly conserved central domain forming two antiparallel α-helices flanked by the less conserved N- and C-terminal regions forming a five-stranded β-sandwich. Amino acids from the two helices participate in the generation of a hydrophobic surface area which is conserved in all eukaryotic and archaeal homologous subunits, and likely constitutes a critical macromolecular interaction interface. The hRPABC14.4 structure accounts for mutagenesis results in Saccharomyces cerevisiae and provides a structural working model for elucidating the role of this subunit in the molecular architecture and function of the human nuclear RNA polymerases.