Professor Achillefs Kapanidis: Publications

Amplification-Free Detection of Viruses in Minutes using Single-Particle Imaging and Machine Learning

Biophysical Journal Elsevier 120:3 (2021) 195a

Authors:

Nicolas Shiaelis, Leon Peto, Andrew McMahon, Chritof Hepp, Erica Bickerton, Cyril Favard, Delphine Muriaux, Monique Andersson, Alison Vaughan, Philippa Matthews, Nicole Stoesser, Derrick Crook, Achillefs N Kapanidis, Nicole C Robb

Single-Molecule Fret Analysis of Key Protein Conformational Changes During Promoter Escape by RNA Polymerase

Biophysical Journal Elsevier 120:3 (2021) 109a

Authors:

Anna Wang, Abhishek Mazumder, Achillefs N Kapanidis

High-throughput nitrogen-vacancy center imaging for nanodiamond photophysical characterization and pH nanosensing

Nanoscale Royal Society of Chemistry 12:42 (2020) 21821-21831

Authors:

Maabur Sow, Horst Steuer, Sanmi Adekanye, Laia Ginés, Soumen Mandal, Barak Gilboa, Oliver A Williams, Jason M Smith, Achillefs N Kapanidis

Abstract:

The fluorescent nitrogen-vacancy (NV) defect in diamond has remarkable photophysical properties, including high photostability which allows stable fluorescence emission for hours; as a result, there has been much interest in using nanodiamonds (NDs) for applications in quantum optics and biological imaging. Such applications have been limited by the heterogeneity of NDs and our limited understanding of NV photophysics in NDs, which is partially due to the lack of sensitive and high-throughput methods for photophysical analysis of NDs. Here, we report a systematic analysis of NDs using two-color wide-field epifluorescence imaging coupled to high-throughput single-particle detection of single NVs in NDs with sizes down to 5-10 nm. By using fluorescence intensity ratios, we observe directly the charge conversion of single NV center (NV- or NV0) and measure the lifetimes of different NV charge states in NDs. We also show that we can use changes in pH to control the main NV charge states in a direct and reversible fashion, a discovery that paves the way for performing pH nanosensing with a non-photobleachable probe.

Transient non-specific DNA binding dominates the target search of bacterial DNA-binding proteins

Cold Spring Harbor Laboratory (2020) 2020.08.13.249771

Authors:

Mathew Stracy, Jakob Schweizer, David J Sherratt, Achillefs N Kapanidis, Stephan Uphoff, Christian Lesterlin

Closing and opening of the RNA polymerase trigger loop

Proceedings of the National Academy of Sciences National Academy of Sciences 117:27 (2020) 15642-15649

Authors:

Abhishek Mazumder, Miaoxin Lin, Achillefs N Kapanidis, Richard H Ebright

Abstract:

The RNA polymerase (RNAP) trigger loop (TL) is a mobile structural element of the RNAP active center that, based on crystal structures, has been proposed to cycle between an "unfolded"/"open" state that allows an NTP substrate to enter the active center and a "folded"/"closed" state that holds the NTP substrate in the active center. Here, by quantifying single-molecule fluorescence resonance energy transfer between a first fluorescent probe in the TL and a second fluorescent probe elsewhere in RNAP or in DNA, we detect and characterize TL closing and opening in solution. We show that the TL closes and opens on the millisecond timescale; we show that TL closing and opening provides a checkpoint for NTP complementarity, NTP ribo/deoxyribo identity, and NTP tri/di/monophosphate identity, and serves as a target for inhibitors; and we show that one cycle of TL closing and opening typically occurs in each nucleotide addition cycle in transcription elongation.

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