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This work describes additive transport in DNA molecules due to a self-assembly of complementary single-stranded deoxyribonucleic acid chains, i.e. DNA hybridization. Charge transport properties in the DNA junctions at the single molecule level were studied experimentally by the break junction technique in an aqueous environment and theoretically including a non-equilibrium Green's function approach within the density functional based tight-binding method and molecular orbital calculations using density functional method and molecular dynamics simulations. Two types of anchoring groups, namely, amino and thiolate moieties were used to connect the single-stranded DNA (anchor-linker-3′-GGCACTCGG-5′-linker-anchor) to gold electrodes. Double-stranded DNA junctions were prepared by hybridization of single-stranded DNA with a complementary oligonucleotide chain (5′-CCGTGAGCC-3′) not containing linkers and anchoring groups. Three stable junction configurations were observed for both single-stranded and double-stranded DNA irrespective of the anchoring group, whereas junction conductance almost doubled upon DNA hybridization. Thiolate anchoring led to more robust and longer junction configurations compared to NH2 groups. Reasons for the observed conductance enhancement and the anchoring group effect on the overall conductance are being discussed. [ABSTRACT FROM AUTHOR]

Byline: James. Annkah, Ivan. Rosenberg, Naina. Hindocha, Syed. Moinuddin, Kate. Ricketts, Abiodun. Adeyemi, Gary. Royle The dosimetric accuracies of CATPhan 504 and CIRS 062 have been evaluated using the kV-CBCT [...]

Cellular 5′‐nucleotidases, enzymes regulating nucleotide/nucleoside pools, are capable of dephosphorylating phosphomonoesters of important nucleoside analogue drugs, thus decreasing their therapeutic efficacy. Human cytosolic (cdN) as well as mitochondrial (mdN) variants of this enzyme represent interesting targets for development of inhibitory compounds. In this work, bisphosphonate nucleoside derivatives were designed by using a structure‐based approach. A second phosphonate group was attached onto a base moiety and by optimization of the linker an increased inhibitor potency towards mdN and cdN was attained. The best compound exhibited inhibition of both enzymes in a nanomolar range, making it the most potent inhibitor of these enzymes prepared to date. In addition, the compounds showed selectivity towards the cdN variant. A series of crystal structures were solved for several inhibitors in the complex with mdN or cdN that provided a structural basis for understanding the inhibition profile of bisphosphonate compounds. By using a structure‐based approach, bisphosphonate nucleoside derivatives have been designed that act as potent inhibitors of human cytosolic and mitochondrial 5′‐nucleotidases. [ABSTRACT FROM AUTHOR]

Suitably protected (R)‐ and (S)‐HPEP {9‐[3‐hydroxy‐2‐(phosphonoethoxy)propyl]} derivatives containing adenine and thymine nucleobases were prepared as monomers for the introduction of acyclic nucleotide units into oligonucleotides. The solid phase synthesis of a series of ribo and 2′‐deoxyribo nonamers containing (R)‐HPEP and (S)‐HPEP units was successfully performed in both 5′ → 3′ and 3′ → 5′ directions. The measurement of thermal characteristics of the complexes of modified nonamers with complementary DNA and RNA strands revealed a general destabilizing effect of the introduced acyclic units on the thermal stability, but in several cases [modif.RNA*RNA and modif.DNA*RNA with (S)‐HPEPA units], the duplexes were characterized in terms of Tm values. A solid‐phase synthesis afforded a series of ribo and 2′‐deoxyribo nonamers containing acyclic nucleotide units. A general destabilizing effect of the introduced acyclic units on the thermal stability of complexes of modified nonamers with the complementary DNA and RNA strands was observed, but in cases with (S)‐HPEPA units, the duplexes were characterized in terms of Tm values. [ABSTRACT FROM AUTHOR]

We report on a new analogue of locked cyclohexane nucleic acids that contains an adenine nucleobase at an alternative position and which resembles homo-DNA. The crucial locked carbocyclic nucleoside monomer was prepared with high enantioselectivity and was subsequently incorporated into a pair of modified oligonucleotides that were subjected to hybridization studies. [ABSTRACT FROM AUTHOR]

Taurine (2-aminoethanesulfonic acid) is a representative substructure in biologically active compounds, but can raise difficulties in direct coupling reactions. In this study, the synthesis of taurine-derived sulfonic acids and analogous aromatic sulfonic acids was accomplished by a performic acid promoted oxidation of corresponding symmetrical disulfide precursors. In some of the products, the taurine or sulfanilic acid nitrogen atom is incorporated in a heterocyclic scaffold or part of a peptide bond in dipeptide mimetics. [ABSTRACT FROM AUTHOR]

We have developed a simple system for the analysis of the affinity of anti-bromodeoxyuridine antibodies. The system is based on the anchored oligonucleotides containing 5-bromo-2'-deoxyuridine (BrdU) at three different positions. It allows a reliable estimation of the reactivity of particular clones of monoclonal anti-bromodeoxyuridine antibodies with BrdU in fixed and permeabilized cells. Using oligonucleotide probes and four different protocols for the detection of BrdU incorporated in cellular DNA, we identified two antibody clones that evinced sufficient reactivity to BrdU in all the tested protocols. One of these clones exhibited higher reactivity to 5-iodo-2'-deoxyuridine (IdU) than to BrdU. It allowed us to increase the sensitivity of the used protocols without a negative effect on the cell physiology as the cytotoxicity of IdU was comparable with BrdU and negligible when compared to 5-ethynyl-2'-deoxyuridine. The combination of IdU and the improved protocol for oxidative degradation of DNA provided a sensitive and reliable approach for the situations when the low degradation of DNA and high BrdU signal is a priority. [ABSTRACT FROM AUTHOR]

