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Tytgat O, Fauvart M, Stakenborg T, Deforce D, Van Nieuwerburgh F. STRide probes: Single-labeled short tandem repeat identification probes. Biosens Bioelectron 2021; 180:113135. [PMID: 33690100 DOI: 10.1016/j.bios.2021.113135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/19/2021] [Accepted: 03/01/2021] [Indexed: 11/16/2022]
Abstract
The demand for forensic DNA profiling at the crime scene or at police stations is increasing. DNA profiling is currently performed in specialized laboratories by PCR amplification of Short Tandem Repeats (STR) followed by amplicon sizing using capillary electrophoresis. The need for bulky equipment to identify alleles after PCR presents a challenge for shifting to a decentralized workflow. We devised a novel hybridization-based STR-genotyping method, using Short Tandem Repeat Identification (STRide) probes, which could help tackle this issue. STRide probes are fluorescently labeled oligonucleotides that rely on the quenching properties of guanine on fluorescein derivatives. Mismatches between STRide probes and amplicons can be detected by melting curve analysis after asymmetric PCR. The functionality of the STRide probes was demonstrated by analyzing synthetic DNA samples for the D16S539 locus. Next, STRide probes were developed for five different CODIS core loci (D16S539, TH01, TPOX, FGA, and D7S820). These probes were validated by analyzing 13 human DNA samples. Successful genotyping was obtained using inputs as low as 31 pg of DNA, demonstrating high sensitivity. The STRide probes are ideally suited to be implemented in a microarray and present an important step towards a portable device for fast on-site forensic DNA fingerprinting.
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Affiliation(s)
- Olivier Tytgat
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, Gent, 9000, Belgium; Imec, Kapeldreef 75, Leuven, 3001, Belgium
| | | | | | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, Gent, 9000, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, Gent, 9000, Belgium.
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2
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Advances in Directly Amplifying Nucleic Acids from Complex Samples. BIOSENSORS-BASEL 2019; 9:bios9040117. [PMID: 31574959 PMCID: PMC6955841 DOI: 10.3390/bios9040117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/23/2019] [Accepted: 09/26/2019] [Indexed: 12/15/2022]
Abstract
Advances in nucleic acid amplification technologies have revolutionized diagnostics for systemic, inherited, and infectious diseases. Current assays and platforms, however, often require lengthy experimental procedures and multiple instruments to remove contaminants and inhibitors from clinically-relevant, complex samples. This requirement of sample preparation has been a bottleneck for using nucleic acid amplification tests (NAATs) at the point of care (POC), though advances in “lab-on-chip” platforms that integrate sample preparation and NAATs have made great strides in this space. Alternatively, direct NAATs—techniques that minimize or even bypass sample preparation—present promising strategies for developing POC diagnostic tools for analyzing real-world samples. In this review, we discuss the current status of direct NAATs. Specifically, we surveyed potential testing systems published from 1989 to 2017, and analyzed their performances in terms of robustness, sensitivity, clinical relevance, and suitability for POC diagnostics. We introduce bubble plots to facilitate our analysis, as bubble plots enable effective visualization of the performances of these direct NAATs. Through our review, we hope to initiate an in-depth examination of direct NAATs and their potential for realizing POC diagnostics, and ultimately transformative technologies that can further enhance healthcare.
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Cornelis S, Tytgat O, Fauvart M, Gansemans Y, Vander Plaetsen AS, Wiederkehr RS, Deforce D, Van Nieuwerburgh F, Stakenborg T. Silicon µPCR Chip for Forensic STR Profiling with Hybeacon Probe Melting Curves. Sci Rep 2019; 9:7341. [PMID: 31089203 PMCID: PMC6517373 DOI: 10.1038/s41598-019-43946-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/01/2019] [Indexed: 11/09/2022] Open
Abstract
The demand to perform forensic DNA profiling outside of centralized laboratories and on the crime scene is increasing. Several criminal investigations would benefit tremendously from having DNA based information available in the first hours rather than days or weeks. However, due to the complexity and time-consuming nature of standard DNA fingerprinting methods, rapid and automated analyses are hard to achieve. We here demonstrate the implementation of an alternative DNA fingerprinting method in a single microchip. By combining PCR amplification and HyBeacon melting assays in a silicon Lab-on-a-chip (LoC), a significant step towards rapid on-site DNA fingerprinting is taken. The small form factor of a LoC reduces reagent consumption and increases portability. Additional miniaturization is achieved through an integrated heating element covering 24 parallel micro-reactors with a reaction volume of 0.14 µl each. The high level of parallelization allows the simultaneous analysis of 4 short tandem repeat (STR) loci and the amelogenin gender marker commonly included in forensic DNA analysis. A reference and crime scene sample can be analyzed simultaneously for direct comparison. Importantly, by using industry-standard semiconductor manufacturing processes, mass manufacturability can be guaranteed. Following assay design and optimization, complete 5-loci profiles could be robustly generated on-chip that are on par with those obtained using conventional benchtop real-time PCR thermal cyclers. Together, our results are an important step towards the development of commercial, mass-produced, portable devices for on-site testing in forensic DNA analysis.
