Dr Timothy D. Craggs

School of Mathematical and Physical Sciences

Senior Lecturer in Biological Chemistry

t.craggs@sheffield.ac.uk
+44 114 222 9347

Dainton Building

Full contact details

Dr Timothy D. Craggs
School of Mathematical and Physical Sciences
Dainton Building
13 Brook Hill
Sheffield
S3 7HF

Profile: 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

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

Journal articles

Akolgo GA, Partridge BM, D. Craggs T & Amewu RK (2023) 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
Agam G, Gebhardt C, Popara M, Mächtel R, Folz J, Ambrose B, Chamachi N, Chung SY, Craggs TD, de Boer M , Grohmann D et al (2023) Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins. Nature Methods, 20, 523-535.
Hill VE, Noy A & Craggs TD (2023) DNA damage competes with sequence to pin a plectoneme. Biophysical Journal, 122(3), 214a-214a.
Rhind-Tutt AV, Fountain SE, Abdelhamid MA & Craggs TD (2023) From single-molecule to synchrotron: New tools for investigating the molecular mechanisms of aberrant DNA diseases. Biophysical Journal, 122(3), 19a-20a.
Jeffet J, Ionescu A, Michaeli Y, Torchinsky D, Perlson E, Craggs TD & Ebenstein Y (2022) Multimodal single-molecule microscopy with continuously controlled spectral resolution (CoCoS). Biophysical Journal, 121(3), 301a-301a.
Abdelhamid MAS, Waller ZAE & Craggs TD (2022) Direct observation of folded human telomeric i-motif at neutral pH by single-molecule FRET. Biophysical Journal, 121(3), 171a-171a.
Ambrose B, Hill VE, Shaw RA, Johnston-Wood T, Willmott M, Johnston C, Mächtel R, Cordes T, Lerner E, Hill JG , Weiss S et al (2022) A novel single molecule fluorescence quenching technique for measuring distances below 3 nm. Biophysical Journal, 121(3), 431a-431a.
Evans GW, Craggs T & Kapanidis AN (2022) The Rate-limiting Step of DNA Synthesis by DNA Polymerase Occurs in the Fingers-closed Conformation. Journal of Molecular Biology, 434(2).
Bennison DJ, Nakamoto JA, Craggs TD, Milón P, Rafferty JB & Corrigan RM (2021) The stringent response inhibits 70S ribosome formation in Staphylococcus aureus by impeding GTPase-ribosome interactions. mBio, 12(6). View this article in WRRO
Jeffet J, Ionescu A, Michaeli Y, Torchinsky D, Perlson E, Craggs TD & Ebenstein Y (2021) Multimodal single-molecule microscopy with continuously controlled spectral resolution. Biophysical Reports, 1(1). View this article in WRRO
George D, Cadby A & Craggs TD (2021) Combinefluent: An Open Source, Low-Cost Laser System for Single-Molecule Microscopy. Biophysical Journal, 120(3), 184a-184a.
Ambrose B, Baxter JM, Cully J, Willmott M, Steele EM, Bateman BC, Martin-Fernandez ML, Cadby A, Shewring J, Aaldering M & Craggs TD (2020) The smfBox is an open-source platform for single-molecule FRET. Nature Communications, 11(1).
Abdu K, Aiertza MK, Wilkinson OJ, Senthong P, Craggs TD, Povey AC, Margison GP & Williams DM (2020) 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
Ambrose B, Willmott M, Johnston-Wood T, Shaw RA, Hill JG & Craggs TD (2020) 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.
Ambrose B, Baxter J, Cully J, Willmott M, Bateman BC, Steele E, Cadby AJ, Shewring J, Aaldering M & Craggs TD (2020) Democratizing Single-Molecule FRET: An Open-Source Microscope for Measuring Precise Distances and Biomolecular Dynamics. Biophysical Journal, 118(3), 614a-614a.
Craggs TD, Sustarsic M, Plochowietz A, Mosayebi M, Kaju H, Cuthbert A, Hohlbein J, Domicevica L, Biggin PC, Doye JPK & Kapanidis AN (2019) Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase. Nucleic Acids Research, 47(20), 10788-10800.
