Dr Timothy D. Craggs
Department of Chemistry
Senior Lecturer in Biological Chemistry and Departmental Director of R&I
t.craggs@sheffield.ac.uk
+44 114 222 9347
+44 114 222 9347
Dainton Building
Full contact details
Dr Timothy D. Craggs
Department of Chemistry
Dainton Building
13 Brook Hill
Sheffield
S3 7HF
Department of Chemistry
Dainton Building
13 Brook Hill
Sheffield
S3 7HF
- Profile
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Dr Tim Craggs obtained his MSci in Chemistry from the University of Cambridge in 2002. After his PhD (Cambridge 2007) and a postdoc in St Andrews, he took up a Lindemann Fellowship at Yale University (2010), followed by senior postdoc positions at Oxford (Kapanidis Lab) and Bristol (Dillingham Lab). In 2016 he was appointed to a Lectureship in Chemical Biology at the University of Sheffield.
- Research interests
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Research Keywords: Single Molecule Spectroscopy
Single-molecule approaches provide unprecedented detail to the understanding of essential biological processes, as was recognized in the awarding of the 2014 Nobel Prize for Chemistry. Their unique advantage stems from the ability to go beyond the ensemble- and time-averaging of common biochemical techniques, enabling the identification and interpretation of asynchronous reactions, transient states, and rare sub-species.
Research in the Craggs Lab involves the development and application of single-molecule fluorescence techniques to addressing crucial questions across physics, chemistry and the life sciences.
Recent work has focussed on the development and application of single-molecule fluorescence resonance energy transfer (smFRET – a molecular ruler for the 30-90 Å scale) to questions of protein folding, and DNA transcription, replication and repair. These methods are capable of observing individual molecules and molecular interactions in real time, and understanding their dynamics.
In addition to this mechanistic work, we have shown we can use smFRET to measure absolute distances with angstrom accuracy, opening the door to FRET driven structural biology.
- Publications
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Journal articles
- Alternative boronic acids in the detection of Mycolactone A/B using the thin layer chromatography (f-TLC) method for diagnosis of Buruli ulcer. BMC Infectious Diseases, 23. View this article in WRRO
- Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins. Nature Methods, 20, 523-535.
- DNA damage competes with sequence to pin a plectoneme. Biophysical Journal, 122(3), 214a-214a.
- From single-molecule to synchrotron: New tools for investigating the molecular mechanisms of aberrant DNA diseases. Biophysical Journal, 122(3), 19a-20a.
- Multimodal single-molecule microscopy with continuously controlled spectral resolution (CoCoS). Biophysical Journal, 121(3), 301a-301a.
- Direct observation of folded human telomeric i-motif at neutral pH by single-molecule FRET. Biophysical Journal, 121(3), 171a-171a.
- A novel single molecule fluorescence quenching technique for measuring distances below 3 nm. Biophysical Journal, 121(3), 431a-431a.
- The Rate-limiting Step of DNA Synthesis by DNA Polymerase Occurs in the Fingers-closed Conformation. Journal of Molecular Biology, 434(2).
- The stringent response inhibits 70S ribosome formation in Staphylococcus aureus by impeding GTPase-ribosome interactions. mBio, 12(6). View this article in WRRO
- Multimodal single-molecule microscopy with continuously controlled spectral resolution. Biophysical Reports, 1(1). View this article in WRRO
- Combinefluent: An Open Source, Low-Cost Laser System for Single-Molecule Microscopy. Biophysical Journal, 120(3), 184a-184a.
- The smfBox is an open-source platform for single-molecule FRET. Nature Communications, 11(1).
- Synthesis of oligodeoxyribonucleotides containing a tricyclic thio analogue of O6-methylguanine and their recognition by MGMT and Atl1. Nucleosides, Nucleotides & Nucleic Acids. View this article in WRRO
- Below the FRET Limit: A New Quantitative Single-Molecule Tool for Measuring Short-Range (0-3 NM) Biomolecular Conformations. Biophysical Journal, 118(3), 615a-615a.