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Affiliation(s)
- Senne Cornelis
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Gent, Belgium
- Department of Life Science Technologies, Imec, 3001, Leuven, Belgium
| | - Olivier Tytgat
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Gent, Belgium
- Department of Life Science Technologies, Imec, 3001, Leuven, Belgium
| | - Maarten Fauvart
- Department of Life Science Technologies, Imec, 3001, Leuven, Belgium
| | - Yannick Gansemans
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Gent, Belgium
| | | | | | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Gent, Belgium.
| | | | - Tim Stakenborg
- Department of Life Science Technologies, Imec, 3001, Leuven, Belgium
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Qiu J, Wilson A, El-Sagheer AH, Brown T. Combination probes with intercalating anchors and proximal fluorophores for DNA and RNA detection. Nucleic Acids Res 2016; 44:e138. [PMID: 27369379 PMCID: PMC5041472 DOI: 10.1093/nar/gkw579] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 06/16/2016] [Indexed: 12/20/2022] Open
Abstract
A new class of modified oligonucleotides (combination probes) has been designed and synthesised for use in genetic analysis and RNA detection. Their chemical structure combines an intercalating anchor with a reporter fluorophore on the same thymine nucleobase. The intercalator (thiazole orange or benzothiazole orange) provides an anchor, which upon hybridisation of the probe to its target becomes fluorescent and simultaneously stabilizes the duplex. The anchor is able to communicate via FRET to a proximal reporter dye (e.g. ROX, HEX, ATTO647N, FAM) whose fluorescence signal can be monitored on a range of analytical devices. Direct excitation of the reporter dye provides an alternative signalling mechanism. In both signalling modes, fluorescence in the unhybridised probe is switched off by collisional quenching between adjacent intercalator and reporter dyes. Single nucleotide polymorphisms in DNA and RNA targets are identified by differences in the duplex melting temperature, and the use of short hybridization probes, made possible by the stabilisation provided by the intercalator, enhances mismatch discrimination. Unlike other fluorogenic probe systems, placing the fluorophore and quencher on the same nucleobase facilitates the design of short probes containing multiple modifications. The ability to detect both DNA and RNA sequences suggests applications in cellular imaging and diagnostics.
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Affiliation(s)
- Jieqiong Qiu
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Adam Wilson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez, 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
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Romsos EL, Vallone PM. Rapid PCR of STR markers: Applications to human identification. Forensic Sci Int Genet 2015; 18:90-9. [DOI: 10.1016/j.fsigen.2015.04.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 04/03/2015] [Accepted: 04/21/2015] [Indexed: 10/23/2022]
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Papadopoulou E, Gale N, Goodchild SA, Cleary DW, Weller SA, Brown T, Bartlett PN. Strain discrimination of Yersinia pestis using a SERS-based electrochemically driven melting curve analysis of variable number tandem repeat sequences. Chem Sci 2015; 6:1846-1852. [PMID: 29449917 PMCID: PMC5701729 DOI: 10.1039/c4sc03084b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/23/2014] [Indexed: 12/05/2022] Open
Abstract
Strain discrimination within genetically highly similar bacteria is critical for epidemiological studies and forensic applications. An electrochemically driven melting curve analysis monitored by SERS has been utilised to reliably discriminate strains of the bacterial pathogen Yersinia pestis, the causative agent of plague. DNA amplicons containing Variable Number Tandem Repeats (VNTRs) were generated from three strains of Y. pestis: CO92, Harbin 35 and Kim. These amplicons contained a 10 base pair VNTR repeated 6, 5, and 4 times in CO92, Harbin 35 and Kim respectively. The assay also included a blocker oligonucleotide comprising 3 repeats of the 10-mer VNTR sequence. The use of the blocker reduced the effective length of the target sequence available to bind to the surface bound probe and significantly improved the sensitivity of the discrimination. The results were consistent during three replicates that were carried out on different days, using different batches of PCR product and different SERS sphere segment void (SSV) substrate. This methodology which combines low cost, speed and sensitivity is a promising alternative to the time consuming current electrophoretic methods.
