Long-lived excited-state dynamics of i-motif structures probed by time-resolved infrared spectroscopy

UV-generated excited states of cytosine (C) nucleobases are precursors to mutagenic photoproduct formation. The i-motif formed from C-rich sequences is known to exhibit high yields of long-lived excited states following UV absorption. Here the excited states of several i-motif structures have been characterized following 267 nm laser excitation using time-resolved infrared spectroscopy (TRIR). All structures possess a long-lived excited state of ∼300 ps and notably in some cases decays greater than 1 ns are observed. These unusually long-lived lifetimes are attributed to the interdigitated DNA structure which prevents direct base stacking overlap

On the influence of a translating inner core in models of outer core convection

It has recently been proposed that the hemispheric seismic structure of the inner core can be explained by a self-sustained rigid-body translation of the inner core material, resulting in melting of the solid at the leading face and a compensating crystallisation at the trailing face. This process induces a hemispherical variation in the release of light elements and latent heat at the inner-core boundary, the two main sources of thermochemical buoyancy thought to drive convection in the outer core. However, the effect of a translating inner core on outer core convection is presently unknown. In this paper we model convection in the outer core with a nonmagnetic Boussinesq fluid in a rotating spherical shell driven by purely thermal buoyancy, incorporating the effect of a translating inner core by a time-independent spherical harmonic degree and order 1 (View the MathML sourceY11) pattern of heat-flux imposed at the inner boundary. The analysis considers Rayleigh numbers up to 10 times the critical value for onset of nonmagnetic convection, a parameter regime where the effects of the inhomogeneous boundary condition are expected to be most pronounced, and focuses on varying q∗q∗, the amplitude of the imposed boundary anomalies. The presence of inner boundary anomalies significantly affects the behaviour of the model system. Increasing q∗q∗ leads to flow patterns dominated by azimuthal jets that span large regions of the shell where radial motion is significantly inhibited. Vigorous convection becomes increasingly confined to isolated regions as q∗q∗ increases; these regions do not drift and always occur in the hemisphere subjected to a higher than average boundary heat-flux. Effects of the inner boundary anomalies are visible at the outer boundary in all inhomogeneous models considered. At low q∗q∗ the expression of inner boundary effects at the core surface is a difference in the flow speed between the two hemispheres. As q∗q∗ increases the spiralling azimuthal jets driven from the inner boundary are clearly visible at the outer boundary. Finally, our results suggest that, when the system is heated from below, a View the MathML sourceY11 heat-flux pattern imposed on the inner boundary has a greater overall influence on the spatio-temporal behaviour of the flow than the same pattern imposed at the outer boundary

Conductive three-dimensional material assembled from silver nanoparticles using a conjugated dithiol linker

A regular three-dimensional conductive nanoparticle network of silver particles constructed by linking the particles via a conjugated organic dithiol bridges demonstrates that the electrical conductivity and surface plasmon resonance frequency can be related to the nature of the linkers employed. The regular packing of the particles was not greatly affected by the nature or length of the linkers and appears to be determined largely by the much larger particles, approximately closed-packed with the nonrigid thiol molecules wrapped partially around in a thin corona-like layers. Ultraviolet Visual Spectra recorded the Surface Plasmon (SP) peak for silver nanoparticles in toluene solution that shifts significantly to longer wavelength (ca. 475 nm) on addition of 1,4-benzenedithiol, but no analogous shift in the SP peak was observed on addition of 1,9-nonanedithiol. A density of states approach taking gold clusters as model for the molecular junctions should compare well with other nanoparticles

Principles of sequence-recognition in aromatic polyimides

Pyrene-based molecular tweezers show sequence-specific binding to aromatic polyimides through sterically-controlled donor-acceptor pi-stacking and hydrogen bonding; H-1 NMR spectra of tweezer-complexes with polyimides having different sequence-restrictions show conclusively that the detection of long range sequence-information results from multiple tweezer-binding at adjacent imide residues

Conformational and hydration effects of site-selective sodium, calcium and strontium ion binding to the DNA Holliday junction structure d(TCGGTACCGA)(4)

The role of metal ions in determining the solution conformation of the Holliday junction is well established, but to date the picture of metal ion binding from structural studies of the four-way DNA junction is very incomplete. Here we present two refined structures of the Holliday junction formed by the sequence d(TCGGTACCGA) in the presence of Na+ and Ca2+, and separately with Sr2+ to resolutions of 1.85 Angstrom and 1.65 Angstrom, respectively. This sequence includes the ACC core found to promote spontaneous junction formation, but its structure has not previously been reported. Almost complete hydration spheres can be defined for each metal cation. The Na+ sites, the most convincing observation of such sites in junctions to date, are one on either face of the junction crossover region, and stabilise the ordered hydration inside the junction arms. The four Ca2+ sites in the same structure are at the CG/CG steps in the minor groove. The Sr2+ ions occupy the TC/AG, GG/CC, and TA/TA sites in the minor groove, giving ten positions forming two spines of ions, spiralling through the minor grooves within each arm of the stacked-X structure. The two structures were solved in the two different C2 lattices previously observed, with the Sr2+ derivative crystallising in the more highly symmetrical form with two-fold symmetry at its centre. Both structures show an opening of the minor groove face of the junction of 8.4degrees in the Ca2+ and Na+ containing structure, and 13.4degrees in the Sr2+ containing structure. The crossover angles at the junction are 39.3degrees and 43.3degrees, respectively. In addition to this, a relative shift in the base pair stack alignment of the arms of 2.3 Angstrom is observed for the Sr2+ containing structure only. Overall these results provide an insight into the so-far elusive stabilising ion structure for the DNA Holliday junction. (C) 2003 Elsevier Science Ltd. All rights reserved