- Democratizing Single-Molecule FRET: An Open-Source Microscope for Measuring Precise Distances and Biomolecular Dynamics. Biophysical Journal, 118(3), 614a-614a.
- Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase. Nucleic Acids Research, 47(20), 10788-10800.
- DNA replication initiation in Bacillus subtilis: structural and functional characterization of the essential DnaA–DnaD interaction. Nucleic Acids Research, 47(4), 2101-2112.
- Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study. Nature Methods, 15(9), 669-676. View this article in WRRO
- Regional conformational flexibility couples substrate specificity and scissile phosphate diester selectivity in human flap endonuclease 1. Nucleic Acids Research, 46(11), 5618-5633. View this article in WRRO
- Publisher Correction: Precision and accuracy of single-molecule
FRET measurements—a multi-laboratory benchmark study. Nature Methods, 15(11), 984-984.
- The structural basis for dynamic DNA binding and bridging interactions which condense the bacterial centromere. eLife, 6. View this article in WRRO
- Cool and dynamic: single-molecule fluorescence-based structural biology. Nature Methods, 14(2), 123-124.
- DNA Polymerase Conformational Dynamics and the Role of Fidelity-Conferring Residues: Insights from Computational Simulations. Frontiers in Molecular Biosciences, 3. View this article in WRRO
- Membraneless organelles can melt nucleic acid duplexes and act as biomolecular filters. Nature Chemistry, 8(6), 569-575.
- DNA and Protein Requirements for Substrate Conformational Changes Necessary for Human Flap Endonuclease-1-catalyzed Reaction. Journal of Biological Chemistry, 291(15), 8258-8268. View this article in WRRO
- Real-time single-molecule studies of the motions of DNA polymerase fingers illuminate DNA synthesis mechanisms. Nucleic Acids Research, 43(12), 5998-6008.
- Phase Transition of a Disordered Nuage Protein Generates Environmentally Responsive Membraneless Organelles. Molecular Cell, 57(5), 936-947.
- Functional Studies of DNA-Protein Interactions Using FRET Techniques, 115-141.
- Additions and corrections published 30th October 2013 to 15th July 2014. Chemical Society Reviews, 43(17), 6470-6470.
- Single-molecule characterization of Fen1 and Fen1/PCNA complexes acting on flap substrates. Nucleic Acids Research, 42(3), 1857-1872. View this article in WRRO
- A Novel FRET-Based Structure of DNA Polymerase Complexed with Kinked Gapped-DNA. Biophysical Journal, 106(2), 274a-274a.
- Alternating-laser excitation: single-molecule FRET and beyond (vol 43, pg 1156, 2014). CHEMICAL SOCIETY REVIEWS, 43(17), 6472-6472.
- The Transcription Bubble of the RNA Polymerase–Promoter Open Complex Exhibits Conformational Heterogeneity and Millisecond-Scale Dynamics: Implications for Transcription Start-Site Selection. Journal of Molecular Biology, 425(5), 875-885.
- Conformational landscapes of DNA polymerase I and mutator derivatives establish fidelity checkpoints for nucleotide insertion. Nature Communications, 4(1). View this article in WRRO
- Six steps closer to FRET-driven structural biology. Nature Methods, 9(12), 1157-1158.
- PCNA and XPF cooperate to distort DNA substrates. Nucleic Acids Research, 38(5), 1664-1675. View this article in WRRO
- ChemInform Abstract: Green Fluorescent Protein: Structure, Folding and Chromophore Maturation. ChemInform, 41(3).
- Green fluorescent protein: structure, folding and chromophore maturation. Chemical Society Reviews, 38(10), 2865-2865.
- Functional Studies of DNA-Protein Interactions Using FRET Techniques, 475-502.