Martin E, Williams HEL, Pitoulias M, Stevens D, Winterhalter C, Craggs TD, Murray H, Searle MS & Soultanas P (2019) DNA replication initiation in Bacillus subtilis: structural and functional characterization of the essential DnaA–DnaD interaction. Nucleic Acids Research, 47(4), 2101-2112.
Hellenkamp B, Schmid S, Doroshenko O, Opanasyuk O, Kühnemuth R, Adariani SR, Ambrose B, Aznauryan M, Barth A, Birkedal V , Bowen ME et al (2018) Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study. Nature Methods, 15(9), 669-676. View this article in WRRO
Bennet I, Finger LD, Baxter NJ, Ambrose B, Hounslow A, Thompson MJ, Exell JC, Shahari NNBM, Craggs TD, Waltho JP & Grasby JA (2018) 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
Hellenkamp B, Schmid S, Doroshenko O, Opanasyuk O, Kühnemuth R, Adariani SR, Ambrose B, Aznauryan M, Barth A, Birkedal V , Bowen ME et al (2018) Publisher Correction: Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study. Nature Methods, 15(11), 984-984.
Fisher GLM, Pastrana CL, Higman VA, Koh A, Taylor JA, Butterer A, Craggs TD, Sobott F, Murray H, Crump MP , Moreno-Herrero F et al (2017) The structural basis for dynamic DNA binding and bridging interactions which condense the bacterial centromere. eLife, 6. View this article in WRRO
Craggs TD (2017) Cool and dynamic: single-molecule fluorescence-based structural biology. Nature Methods, 14(2), 123-124.
Meli M, Sustarsic M, Craggs TD, Kapanidis AN & Colombo G (2016) 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
Nott TJ, Craggs TD & Baldwin AJ (2016) Membraneless organelles can melt nucleic acid duplexes and act as biomolecular filters. Nature Chemistry, 8(6), 569-575.
Algasaier SI, Exell JC, Bennet IA, Thompson MJ, Gotham VJB, Shaw SJ, Craggs TD, Finger LD & Grasby JA (2016) 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
Evans GW, Hohlbein J, Craggs T, Aigrain L & Kapanidis AN (2015) Real-time single-molecule studies of the motions of DNA polymerase fingers illuminate DNA synthesis mechanisms. Nucleic Acids Research, 43(12), 5998-6008.
Nott TJ, Petsalaki E, Farber P, Jervis D, Fussner E, Plochowietz A, Craggs TD, Bazett-Jones DP, Pawson T, Forman-Kay JD & Baldwin AJ (2015) Phase Transition of a Disordered Nuage Protein Generates Environmentally Responsive Membraneless Organelles. Molecular Cell, 57(5), 936-947.
Blouin S, Craggs TD, Lafontaine DA & Penedo JC (2015) Functional Studies of DNA-Protein Interactions Using FRET Techniques, 115-141.
(2014) Additions and corrections published 30th October 2013 to 15th July 2014. Chemical Society Reviews, 43(17), 6470-6470.
Craggs TD, Hutton RD, Brenlla A, White MF & Penedo JC (2014) 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
Craggs TD, Sustarsic M, Hohlbein J, Cuthbert A, Taylor N, Evans G & Kapanidis AN (2014) A Novel FRET-Based Structure of DNA Polymerase Complexed with Kinked Gapped-DNA. Biophysical Journal, 106(2), 274a-274a.
Hohlbein J, Craggs TD & Cordes T (2014) Alternating-laser excitation: single-molecule FRET and beyond (vol 43, pg 1156, 2014). CHEMICAL SOCIETY REVIEWS, 43(17), 6472-6472.
Robb NC, Cordes T, Hwang LC, Gryte K, Duchi D, Craggs TD, Santoso Y, Weiss S, Ebright RH & Kapanidis AN (2013) 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.
Hohlbein J, Aigrain L, Craggs TD, Bermek O, Potapova O, Shoolizadeh P, Grindley NDF, Joyce CM & Kapanidis AN (2013) Conformational landscapes of DNA polymerase I and mutator derivatives establish fidelity checkpoints for nucleotide insertion. Nature Communications, 4(1). View this article in WRRO
Craggs TD & Kapanidis AN (2012) Six steps closer to FRET-driven structural biology. Nature Methods, 9(12), 1157-1158.