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Affiliation(s)
- E Papadopoulou
- Chemistry , University of Southampton , Highfield , Southampton SO17 1BJ , UK .
| | - N Gale
- ATDBio Ltd , Chemistry , University of Southampton , Highfield , Southampton SO17 1BJ , UK
| | - S A Goodchild
- DSTL , Wiltshire SP4 0JQ , Salisbury , Porton Down , UK
| | - D W Cleary
- DSTL , Wiltshire SP4 0JQ , Salisbury , Porton Down , UK
| | - S A Weller
- DSTL , Wiltshire SP4 0JQ , Salisbury , Porton Down , UK
| | - T Brown
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , Oxford OX1 3TA , UK
| | - P N Bartlett
- Chemistry , University of Southampton , Highfield , Southampton SO17 1BJ , UK .
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7
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Liu JY. Direct qPCR quantification of unprocessed forensic casework samples. Forensic Sci Int Genet 2014; 11:96-104. [DOI: 10.1016/j.fsigen.2014.03.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Revised: 02/16/2014] [Accepted: 03/02/2014] [Indexed: 11/16/2022]
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8
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Shelbourne M, Brown T, El-Sagheer AH, Brown T. Fast and efficient DNA crosslinking and multiple orthogonal labelling by copper-free click chemistry. Chem Commun (Camb) 2013; 48:11184-6. [PMID: 22892959 DOI: 10.1039/c2cc35084j] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two new dibenzocyclooctyne-thymidine monomers were incorporated into oligonucleotides and crosslinked to azide-labelled complementary strands across the DNA grooves. Equivalent reactions were successful using a (bicyclo[6.1.0]nonyne) alkyne. Oligonucleotides containing internal cyclooctyne and amino groups were simultaneously reacted with azides and NHS esters of different fluorescent dyes to produce functional genetic probes.
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9
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Efficient reverse click labeling of azide oligonucleotides with multiple alkynyl Cy-Dyes applied to the synthesis of HyBeacon probes for genetic analysis. Tetrahedron 2012. [DOI: 10.1016/j.tet.2011.11.041] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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10
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Gale N, Kocalka P, Mardle C, Brown T. PNA HyBeacons for analysis of human mutations related to statin-induced myopathy. ARTIFICIAL DNA, PNA & XNA 2011; 2:79-89. [PMID: 22567191 PMCID: PMC3324338 DOI: 10.4161/adna.18179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Aminoalkyl and alkyne-tagged PNA HyBeacons have been synthesized, labeled with fluorescein via conventional amide bond or triazole formation (click chemistry) and used to detect single nucleotide polymorphisms (SNPs) implicated in statin-induced myopathy. The PNA HyBeacons gave much better mismatch/mutant discrimination than conventional DNA HyBeacons but smaller fluorescence changes on melting.