- Evidence of an Intermediate and Parallel Pathways in Protein Unfolding from Single-Molecule Fluorescence. Journal of the American Chemical Society, 130(25), 7898-7907.
- Spin Relaxation Effects in Photochemically Induced Dynamic Nuclear Polarization Spectroscopy of Nuclei with Strongly Anisotropic Hyperfine Couplings. Journal of the American Chemical Society, 129(29), 9004-9013.
- Stable Intermediate States and High Energy Barriers in the Unfolding of GFP. Journal of Molecular Biology, 370(2), 356-371.
- Understanding the folding of GFP using biophysical techniques. Expert Review of Proteomics, 3(5), 545-559.
- 19F NMR Studies of the Native and Denatured States of Green Fluorescent Protein. Journal of the American Chemical Society, 128(33), 10729-10737.
- High-Force Application by a Nanoscale DNA Force Spectrometer. ACS Nano.
- Making Precise and Accurate Single-Molecule FRET Measurements using the Open-Source smfBox. Journal of Visualized Experiments(173).
- FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. eLife, 10.
- DNA replication initiation in Bacillus subtilis; Structural and functional characterisation of the essential DnaA-DnaD interaction.
- Substrate conformational dynamics drive structure-specific recognition of gapped DNA by DNA polymerase.
- The C-terminal domain of ParB is critical for dynamic DNA binding and bridging interactions which condense the bacterial centromere.
- Alternating-laser excitation: single-molecule FRET and beyond. Chem. Soc. Rev., 43(4), 1156-1171.
- The FRET-based structural dynamics challenge -- community contributions
to consistent and open science practices. View this article in WRRO
- The smfBox: an open-source platform for single-molecule FRET.
- CHARMM-DYES: Parameterization of fluorescent dyes for use with the CHARMM force field. Journal of Chemical Theory and Computation.
Conference proceedings papers
- The Conformational Landscape of SMC: A FRET Study. Biophysical Journal, Vol. 114(3) (pp 209a-209a)
- How Structure-Specific DNA-Binding Proteins Recognise their Substrates. Biophysical Journal, Vol. 110(3) (pp 514a-515a)
- A Novel FRET-Based Structure of DNA Polymerase Complexed with Kinked Gapped-DNA. BIOPHYSICAL JOURNAL, Vol. 106(2) (pp 273A-273A)
- YFP unfolding kinetics studied in a single-molecule nano-flow cell. BIOPHYSICAL JOURNAL (pp 660A-660A)
Preprints
- Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins, Cold Spring Harbor Laboratory.
- An Open-source, Cost-Efficient Excitation Module for Single-molecule Microscopy, Cold Spring Harbor Laboratory.
- (p)ppGpp inhibits 70S ribosome formation in Staphylococcus aureus by impeding GTPase-ribosome interactions.
- Multi-modal Single-molecule Imaging with Continuously Controlled Spectral-resolution (CoCoS) Microscopy.
- Alternative boronic acids in the detection of Mycolactone A/B using the thin layer chromatography (f-TLC) method for diagnosis of Buruli ulcer. BMC Infectious Diseases, 23. View this article in WRRO
- Teaching interests
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Biological Chemistry
- Teaching activities
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Undergraduate and postgraduate taught modules
- An Introduction to Biology for Physical Scientists (Level 1)
This unit provides a basic knowledge and understanding of the occurrence, structure and function of important types of biopolymers such as proteins and nucleic acids, their organisation into biomaterials and their function in living systems. - Biopolymers and Biomaterials (Post-graduate Level)
This course explores the occurrence, structure and function of important types of biopolymers such as proteins and nucleic acids, their organisation into biomaterials and their function in living systems.
Support Teaching:
- Level 3 Literature Review
Laboratory Teaching:
- Level 2 Organic Laboratories
- Level 3 Research Project
- Level 4 Research Project
- An Introduction to Biology for Physical Scientists (Level 1)