Hutton RD, Craggs TD, White MF & Penedo JC (2010) PCNA and XPF cooperate to distort DNA substrates. Nucleic Acids Research, 38(5), 1664-1675. View this article in WRRO
Craggs TD (2010) ChemInform Abstract: Green Fluorescent Protein: Structure, Folding and Chromophore Maturation. ChemInform, 41(3).
Craggs TD (2009) Green fluorescent protein: structure, folding and chromophore maturation. Chemical Society Reviews, 38(10), 2865-2865.
Blouin S, Craggs TD, Lafontaine DA & Penedo JC (2009) Functional Studies of DNA-Protein Interactions Using FRET Techniques, 475-502.
Orte A, Craggs TD, White SS, Jackson SE & Klenerman D (2008) Evidence of an Intermediate and Parallel Pathways in Protein Unfolding from Single-Molecule Fluorescence. Journal of the American Chemical Society, 130(25), 7898-7907.
Kuprov I, Craggs TD, Jackson SE & Hore PJ (2007) 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.
Huang J-R, Craggs TD, Christodoulou J & Jackson SE (2007) Stable Intermediate States and High Energy Barriers in the Unfolding of GFP. Journal of Molecular Biology, 370(2), 356-371.
Jackson SE, Craggs TD & Huang J-R (2006) Understanding the folding of GFP using biophysical techniques. Expert Review of Proteomics, 3(5), 545-559.
Khan F, Kuprov I, Craggs TD, Hore PJ & Jackson SE (2006) 19F NMR Studies of the Native and Denatured States of Green Fluorescent Protein. Journal of the American Chemical Society, 128(33), 10729-10737.
Darcy M, Crocker K, Wang Y, Le JV, Mohammadiroozbahani G, Abdelhamid MAS, Craggs TD, Castro CE, Bundschuh R & Poirier MG () High-Force Application by a Nanoscale DNA Force Spectrometer. ACS Nano.
Abdelhamid MAS, Rhind-Tutt AV, Ambrose B & Craggs TD () Making Precise and Accurate Single-Molecule FRET Measurements using the Open-Source smfBox. Journal of Visualized Experiments(173).
Abdelhamid MAS, Rhind-Tutt AV, Ambrose B & Craggs TD () Making Precise and Accurate Single-Molecule FRET Measurements using the Open-Source smfBox. Journal of Visualized Experiments(173).
Lerner E, Barth A, Hendrix J, Ambrose B, Birkedal V, Blanchard SC, Börner R, Sung Chung H, Cordes T, Craggs TD , Deniz AA et al () FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. eLife, 10.
Martin E, Williams HEL, Pitoulias M, Stevens D, Winterhalter C, Craggs TD, Murray H, Searle MS & Soultanas P () DNA replication initiation in Bacillus subtilis; Structural and functional characterisation of the essential DnaA-DnaD interaction.
Craggs TD, Sustarsic M, Plochowietz A, Mosayebi M, Kaju H, Cuthbert A, Hohlbein J, Domicevica L, Biggin PC, Doye JPK & Kapanidis AN () Substrate conformational dynamics drive structure-specific recognition of gapped DNA by DNA polymerase.
Fisher GLM, Pastrana CL, Higman VA, Koh A, Taylor JA, Butterer A, Craggs TD, Sobott F, Murray H, Crump MP , Moreno-Herrero F et al () The C-terminal domain of ParB is critical for dynamic DNA binding and bridging interactions which condense the bacterial centromere.
Hohlbein J, Craggs TD & Cordes T () Alternating-laser excitation: single-molecule FRET and beyond. Chem. Soc. Rev., 43(4), 1156-1171.
Lerner E, Ambrose B, Barth A, Birkedal V, Blanchard SC, Borner R, Cordes T, Craggs TD, Ha T, Haran G , Hugel T et al () The FRET-based structural dynamics challenge -- community contributions to consistent and open science practices. View this article in WRRO
Ambrose B, Baxter J, Cully J, Willmott M, Steele E, Bateman BC, Martin-Fernandez ML, Cadby A, Shewring J, Aaldering M & Craggs TD () The smfBox: an open-source platform for single-molecule FRET.
Shaw R, Johnston-Wood T, Ambrose B, Craggs T & Hill J () CHARMM-DYES: Parameterization of fluorescent dyes for use with the CHARMM force field. Journal of Chemical Theory and Computation.

