Recognition of abasic sites and single base bulges in DNA by a metalloinsertor

Abasic sites and single base bulges are thermodynamically destabilizing DNA defects that can lead to cancerous transformations if left unrepaired by the cell. Here we discuss the binding properties with abasic sites and single base bulges of Rh(bpy)_2(chrysi)^(3+), a complex previously shown to bind thermodynamically destabilized mismatch sites via metalloinsertion. Photocleavage experiments show that Rh(bpy)_2(chrysi)^(3+) selectively binds abasic sites with affinities of 1−4 × 10^6 M^(−1); specific binding is independent of unpaired base identity but is somewhat contingent on sequence context. Single base bulges are also selectively bound and cleaved, but in this case, the association constants are significantly lower (~10^5 M^(−1)), and the binding is dependent on both unpaired base identity and bulge sequence context. A wide variety of evidence, including strand scission asymmetry, binding enantiospecificity, and MALDI-TOF cleavage fragment analysis, suggests that Rh(bpy)_2(chrysi)^(3+) binds abasic sites, like mismatches, through insertion of the bulky chrysi ligand into the base pair stack from the minor groove side and ejection of the unpaired base. At single base bulge sites, a similar, though not identical, metalloinsertion mode is suggested. The recognition of abasic sites and single base bulges with bulky metalloinsertors holds promise for diagnostic and therapeutic applications

Single-Step Charge Transport through DNA over Long Distances

Quantum yields for charge transport across adenine tracts of increasing length have been measured by monitoring hole transport in synthetic oligonucleotides between photoexcited 2-aminopurine, a fluorescent analogue of adenine, and N_2-cyclopropyl guanine. Using fluorescence quenching, a measure of hole injection, and hole trapping by the cyclopropyl guanine derivative, we separate the individual contributions of single- and multistep channels to DNA charge transport and find that with 7 or 8 intervening adenines the charge transport is a coherent, single-step process. Moreover, a transition occurs from multistep to single-step charge transport with increasing donor/acceptor separation, opposite to that generally observed in molecular wires. These results establish that coherent transport through DNA occurs preferentially across 10 base pairs, favored by delocalization over a full turn of the helix

Metallo-intercalators and metallo-insertors

Since the elucidation of the structure of double helical DNA, the construction of small molecules that recognize and react at specific DNA sites has been an area of considerable interest. In particular, the study of transition metal complexes that bind DNA with specificity has been a burgeoning field. This growth has been due in large part to the useful properties of metal complexes, which possess a wide array of photophysical attributes and allow for the modular assembly of an ensemble of recognition elements. Here we review recent experiments in our laboratory aimed at the design and study of octahedral metal complexes that bind DNA non-covalently and target reactions to specific sites. Emphasis is placed both on the variety of methods employed to confer site-specificity and upon the many applications for these complexes. Particular attention is given to the family of complexes recently designed that target single base mismatches in duplex DNA through metallo-insertion

Performance of a Functionalised Polymer-Coated Silica at Treating Uranium Contaminated Groundwater from a Hungarian Mine Site

The performance of an active material for treating uranium contaminated groundwater within a permeable reactive barrier (PRB) is reported. This material, called PANSIL, has a tailored ligand system that selectively removes the uranyl (UO22+) cation from solution. The active uranyl ligand in PANSIL is a polyacryloamidoxime resin derived from polyacrylonitrile, which is deposited from solution onto the surface of quartz sand to form a thin film coating. PANSIL is effective at sequestering cationic and neutral uranyl species when the solution pH is above 4, due to the stability of the polyacryloamidoxime-uranyl complex formed. However the rate of sequestration decreases rapidly when the pH exceeds about 8 where neutral uranyl species are present only at very low concentrations. It can preferentially sequester UO22+ in the presence of typical divalent groundwater cations. In mildly alkaline conditions the sequestration performance in groundwater is sensitive to the concentration of uranyl complexing ligands, such as bicarbonate. Such behaviour has important consequences for PRB design as it will determine the barrier thickness required to treat a particular groundwater flow rate

A benign, low Z electron capture agent for negative ion TPCs

We have identified nitromethane (CH$_3$NO$_2$) as an effective electron capture agent for negative ion TPCs (NITPCs). We present drift velocity and longitudinal diffusion measurements for negative ion gas mixtures using nitromethane as the capture agent. Not only is nitromethane substantially more benign than the only other identified capture agent, CS$_2$, but its low atomic number will enable the use of the NITPC as a photoelectric X{}-ray polarimeter in the 1{}-10 keV band

Local and Global Casimir Energies for a Semitransparent Cylindrical Shell

The local Casimir energy density and the global Casimir energy for a massless scalar field associated with a $\lambda\delta$-function potential in a 3+1 dimensional circular cylindrical geometry are considered. The global energy is examined for both weak and strong coupling, the latter being the well-studied Dirichlet cylinder case. For weak-coupling,through $\mathcal{O}(\lambda^2)$, the total energy is shown to vanish by both analytic and numerical arguments, based both on Green's-function and zeta-function techniques. Divergences occurring in the calculation are shown to be absorbable by renormalization of physical parameters of the model. The global energy may be obtained by integrating the local energy density only when the latter is supplemented by an energy term residing precisely on the surface of the cylinder. The latter is identified as the integrated local energy density of the cylindrical shell when the latter is physically expanded to have finite thickness. Inside and outside the delta-function shell, the local energy density diverges as the surface of the shell is approached; the divergence is weakest when the conformal stress tensor is used to define the energy density. A real global divergence first occurs in $\mathcal{O}(\lambda^3)$, as anticipated, but the proof is supplied here for the first time; this divergence is entirely associated with the surface energy, and does {\em not} reflect divergences in the local energy density as the surface is approached.Comment: 28 pages, REVTeX, no figures. Appendix added on perturbative divergence

A Note on the Protection of Wooden Beams Exposed to an Acidic, Humid Atmosphere

By means of standard lignin and carbohydrate analyses, together with pH measurements, the cause of strength losses in beams exposed to an acidic, humid atmosphere was shown to be due to acid hydrolysis of wood carbohydrates. It is recommended that wooden beams used in such an acidic environment be adequately finished with a flexible, moisture-proof coating and the finish be inspected and maintained at regular intervals

A Mismatch-Selective Bifunctional Rhodium−Oregon Green Conjugate: A Fluorescent Probe for Mismatched DNA

A fluorescent metallointercalator conjugate that selectively targets DNA base mismatches has been synthesized by coupling an organic fluorophore to a bulky Rh intercalator containing the chrysenequinone diimine ligand. Ion pairing between the cationic Rh and anionic fluorophore moieties dramatically quenches the fluorescence of the conjugate in solution and in the presence of matched DNA. However, in the presence of mismatched DNA, the fluorescence of the conjugate is increased >300%. This increase in fluorescence is attributed to the loss in intramolecular quenching associated with DNA binding; intercalation of the Rh moiety into the mismatched site can lead to electrostatic repulsion of the anionic fluorophore away from the DNA phosphate backbone and Rh. Denaturing PAGE experiments with ^(32)P-labeled oligonucleotides indicate that the conjugate selectively binds the mismatched DNA with a binding affinity of 6 × 10^5 M^(-1) and, upon irradiation, cleaves the DNA backbone neighboring the mismatched site