Anita C. Jones

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Organization: The University of Edinburgh , England

Department: Department of Chemistry

Title: (PhD)

Chemicals
References

A DFT study of 2-aminopurine-containing dinucleotides: prediction of stacked conformations with B-DNA structure

Co-reporter:Darren A. Smith, Leo F. Holroyd, Tanja van Mourik and Anita C. Jones

Physical Chemistry Chemical Physics 2016 vol. 18(Issue 21) pp:14691-14700

Publication Date(Web):11 May 2016

DOI:10.1039/C5CP07816D

The fluorescence properties of dinucleotides incorporating 2-aminopurine (2AP) suggest that the simplest oligonucleotides adopt conformations similar to those found in duplex DNA. However, there is a lack of structural data for these systems. We report a density functional theory (DFT) study of the structures of 2AP-containing dinucleotides (deoxydinucleoside monophosphates), including full geometry optimisation of the sugar-phosphate backbone. Our DFT calculations employ the M06-2X functional for reliable treatment of dispersion interactions and include implicit aqueous solvation. Dinucleotides with 2AP in the 5′-position and each of the natural bases in the 3′-position are examined, together with the analogous 5′-adenine-containing systems. Computed structures are compared in detail with typical B-DNA base-step parameters, backbone torsional angles and sugar pucker, derived from crystallographic data. We find that 2AP-containing dinucleotides adopt structures that closely conform to B-DNA in all characteristic parameters. The structures of 2AP-containing dinucleotides closely resemble those of their adenine-containing counterparts, demonstrating the fidelity of 2AP as a mimic of the natural base. As a first step towards exploring the conformational heterogeneity of dinucleotides, we also characterise an imperfectly stacked conformation and one in which the bases are completely unstacked.

Taking Two-Photon Excitation to Exceptional Path-Lengths in Photonic Crystal Fiber

Co-reporter:Gareth O. S. Williams, Tijmen G. Euser, Jochen Arlt, Philip St.J. Russell, and Anita C. Jones

ACS Photonics 2014 Volume 1(Issue 9) pp:790

Publication Date(Web):August 25, 2014

DOI:10.1021/ph5002236

The well-known, defining feature of two-photon excitation (TPE) is the tight, three-dimensional confinement of excitation at the intense focus of a laser beam. The extremely small excitation volume, on the order of 1 μm3 (1 femtoliter), is the basis of far-reaching applications of TPE in fluorescence imaging, photodynamic therapy, nanofabrication, and three-dimensional optical memory. Paradoxically, the difficulty of detecting photochemical events in such a small volume is a barrier to the development of the two-photon-activated molecular systems that are essential to the realization of such applications. We show, using two-photon-excited fluorescence to directly visualize the excitation path, that confinement of both laser beam and sample solution within the 20 μm hollow core of a photonic crystal fiber permits TPE to be sustained over an extraordinary path-length of more than 10 cm, presenting a new experimental paradigm for ultrasensitive studies of two-photon-induced processes in solution.Keywords: fluorescence; nonlinear optics; optofluidics; photochemistry; two-photon absorption; two-photon cross-section

Photonic crystal fibre as an optofluidic reactor for the measurement of photochemical kinetics with sub-picomole sensitivity

Co-reporter:Gareth O. S. Williams, Jocelyn S. Y. Chen, Tijmen G. Euser, Philip St.J. Russell and Anita C. Jones

Lab on a Chip 2012 vol. 12(Issue 18) pp:3356-3361

Publication Date(Web):06 Jul 2012

DOI:10.1039/C2LC40062F

Photonic crystal fibre constitutes an optofluidic system in which light can be efficiently coupled into a solution-phase sample, contained within the hollow core of the fibre, over long path-lengths. This provides an ideal arrangement for the highly sensitive monitoring of photochemical reactions by absorption spectroscopy. We report here the use of UV/vis spectroscopy to measure the kinetics of the photochemical and thermal cis–trans isomerisation of sub-picomole samples of two azo dyes within the 19-μm diameter core of a photonic crystal fibre, over a path length of 30 cm. Photoisomerisation quantum yields are the first reported for “push–pull” azobenzenes in solution at room temperature; such measurements are challenging because of the fast thermal isomerisation process. Rate constants obtained for thermal isomerisation are in excellent agreement with those established previously in conventional cuvette-based measurements. The high sensitivity afforded by this intra-fibre method enables measurements in solvents in which the dyes are too insoluble to permit conventional cuvette-based measurements. The results presented demonstrate the potential of photonic crystal fibres as optofluidic elements in lab-on-a-chip devices for photochemical applications.