Chapters

Tor Y, Gehring K, Fabris D, Egli M, Korostelev AA, Craggs TD, Pyne A, Gagnon KT, Watts JK, Cheatham III TE & Richards NGJ (2022) Online Content: Physical and Structural Techniques Applied to Nucleic Acids, Nucleic Acids in Chemistry and Biology (pp. E1-E50). The Royal Society of Chemistry

Conference proceedings papers

Fisher GLM, Bateman BC, Craggs TD & Dillingham MS (2018) The Conformational Landscape of SMC: A FRET Study. Biophysical Journal, Vol. 114(3) (pp 209a-209a)
Craggs TD, Sustarsic M, Mosayebi M, Kaju H, Hohlbein J, Biggin PC, Doye JPK & Kapanidis AN (2016) How Structure-Specific DNA-Binding Proteins Recognise their Substrates. Biophysical Journal, Vol. 110(3) (pp 514a-515a)
Craggs TD, Sustarsic M, Hohlbein J, Cuthbert A, Taylor N, Evans G & Kapanidis AN (2014) A Novel FRET-Based Structure of DNA Polymerase Complexed with Kinked Gapped-DNA. BIOPHYSICAL JOURNAL, Vol. 106(2) (pp 273A-273A)
Orte A, Craggs TD, White SS, Jackson SE & Klenerman D (2007) YFP unfolding kinetics studied in a single-molecule nano-flow cell. BIOPHYSICAL JOURNAL (pp 660A-660A)

Preprints

Howard JAL, Ambrose B, Abdelhamid MAS, Alevropoulos-Borrill A, Ejaz A, Dresser L, Dienerowitz M, Quinn SD, Squires AH, Noy A , Craggs TD et al (2024) Rep structures can be tuned by ionicity via metastable intermediates in the absence of DNA, Cold Spring Harbor Laboratory.
Gelder KL, Carruthers NA, Ball SS, Dunning M, Craggs TD, Twelvetrees AE & Bose DA (2024) Cooperation between Intrinsically Disordered Regions regulates CBP condensate behaviour., Cold Spring Harbor Laboratory.
Agam G, Gebhardt C, Popara M, Mächtel R, Folz J, Ambrose B, Chamachi N, Chung SY, Craggs TD, de Boer M , Grohmann D et al () Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins, Cold Spring Harbor Laboratory.
George DR, Ambrose B, Cadby AJ & Craggs TD () An Open-source, Cost-Efficient Excitation Module for Single-molecule Microscopy, Cold Spring Harbor Laboratory.
Bennison DJ, Nakamoto JA, Craggs TD, Milón P, Rafferty JB & Corrigan RM () (p)ppGpp inhibits 70S ribosome formation in Staphylococcus aureus by impeding GTPase-ribosome interactions.
Jeffet J, Michaeli Y, Torchinsky D, Israel-Elgali I, Shomron N, Craggs TD & Ebenstein Y () Multi-modal Single-molecule Imaging with Continuously Controlled Spectral-resolution (CoCoS) Microscopy.

Teaching interests: Biological Chemistry

Teaching activities

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