Crystal structure of the complementary quadruplex formed by d(GCATGCT) at atomic resolution

Here we report the crystal structure of the DNA heptanucleotide sequence d(GCATGCT) determined to a resolution of 1.1 Angstrom. The sequence folds into a complementary loop structure generating several unusual base pairings and is stabilised through cobalt hexammine and highly defined water sites. The single stranded loop is bound together through the G(N2)-C(O2) intra-strand H-bonds for the available G/C residues, which form further Watson-Crick pairings to a complementary sequence, through 2-fold symmetry, generating a pair of non-planar quadruplexes at the heart of the structure. Further, four adenine residues stack in pairs at one end, H-bonding through their N7-N6 positions, and are additionally stabilised through two highly conserved water positions at the structural terminus. This conformation is achieved through the rotation of the central thymine base at the pinnacle of the loop structure, where it stacks with an adjacent thymine residue within the lattice. The crystal packing yields two halved biological units, each related across a 2-fold symmetry axis spanning a cobalt hexammine residue between them, which stabilises the quadruplex structure through H-bonds to the phosphate oxygens and localised hydration

Crystal structure of (2-pyridinecarboxaldehydeisonicotinoyl-hydrazonato)copper(I) thiocyanate, [Cu(C12H9N4O)]NCS

C13H9CuN5OS, monoclinic, P12(1)/c1 (no. 14), a = 9.900(2) angstrom, b = 11.018(1) angstrom, c = 12.861(2) angstrom, beta = 103.55(1)degrees, V = 1363.8 angstrom(3), Z = 4, R-gt(F) = 0.029, wR(ref)(F-2) = 0.088, T = 150 K

Crystal structure of (isothiocyanato)(2-pyridinecarboxaldehydebenzoylhydrazonato)copper(I),Cu(C13H10N3O)(NCS)

C14H10CuN4OS, monoclinic, P12(1)/nl (no. 14), a = 8.837(1) angstrom, b = 15.625(2) angstrom, c = 10.366(1) angstrom, beta = 103.36(1)degrees, V = 1392.6 angstrom(3), Z = 4, R-gt(F) = 0.029, WRref(F-2) = 0.076, T = 150 K

Recognition of sequence-information in synthetic copolymer chains by a conformationally-constrained tweezer molecule

A novel type of tweezer molecule containing electron-rich 2-pyrenyloxy arms has been designed to exploit intramolecular hydrogen bonding in stabilising a preferred conformation for supramolecular complexation to complementary sequences in aromatic copolyimides. This tweezer-conformation is demonstrated by single-crystal X-ray analyses of the tweezer molecule itself and of its complex with an aromatic diimide model-compound. In terms of its ability to bind selectively to polyimide chains, the new tweezer molecule shows very high sensitivity to sequence effects. Thus, even low concentrations of tweezer relative to diimide units (<2.5 mol%) are sufficient to produce dramatic, sequence-related splittings of the pyromellitimide proton NMR resonances. These induced resonance-shifts arise from ring-current shielding of pyromellitimide protons by the pyrenyloxy arms of the tweezer-molecule, and the magnitude of such shielding is a function of the tweezer-binding constant for any particular monomer sequence. Recognition of both short-range and long-range sequences is observed, the latter arising from cumulative ring-current shielding of diimide protons by tweezer molecules binding at multiple adjacent sites on the copolymer chain

High-resolution crystal structure of the intramolecular d(TpA) thymine-adenine photoadduct and its mechanistic implications

A high-resolution crystal structure is reported for d(TpA)*, the intramolecular thymine-adenine photoadduct that is produced by direct ultraviolet excitation of the dinucleoside monophosphate d(TpA). It confirms the presence of a central 1,3-diazacyclooctatriene ring linking the remnants of the T and A bases, as previously deduced from heteronuclear NMR measurements by Zhao et al. (The structure of d(TpA)*, the major photoproduct of thymidylyl-(3'-5')-deoxyadenosine. Nucleic Acids Res., 1996, 24, 1554-1560). Within the crystal, the d(TpA)* molecules exist as zwitterions with a protonated amidine fragment of the eight-membered ring neutralizing the charge of the internucleotide phosphate monoanion. The absolute configuration at the original thymine C5 and C6 atoms is determined as 5S,6R. This is consistent with d(TpA)* arising by valence isomerization of a precursor cyclobutane photoproduct with cis-syn stereochemistry that is generated by [2 + 2] photoaddition of the thymine 5,6-double bond across the C6 and C5 positions of adenine. This mode of photoaddition should be favoured by the stacked conformation of adjacent T and A bases in B-form DNA. It is probable that the primary photoreaction is mechanistically analogous to pyrimidine dimerization despite having a much lower quantum yield