Using the fluorescence decay of 2-aminopurine to investigate conformational change in the recognition sequence of the EcoRV DNA-(adenine-N6)-methyltransferase on enzyme binding

Co-reporter:Eleanor Y.M. Bonnist, Kirsten Liebert, David T.F. Dryden, Albert Jeltsch, Anita C. Jones

Biophysical Chemistry 2012 160(1) pp: 28-34

Publication Date(Web):January 2012

DOI:10.1016/j.bpc.2011.09.001

The EcoRV DNA methyltransferase methylates the first adenine in the GATATC recognition sequence. It is presumed that methylation proceeds by a nucleotide flipping mechanism but no crystal structure is available to confirm this. A popular solution-phase assay for nucleotide flipping employs the fluorescent adenine analogue, 2-aminopurine (2AP), substituted at the methylation target site; a substantial increase in fluorescence intensity on enzyme binding indicates flipping. However, this appeared to fail for M.EcoRV, since 2AP substituted for the non-target adenine in the recognition sequence showed a much greater intensity increase than 2AP at the target site. This anomaly is resolved by recording the fluorescence decay of 2AP which shows that the target 2AP is indeed flipped by the enzyme, but its fluorescence is quenched by interaction with aromatic residues in the catalytic site, whereas bending of the duplex at the non-target site alleviates inter-base quenching and exposes the 2AP to solvent.Highlights► The anomalous response of 2AP intensity to M.EcoRV binding is resolved by measuring the fluorescence decay. ► The fluorescence decay parameters of 2AP report unambiguously and informatively on DNA conformation and the DNA-enzyme interface. ► When M.EcoRV binds to its recognition sequence it induces different local distortions at the two adenine positions. ► The target 2AP is flipped, but its fluorescence is quenched by interaction with aromatic residues in the catalytic site. ► Bending of the duplex at the non-target site alleviates inter-base quenching and exposes the 2AP to solvent.

Optically trapped microsensors for microfluidic temperature measurement by fluorescence lifetime imaging microscopy

Co-reporter:Mathieu A. Bennet, Patricia R. Richardson, Jochen Arlt, Aongus McCarthy, Gerald S. Buller and Anita C. Jones

Lab on a Chip 2011 vol. 11(Issue 22) pp:3821-3828

Publication Date(Web):28 Sep 2011

DOI:10.1039/C1LC20391F

The novel combination of optical tweezers and fluorescence lifetime imaging microscopy (FLIM) has been used, in conjunction with specially developed temperature-sensitive fluorescent microprobes, for the non-invasive measurement of temperature in a microfluidic device. This approach retains the capability of FLIM to deliver quantitative mapping of microfluidic temperature without the disadvantageous need to introduce a fluorescent dye that pervades the entire micofluidic system. This is achieved by encapsulating the temperature-sensitive Rhodamine B fluorophore within a microdroplet which can be held and manipulated in the microfluidic flow using optical tweezers. The microdroplet is a double bubble in which an aqueous droplet of the fluorescent dye is surrounded by an oil shell which serves both to contain the fluorophore and to provide the refractive index differential required for optical trapping of the droplet in an external aqueous medium.

