Comparison of the phosphorus magnetic resonance and circular dichroism properties of calf thymus DNA and chromatin

Unspinning chromatin: Revealing the dynamic nucleosome landscape by NMR

NMR is an essential technique for obtaining information at atomic resolution on the structure, motions and interactions of biomolecules. Here, we review the contribution of NMR to our understanding of the fundamental unit of chromatin: the nucleosome. Nucleosomes compact the genome by wrapping the DNA around a protein core, the histone octamer, thereby protecting genomic integrity. Crucially, the imposed barrier also allows strict regulation of gene expression, DNA replication and DNA repair processes through an intricate system of histone and DNA modifications and a wide range of interactions between nucleosomes and chromatin factors. In this review, we describe how NMR has contributed to deciphering the molecular basis of nucleosome function. Starting from pioneering studies in the 1960s using natural abundance NMR studies, we focus on the progress in sample preparation and NMR methodology that has allowed high-resolution studies on the nucleosome and its subunits. We summarize the results and approaches of state-of-the-art NMR studies on nucleosomal DNA, histone complexes, nucleosomes and nucleosomal arrays. These studies highlight the particular strength of NMR in studying nucleosome dynamics and nucleosome-protein interactions. Finally, we look ahead to exciting new possibilities that will be afforded by on-going developments in solution and solid-state NMR. By increasing both the depth and breadth of nucleosome NMR studies, it will be possible to offer a unique perspective on the dynamic landscape of nucleosomes and its interacting proteins.

ENDOR of metalloenzymes

This Account examines the role of electron-nuclear double resonance (endor) spectroscopy in furthering our understanding of how metal ions function in biological systems. It briefly describes endor and electron spin-echo envelope modulation (eseem) spectroscopies and then illustrates the uses of endor with several case studies from our own research: cytochrome c peroxidase compound ES; ribonucleotide reductase intermediate X; allylbenzene-inactivated chloroperoxidase; the role of the [4Fe-4S](+) cluster in enzymes of the "radical S-adenosylmethionine" superfamily; dioxygen activation by heme enzymes. Finally, it briefly considers future developments.

A 31P NMR study of the interaction of the antitumor active metallocene Cp2MoCl2 with calf thymus DNA

Treatment of sonicated calf thymus DNA with the antitumor active metallocene Cp2MoCl2 afforded a metallocene-DNA complex which was characterized by 31P NMR spectroscopy. In addition to the resonance for the phosphate backbone (delta-1.6), the spectrum contained 2 signals assigned to a phosphate bound Mo-DNA complex(es) (delta 37.2, 36.5) and a broad signal at delta 6.2 ppm. This result suggests that covalent attachment of the metallocene Cp2MoCl2 occurs via phosphate(O) coordination and is accompanied by local distortion of the DNA backbone. This result supports recent ICP studies with Cp2TiCl2 that have DNA detected DNA-metallocene adducts.

Phosphorus-31 nuclear magnetic resonance of double- and triple-helical nucleic acids. Phosphorus-31 chemical shifts as a probe of phosphorus-oxygen ester bond torsional angles

The temperature dependence to the 31P NMR spectra of poly[d(GC)] . poly [d(GC)],d(GC)4, phenylalanine tRNA (yeast) and mixtures of poly(A) + oligo(U) is presented. The 31P NMR spectra of mixtures of complementary RNA and of the poly d(GC) self-complementary DNA provide torsional information on the phosphate ester conformation in the double, triple, and "Z" helix. The increasing downfield shift with temperature of the single-strand nucleic acids provides a measure of the change in the phosphate ester conformation in the single helix to coil conversion. A separate upfield peak (20-60% of the total phosphates) is observed at lower temperatures in the oligo(U) . poly(A) mixtures which is assigned to the double helix/triple helix. Proton NMR and UV spectra confirm the presence of the multistrand forms. The 31P chemical shift for the double helix/triple helix is 0.2-0.5 ppm upfield from the chemical shift for the single helix which in turn is 1.0 ppm upfield from the chemical shift for the random coil conformation.

Characterization of alternating deoxyribonucleic acid conformations in solution by phosphorus-31 nuclear magnetic resonance spectroscopy

Medium length (500-200 bp) alternating purine-pyrimidine DNAs were prepared by sonication of synthetic polymers at low temperature. The products, and the hairpin structures derived from them after melting, were sufficiently small for high-resolution 31P NMR studies. Of the five sequences studied, two DNAs, poly(dG-dC).poly(dG-dC) and poly(dA-dU).poly(dA-dU), gave singlet 31P resonances, while three others, poly(dA-dT).poly(dA-dT), poly(dA-br5U).poly(dA-br5U), and poly(dI-dC).poly(dI-dC), exhibited two resolved signals of equal area. This indicates the existence of two distinct alternating phosphodiester backbone conformations for these latter three B-DNAs in solution. Controls of homopolymers, which were also prepared by sonication, showed only singlet 31P resonances. Of the alternating sequences DNAs, only sonicated poly(dG-dC).poly(dG-dC) exhibited a conformational transition to a high salt (greater than 2.5 M) form which exhibited two well-resolved 31P resonances of equal area. This indicates that the high salt form of poly(dG-dC).poly(dG-dC) also has an alternating backbone structure, and it is presumed to be a Z-DNA. These results indicate a general response of the DNA backbone conformation to alternating purine-pyrimidine base sequences but with a degree of sequence and environmental specificity which might have functional genetic significance.

Deoxyribonucleic acid dynamics from phosphorus-31 nuclear magnetic resonance

31P NMR of native high molecular weight DNA shows that the phosphodiester backbone undergoes reorientation with a rotational correlation time of about 2 X 10(-6) s at 30 degrees C. This rate is consistent with the flexibility of the polymer and does not require the presence of internal phosphate motions. The line width of the phosphorus resonance of DNA is due to incompletely averaged 31P-1H dipolar couplings and 31P chemical shift anisotropy relaxation; high-power proton decoupling and magnetic field dependence experiments separate the two effects and allow the use of the line width for determination of the rotational correlation time. The line width is dependent on temperature, and an activation energy of 5-8 kcal/mol is calculated for the motion of DNA.

31P magnetic resonance of DNA in nucleosome core particles of chromatin

The 31P magnetic resonance spectrum of nucleosome cores from calf thymus nuclei has been measured. The spectrum consists of a single symmetric line, with a maximum second component of 5%. It is argued that this reflects a single average state of the DNA backbone, and does not support models that invoke backbone kinking at a frequency of 1 in 10 base pairs.

Analysis of living tissue by phosphorus-31 magnetic resonance

Nuclear magnetic resonance is a new method for assaying the content of phosphate metabolites in intact tissues. Its nondestructive nature allows simultaneous and repeated determinations of these compounds with a minimum perturbation of tissue. Changes in the concentrations of the phosphates as a function of time characterize the metabolic machinery of the tissue and reveal alterations in enzymic activity that result from drug treatment or disease. The entire phosphate profile shows differences between normal and diseased muscle which should be of diagnostic value. Further, by examining phosphate profiles we detected a family of chemical compounds that were not previously known to exist as major constituents in muscle. Of these, two have been isolated and one has been identified as glycerol 3-phosphorylcholine. Finally, shifts in the positions of resonances monitor the internal environment of the living system, its hydrogen ion concentration, the complexing of alkaline earth metals with ATP, and compartmentalization within the cell.