Neutron crystallography of B-DNA decamer d(CCATTAATGG)

Arai, Shigeki; Chatake, Toshiyuki; Kurihara, Kazuo; Tanaka, I.; Ohhara, Takashi; Nakabayashi, Nobuo

doi:10.2142/biophys.43.s27_1

Cited by 10 publications

(20 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Consequently, the hydrogenbonding network is quite complicated. Very recently, we have solved the neutron structure of the B-DNA decamer d(CCATTAATGG) at 3.0 Å resolution (Arai et al, 2005), in which the hydrogen-bonding network is also complicated, as in the present Z-DNA. This coincides with the present observation.…”

Section: Tablementioning

confidence: 96%

The hydration structure of a Z-DNA hexameric duplex determined by a neutron diffraction technique

Chatake

Tanaka

Umino³

et al. 2005

Acta Cryst D

View full text Add to dashboard Cite

In order to reveal the hydration structure of Z-DNA, a neutron diffraction study has been carried out at 1.8 A resolution on a Z-DNA hexamer d(CGCGCG). Neutron diffraction data were collected with the BIX-3 single-crystal diffractometer at the JRR-3 reactor in the Japan Atomic Energy Research Institute (JAERI) using a large crystal (1.6 mm3) obtained from D2O solution. It has been found that almost all the guanine bases have participated in H/D exchange at the C8-H8 group, consistent with the acidic nature of this bond. 44 water molecules were found in the nuclear density maps, of which 29 showed the entire contour of all three atoms (D-O-D). The remaining 15 water molecules had a simple spherical shape, indicating that they were rotationally disordered. An interesting relationship was found between the orientational disorder of the water molecules and their locations. Almost all water molecules in the minor groove were well ordered in the crystal, while 40% of the water molecules in the major groove were rotationally disordered. The hydrogen-bonding networks in the hydration shells have two structural aspects: flexibility and regularity.

show abstract

Section: Tablementioning

confidence: 96%

The hydration structure of a Z-DNA hexameric duplex determined by a neutron diffraction technique

Chatake

Tanaka

Umino³

et al. 2005

Acta Cryst D

View full text Add to dashboard Cite

show abstract

“…84 The 25H 2 O molecules in the crystal structure are from the solvent and are hydrogen-bonded to the B-DNA as shown in Fig. 84 The 25H 2 O molecules in the crystal structure are from the solvent and are hydrogen-bonded to the B-DNA as shown in Fig.…”

Section: Reproducing the Electrostatic Potential In One System Conformentioning

confidence: 99%

Introducing DDEC6 atomic population analysis: part 2. Computed results for a wide range of periodic and nonperiodic materials

2016

View full text Add to dashboard Cite

Net atomic charges (NACs) are widely used throughout the chemical sciences to concisely summarize key information about charge transfer between atoms in materials. The vast majority of NAC definitions proposed to date are unsuitable for describing the wide range of material types encountered across the chemical sciences. In this article, we show the DDEC6 method reproduces important chemical, theoretical, and experimental properties across an extremely broad range of material types including small and large molecules, organometallics, nanoclusters, porous solids, nonporous solids, and solid surfaces. Some important comparisons we make are: (a) correlations between various NAC models and spectroscopically measured core-electron binding energy shifts for Ti-, Fe-, and Mo-containing solids, (b) comparisons between DDEC6 and experimentally extracted NACs for formamide and natrolite, (c) comparisons of accuracy of different NAC methods for reproducing the electrostatic potential surrounding a material across one and multiple system conformations, (d) comparisons between calculated and chemically expected electron transfer trends for atoms in numerous dense solids, solid surfaces, and molecules, (e) an assessment of NAC transferability between three crystal phases of the diisopropylammonium bromide organic ferroelectric, and (f) comparisons between DDEC6 and polarized neutron diffraction atomic spin moments for the Mn 12 -acetate single-molecule magnet. We find the DDEC6 NACs are ideally suited for constructing flexible force-fields and give reasonable agreement with force-fields commonly used to simulate biomolecules and water. We find the DDEC6 method is more accurate than the DDEC3 method for analyzing a broad range of materials. This broad applicability to periodic and non-periodic materials irrespective of the basis set type makes the DDEC6 method suited for use as a default atomic population analysis method in quantum chemistry programs. † Electronic supplementary information (ESI) available: Tables listing spectroscopically measured core electron energies and Bader, CM5, DDEC3, DDEC6, HD NACs for Ti-and Mo-containing solids; plot comparing DDEC6 to DDEC3 NACs for 14 systems comprised almost entirely of surface atoms; DDEC6 and DDEC3 NACs for Mo 2 C(110) surface with K adatom and NaF (001) surface; DDEC6 and DDEC3 NACs, atomic dipoles, and atomic quadrupoles for SrTiO 3 (100) surface and bulk crystal; DDEC6, DDEC3, Bader, and IH NACs for NaF and SrTiO 3 bulk crystals; xyz les (which can be read using any text editor or the free Jmol visualization program downloadable from jmol.sourceforge.net) containing geometries, NACs, atomic dipoles and quadrupoles, tted tail decay exponents, and ASMs. See

show abstract

“…In aqueous solution, DNA is heavily hydrated and it seems that its interaction with water largely determines its conformation, stability, and ligand binding properties 10–14. According to crystallography and NMR spectroscopy, the state of water is very different in the minor and major DNA grooves of AT‐rich sequences: in the minor groove water is arranged regularly, forming an extended well‐ordered cooperative spine 15–21. The anomalously high hydration of AT‐rich sequences was shown also by measuring ultrasonic velocities 22.…”

Section: Introductionmentioning

confidence: 99%

DNA hydration studied by pressure perturbation scanning microcalorimetry

2008

View full text Add to dashboard Cite

Pressure perturbation differential scanning calorimetry was used to determine thermal expansion coefficients and thus temperature-induced volume changes of DNA duplexes differing in their GC/AT content. It was shown that the temperature-induced unfolding of the DNA duplexes proceeds with a significant increase of the thermal expansion coefficient and the partial volume of the DNA. Unusually, large temperature-induced changes in the partial volume were observed for an AT-rich dodecamer, a finding consistent with previous crystallographic studies showing the presence of highly ordered water molecules hydrating the minor groove of such duplexes. The data show that the density of this ordered water is substantially higher than that of the bulk water. This ordered water cannot, therefore, be equated to ice at normal pressures but it thermodynamically resembles ice formed at high pressures.

show abstract

Neutron crystallography of B-DNA decamer d(CCATTAATGG)

Cited by 10 publications

References 0 publications

The hydration structure of a Z-DNA hexameric duplex determined by a neutron diffraction technique

The hydration structure of a Z-DNA hexameric duplex determined by a neutron diffraction technique

Introducing DDEC6 atomic population analysis: part 2. Computed results for a wide range of periodic and nonperiodic materials

DNA hydration studied by pressure perturbation scanning microcalorimetry

Contact Info

Product

Resources

About