Quantitative mapping of aqueous microfluidic temperature with sub-degree resolution using fluorescence lifetime imaging microscopy

Co-reporter:Emmelyn M. Graham, Kaoru Iwai, Seiichi Uchiyama, A. Prasanna de Silva, Steven W. Magennis and Anita C. Jones

Lab on a Chip 2010 vol. 10(Issue 10) pp:1267-1273

Publication Date(Web):25 Feb 2010

DOI:10.1039/B924151E

The use of a water-soluble, thermo-responsive polymer as a highly sensitive fluorescence-lifetime probe of microfluidic temperature is demonstrated. The fluorescence lifetime of poly(N-isopropylacrylamide) labelled with a benzofurazan fluorophore is shown to have a steep dependence on temperature around the polymer phase transition and the photophysical origin of this response is established. The use of this unusual fluorescent probe in conjunction with fluorescence lifetime imaging microscopy (FLIM) enables the spatial variation of temperature in a microfluidic device to be mapped, on the micron scale, with a resolution of less than 0.1 °C. This represents an increase in temperature resolution of an order of magnitude over that achieved previously by FLIM of temperature-sensitive dyes.

Long-Wavelength Fluorescence from 2-Aminopurine-Nucleobase Dimers in DNA

Co-reporter:Eleanor Y. M. Bonnist Dr.

ChemPhysChem 2008 Volume 9( Issue 8) pp:1121-1129

Publication Date(Web):

DOI:10.1002/cphc.200700813

Abstract

When 2-aminopurine (2AP) is substituted for adenine in DNA, it is widely accepted that its fluorescence spectrum is essentially unchanged from that of the free fluorophore. We show that 2AP in DNA exhibits long-wavelength emission and excitation bands, in addition to the familiar short-wavelength spectra, as a result of formation of a ground-state heterodimer with an adjacent, π-stacked, natural base. The observation of dual emission from 2AP in a variety of oligodeoxynucleotide duplexes and single strands demonstrates the generality of this phenomenon. The photophysical and conformational properties of the long-wavelength-emitting 2AP-nucleobase dimer are examined. Analogous long-wavelength fluorescence is seen when 2AP π-stacks with aromatic amino acid sidechains in the active sites of methyltransferase enzymes during DNA nucleotide flipping.

Cover Picture: Long-Wavelength Fluorescence from 2-Aminopurine-Nucleobase Dimers in DNA (ChemPhysChem 8/2008)

Co-reporter:Eleanor Y. M. Bonnist Dr.

ChemPhysChem 2008 Volume 9( Issue 8) pp:

Publication Date(Web):

DOI:10.1002/cphc.200890030

Structural characterisation of the photoisomers of reactive sulfonated azo dyes by NMR spectroscopy and DFT calculations

Co-reporter:Katrina M. Tait, John A. Parkinson, David I. Gibson, Patricia R. Richardson, Warren J. Ebenezer, Michael G. Hutchings and Anita C. Jones

Photochemical & Photobiological Sciences 2007 vol. 6(Issue 9) pp:1010-1018

Publication Date(Web):20 Apr 2007

DOI:10.1039/B703044D

1H NMR spectroscopy coupled with in situ laser irradiation has been used together with density functional theory (DFT) computation to examine the structures of the photoisomers of a series of sulfonated reactive azo dyes. Assignment of 1H NMR spectra acquired at the photostationary state has allowed, for the first time, NMR characterisation of unstable cis isomers of commercially relevant water-soluble azo dyes. Structural features of the two isomeric forms predicted by DFT calculations are clearly reflected in the experimental NMR data. The trans–cis photoisomerisation process could be unambiguously identified in each case, based on the large chemical shift change observed for resonances associated with aromatic protons adjacent to the azo linkage.

Photophysics and X-ray Structure of Crystalline 2-Aminopurine

Co-reporter:Robert K. Neely Dr.;Steven W. Magennis Dr. Dr.;Simon Parsons Dr.

ChemPhysChem 2007 Volume 8(Issue 7) pp:1095-1102

Publication Date(Web):27 MAR 2007

DOI:10.1002/cphc.200600593

To explore the effect of intermolecular interactions on the photophysics of 2-aminopurine (2AP) in a well-defined environment, we have investigated the fluorescence properties of single 2AP crystals, having determined their X-ray structure. In the crystal, 2AP is subject to base-stacking and hydrogen-bonding interactions similar to those found in DNA. The crystal shows dual fluorescence: π-stacked molecules in the bulk of the lattice have redshifted excitation and emission spectra, while molecules at defect sites have spectra similar to those of 2AP in solution or in DNA. Heterogeneous intermolecular interactions in the crystal give rise to multiexponential fluorescence decay characteristics similar to those observed for 2AP-labelled DNA. The presence of about 13 % of the 7H tautomer in the crystal confirms that 9H–7H tautomerisation of 2AP occurs in the ground state. Long-wavelength excitation of a 2AP-labelled oligonucleotide duplex produced redshifted emission similar to that observed in the crystal, indicating that π-stacking interaction of 2AP with nucleobases gives rise to a low energy excited state.