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Affiliation(s)
- Nittaya Gale
- ATDBio Ltd., School of Chemistry, University of Southampton; Southampton, UK
| | - Petr Kocalka
- School of Chemistry, University of Southampton; Southampton, UK
| | | | - Tom Brown
- School of Chemistry, University of Southampton; Southampton, UK
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11
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Cha YS, Choi SH, Lee JH, Shin SK, Lee SH, Lee SD, Kim SO, Hong SP. Analysis of TPOX short tandem repeat locus with matrix-associated laser desorption/ionization time-of-flight-based restriction fragment mass polymorphism assay. Anal Biochem 2011; 412:79-84. [DOI: 10.1016/j.ab.2011.01.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Revised: 01/12/2011] [Accepted: 01/15/2011] [Indexed: 12/21/2022]
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12
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Hopwood AJ, Hurth C, Yang J, Cai Z, Moran N, Lee-Edghill JG, Nordquist A, Lenigk R, Estes MD, Haley JP, McAlister CR, Chen X, Brooks C, Smith S, Elliott K, Koumi P, Zenhausern F, Tully G. Integrated microfluidic system for rapid forensic DNA analysis: sample collection to DNA profile. Anal Chem 2010; 82:6991-9. [PMID: 20704389 DOI: 10.1021/ac101355r] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We demonstrate a conduit for the delivery of a step change in the DNA analysis process: A fully integrated instrument for the analysis of multiplex short tandem repeat DNA profiles from reference buccal samples is described and is suitable for the processing of such samples within a forensic environment such as a police custody suite or booking office. The instrument is loaded with a DNA processing cartridge which incorporates on-board pumps and valves which direct the delivery of sample and reagents to the various reaction chambers to allow DNA purification, amplification of the DNA by PCR, and collection of the amplified product for delivery to an integral CE chip. The fluorescently labeled product is separated using micro capillary electrophoresis with a resolution of 1.2 base pairs (bp) allowing laser induced fluorescence-based detection of the amplified short tandem repeat fragments and subsequent analysis of data to produce a DNA profile which is compatible with the data format of the UK DNA database. The entire process from taking the sample from a suspect, to database compatible DNA profile production can currently be achieved in less than 4 h. By integrating such an instrument and microfluidic cartridge with the forensic process, we believe it will be possible in the near future to process a DNA sample taken from an individual in police custody and compare the profile with the DNA profiles held on a DNA Database in as little as 3 h.
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Affiliation(s)
- Andrew J Hopwood
- Research and Development, Forensic Science Service, Trident Court 2960 Solihull Parkway, Birmingham Business Park, Birmingham, UK B37 7YN.
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13
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Halpern MD, Ballantyne J. An STR Melt Curve Genotyping Assay for Forensic Analysis Employing an Intercalating Dye Probe FRET*. J Forensic Sci 2010; 56:36-45. [DOI: 10.1111/j.1556-4029.2010.01549.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Corrigan D, Gale N, Brown T, Bartlett P. Analysis of Short Tandem Repeats by Using SERS Monitoring and Electrochemical Melting. Angew Chem Int Ed Engl 2010; 49:5917-20. [DOI: 10.1002/anie.201001389] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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15
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Corrigan D, Gale N, Brown T, Bartlett P. Analysis of Short Tandem Repeats by Using SERS Monitoring and Electrochemical Melting. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001389] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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16
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van Schie RMF, Wadelius M, Kamali F, Daly AK, Manolopoulos VG, de Boer A, Barallon R, Verhoef TI, Kirchheiner J, Haschke-Becher E, Briz M, Rosendaal FR, Redekop WK, Pirmohamed M, Maitland-van der Zee AH. Genotype-guided dosing of coumarin derivatives: the European pharmacogenetics of anticoagulant therapy (EU-PACT) trial design. Pharmacogenomics 2009; 10:1687-95. [DOI: 10.2217/pgs.09.125] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The narrow therapeutic range and wide interpatient variability in dose requirement make anticoagulation response to coumarin derivatives unpredictable. As a result, patients require frequent monitoring to avert adverse effects and maintain therapeutic efficacy. Polymorphisms in VKORC1 and CYP2C9 jointly account for about 40% of the interindividual variability in dose requirements. To date, several pharmacogenetic-guided dosing algorithms for coumarin derivatives, predominately for warfarin, have been developed. However, the potential benefit of these dosing algorithms in terms of their safety and clinical utility has not been adequately investigated in randomized settings. The European Pharmacogenetics of Anticoagulant Therapy (EU-PACT) trial will assess, in a single-blinded and randomized controlled trial with a follow-up period of 3 months, the safety and clinical utility of genotype-guided dosing in daily practice for the three main coumarin derivatives used in Europe. The primary outcome measure is the percentage time in the therapeutic range for international normalized ratio. This report describes the design and protocol for the trial.
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Affiliation(s)
| | | | | | - Ann K Daly
- Newcastle University, Newcastle upon Tyne, UK
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Affiliation(s)
- T. A. Brettell
- Department of Chemical and Physical Sciences, Cedar Crest College, 100 College Drive, Allentown, Pennsylvania 18104-6196
| | - J. M. Butler
- Biochemical Science Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8312
| | - J. R. Almirall
- Department of Chemistry and Biochemistry and International Forensic Research Institute, Florida International University, University Park, Miami, Florida 33199
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