A new potential quality assurance (QA) method is explored (including assessment of depth dose, dose linearity, dose rate linearity and beam profile) for clinical electron beams based on imaging Cerenkov light. The potential of using a standard commercial camera to image Cerenkov light generated from electrons in water for fast QA measurement of a clinical electron beam was explored and compared to ionization chamber measurements. The new method was found to be linear with dose and independent of dose rate (to within 3%). The uncorrected practical range measured in Cerenkov images was found to overestimate the actual value by 3 mm in the worst case. The field size measurements underestimated the dose at the edges by 5% without applying any correction factor. Still, the measured field size could be used to monitor relative changes in the beam profile. Finally, the beam-direction profile measurements were independent of the field size within 2%. A simulation was also performed of the deposited energy and of Cerenkov production in water using GEANT4. Monte Carlo simulation was used to predict the measured light distribution around the water phantom, to reproduce Cerenkov images and to find the relation between deposited energy and Cerenkov production. The camera was modelled as a pinhole camera in GEANT4, to attempt to reproduce Cerenkov images. Simulations of the deposited energy and the Cerenkov light production agreed with each other for a pencil beam of electrons, while for a realistic field size, Cerenkov production in the build-up region overestimated the dose by +8%. [ABSTRACT FROM AUTHOR]

A new method of the light microscopy detection of BrdU-labeled DNA in situ is described. It is based on the oxidative attack at the deoxyribose moiety by copper(I) in the presence of oxygen, which leads to the abstraction of hydrogen atom from deoxyribose culminating in the elimination of the nucleobase, scission of the nucleic-acid strand and formation of frequent gaps. The gaps allow the reaction of the antibodies with the commonly used markers of replication (e.g. 5-bromo-29- deoxyuridine), which are otherwise masked. The method developed makes it possible to detect nuclear and mitochondrial DNA replication efficiently. In most cases, it does not inhibit effective protein detections and in addition enables simultaneous localization of newly-synthesized RNA. The alternative presently-used methods result in protein denaturation and/or extensive DNA cleavage followed by the DNA-bound proteins peeling off. [ABSTRACT FROM AUTHOR]

5-Bromo-2'-deoxyuridine (BrdU) and 2'-deoxy-5-ethynyluridine (EdU) are widely used as markers of replicated DNA. While BrdU is detected using antibodies, the click reaction typically with fluorescent azido-dyes is used for EdU localisation. We have performed an analysis of ten samples of antibodies against BrdU with respect to their reactivity with EdU. Except for one sample all the others evinced reactivity with EdU. A high level of EdU persists in nuclear DNA even after the reaction of EdU with fluorescent azido-dyes if the common concentration of dye is used. Although a ten-time increase of azido-dye concentration resulted in a decrease of the signal provided by anti-BrdU antibodies, it also resulted in a substantial increase of the non-specific signal. We have shown that this unwanted reactivity is effectively suppressed by non-fluorescent azido molecules. In this respect, we have tested two protocols of the simultaneous localisation of incorporated BrdU and EdU. They differ in the mechanism of the revelation of incorporated BrdU for the reaction with antibodies. The first one was based on the use of hydrochloric acid, the second one on the incubation of samples with copper(I) ions. The use of hydrochloric acid resulted in a significant increase of the non-specific signal. In the case of the second method, no such effect was observed. [ABSTRACT FROM AUTHOR]

INTRODUCTION Intensity-modulated radiotherapy (IMRT) improves planning target volume (PTV) coverage and organ at risk (OAR) avoidance in the brain compared to three-dimensional conformal radiotherapy (3-D CRT). However, IMRT is time consuming with considerable resource implications. Volumetric modulated arc therapy (VMAT) offers a quicker method of delivering an IMRT plan and requires less monitor units. Planning studies have shown VMAT compares well to IMRT in the brain but there is little data regarding clinical experience, particularly in fractionated schedules. METHODS Prospectively collected data (treatment details, delivery parameters, dosimetry, time, toxicity, and quality assurance) from the first 10 patients treated with RapidArc (a VMAT product) for brain tumors at our institution was analyzed in an observational study to establish whether the theoretical advantages of VMAT in the treatment of brain tumors translate into clinical practice. RESULTS Patients were selected for RapidArc due to the proximity of PTV to OAR and complex geometric tumor volumes. These included a range of tumor sites, histology, treatment volumes, and dose schedules. In all cases the PTV received >95% prescribed dose and dose to OAR was within tolerance. One patient required a second noncoplanar arc. Quality assurance parameters were easily met. Treatment time and monitor units were approximately half that taken to deliver IMRT. Patients tolerated treatment well and experienced minimal alopecia. CONCLUSION In practice RapidArc provides excellent radiotherapy plan conformity for a wide range of brain tumors with reduced treatment times and monitor units compared to IMRT. Our experience suggests patients treated with RapidArc may suffer minimal alopecia. [ABSTRACT FROM AUTHOR]