Quantitative Spatial Mapping of Mixing in Microfluidic Systems

Co-reporter:Steven W. Magennis Dr.;Emmelyn M. Graham Dr.

Angewandte Chemie 2005 Volume 117(Issue 40) pp:

Publication Date(Web):21 SEP 2005

DOI:10.1002/ange.200500558

Das Miniaturisierungsproblem bei Mischprozessen steht Fortschritten auf dem Gebiet der Mikrofluidik im Wege. Durch Fluoreszenzlebensdauer-Imaging sind quantitative Informationen über den Mischpozess in Mikrofluidsystemen zugänglich, die entscheidend für die Entwicklung neuer Bauteile sind. Mithilfe eines gepulsten Lasers (B) wird der Mischprozess in einer Mikrofluidzelle (A) anhand von Fluoreszenz (C) verfolgt; der rechte Bildteil zeigt eine Probe.

Quantitative Spatial Mapping of Mixing in Microfluidic Systems

Co-reporter:Steven W. Magennis, Emmelyn M. Graham,Anita C. Jones

Angewandte Chemie International Edition 2005 44(40) pp:6512-6516

Publication Date(Web):

DOI:10.1002/anie.200500558

The novel use of NMR spectroscopy with in situ laser irradiation to study azo photoisomerisation

Co-reporter:Katrina M Tait, John A Parkinson, Simon P Bates, Warren J Ebenezer, Anita C Jones

Journal of Photochemistry and Photobiology A: Chemistry 2003 Volume 154(2–3) pp:179-188

Publication Date(Web):24 January 2003

DOI:10.1016/S1010-6030(02)00347-7

Cis–trans photoisomerisation of four azo dyes has been studied by nuclear magnetic resonance (NMR) spectroscopy, with in situ laser irradiation of the sample. The laser radiation was coupled into the sample within the NMR magnet via an optical fibre. This enabled the first NMR measurements to be made of the transient cis isomers of 4-(4-nitrophenylazo)aniline (CI Disperse Orange 3) and 4-[N-ethyl-N-(2-hydroxyethyl)amino]-4′-nitroazobenzene (CI Disperse Red 1). Typical NMR methods, including 1D, – 2D COSY and – 2D EXSY/NOESY, were used to assign resonances of the trans and cis isomers. Ab initio calculations were used to predict the chemical shifts of cis- and trans-azobenzene, in good agreement with the experimental results, and to rationalise the chemical shift changes observed on isomerisation.

Observation of a Fluorescent Dimer of a Sulfonated Phthalocyanine

Co-reporter:Warren J. Ebenezer;Neil M. Speirs

Photochemistry and Photobiology 2002 Volume 76(Issue 3) pp:247-251

Publication Date(Web):1 MAY 2007

DOI:10.1562/0031-8655(2002)0760247OOAFDO2.0.CO2

With very few exceptions, phthalocyanine dimers are found to be nonfluorescent. We report here the observation of a fluorescent dimer of a tetrasulfonated copper phthalocyanine in ethanol and water. Fluorescence excitation and emission spectra at room temperature and at 77 K are presented. These are consistent with the conventional model of exciton coupling in a cofacial dimer.

A DFT study of 2-aminopurine-containing dinucleotides: prediction of stacked conformations with B-DNA structure

Co-reporter:Darren A. Smith, Leo F. Holroyd, Tanja van Mourik and Anita C. Jones

Physical Chemistry Chemical Physics 2016 - vol. 18(Issue 21) pp:NaN14700-14700

Publication Date(Web):2016/05/11

DOI:10.1039/C5CP07816D