Structural polymorphism in a tubercidin analogue of the DNA double helix

Altering the electrostatic potential in the major groove: thermodynamic and structural characterization of 7-deaza-2'-deoxyadenosine:dT base pairing in DNA

As part of an ongoing effort to explore the effect of major groove electrostatics on the thermodynamic stability and structure of DNA, a 7-deaza-2′-deoxyadenosine:dT (7-deaza-dA:dT) base pair in the Dickerson–Drew dodecamer (DDD) was studied. The removal of the electronegative N7 atom on dA and the replacement with an electropositive C–H in the major groove was expected to have a significant effect on major groove electrostatics. The structure of the 7-deaza-dA:dT base pair was determined at 1.1 Å resolution in the presence of Mg²⁺. The 7-deaza-dA, which is isosteric for dA, had minimal effect on the base pairing geometry and the conformation of the DDD in the crystalline state. There was no major groove cation association with the 7-deaza-dA heterocycle. In solution, circular dichroism showed a positive Cotton effect centered at 280 nm and a negative Cotton effect centered at 250 nm that were characteristic of a right-handed helix in the B-conformation. However, temperature-dependent NMR studies showed increased exchange between the thymine N3 imino proton of the 7-deaza-dA:dT base pair and water, suggesting reduced stacking interactions and an increased rate of base pair opening. This correlated with the observed thermodynamic destabilization of the 7-deaza-dA modified duplex relative to the DDD. A combination of UV melting and differential scanning calorimetry experiments were conducted to evaluate the relative contributions of enthalpy and entropy in the thermodynamic destabilization of the DDD. The most significant contribution arose from an unfavorable enthalpy term, which probably results from less favorable stacking interactions in the modified duplex, which was accompanied by a significant reduction in the release of water and cations from the 7-deaza-dA modified DNA.

Neutron fibre diffraction studies of amyloid using H2O/D2O isotopic replacement

The first neutron fibre diffraction studies of an amyloid system are presented. The techniques used to prepare the large samples needed are described, as well as the procedures used to isotopically replace H2O in the sample by D2O. The results demonstrate the feasibility of this type of approach for the pursuit of novel structural analyses that will strongly complement X-ray fibre diffraction studies and probe aspects of amyloid structure that to date have remained obscure. The approach is demonstrated using an amyloid form of the peptide NSGAITIG, but is equally applicable for the study of other systems such as Alzheimer's Aβ peptide.

Phonon dispersion of oriented DNA by inelastic x-ray scattering

Films of oriented deoxyribonucleic acid (DNA), prepared by the wet spinning method, have been studied using inelastic x-ray scattering. Spectra were recorded within the range of energy transfers -30< homega <30 meV at momentum transfers homegaQ ranging from 2.5 to 30 nm(-1) whereby the direction of Q essentially coincided with the helical axis. Measurements at ambient temperature cover samples in the A, B, C, and D conformations of DNA. Within the limits of the instrumental resolution, the spectra were analyzed by the response of a damped harmonic oscillator delivering dispersion and damping of modes having displacements with nonzero projections onto Q, i.e., essentially the compression waves traveling along the helical axis. The longitudinal speed of sound resulting from the sinusoidal dispersion varies only weakly with conformation. Our sound speed values are compared to results from Brillouin spectroscopy. The dispersion curves exhibit a minimum at about the inverse rise per residue, which -- together with strong elastic scattering -- reflect the large degree of disorder. Overdamping of the modes is observed for Q>5 nm(-1). The possibility that the observed large damping parameters are due to several contributing modes is discussed in terms of a simple model calculation for an idealized double helix. Whereas the quasicrystalline approximation for an effective disordered chain could well describe the sinusoidal dispersion, it fails to reproduce the observed damping by one order of magnitude. Our results indicate that the high-frequency dynamics of DNA is liquidlike and is most appropriately described by instantaneous normal modes of short correlation length.

Water-DNA interactions as studied by X-ray and neutron fibre diffraction

X-ray fibre-diffraction studies indicate a high degree of stereochemical specificity in interactions between water and the DNA double helix. Evidence for this comes from data that show that the molecular conformations assumed by DNA in fibres are highly reproducible and that the hydration-driven transitions between these conformations are fully reversible. These conformational transitions are induced by varying the relative humidity of the fibre environment and hence its water content. Further evidence for stereochemical specificity comes from the observed dependence of the conformation assumed on the ionic content of the fibre and the nucleotide sequence of the DNA. For some transitions, information on stereochemical pathways has come from real-time X-ray fibre diffraction using synchrotron radiation; information on the location of water with respect to the double helix for a number of DNA conformations has come from neutron fibre diffraction. This structural information from fibre-diffraction studies of DNA is complemented by information from X-ray single-crystal studies of oligonucleotides. If the biochemical processes involving DNA have evolved to exploit the structural features observed in DNA fibres and oligonucleotide single crystals, the challenges in developing alternatives to a water environment can be expected to be very severe.

Developments in fiber diffraction

Improved specimen preparation methods, third generation synchrotron sources, new data processing algorithms and molecular dynamics refinement techniques are, together, allowing the high-resolution structure determination of larger and larger macromolecular complexes by fiber diffraction. New synchrotron sources are also making possible both time-resolved studies and studies of ordered fibers only a few microns in diameter.