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Pérez-García L, Selin M, Ciarlo A, Magazzù A, Pesce G, Sasso A, Volpe G, Pérez Castillo I, Arzola AV. Optimal calibration of optical tweezers with arbitrary integration time and sampling frequencies: a general framework [Invited]. BIOMEDICAL OPTICS EXPRESS 2023; 14:6442-6469. [PMID: 38420310 PMCID: PMC10898575 DOI: 10.1364/boe.495468] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/31/2023] [Accepted: 09/03/2023] [Indexed: 03/02/2024]
Abstract
Optical tweezers (OT) have become an essential technique in several fields of physics, chemistry, and biology as precise micromanipulation tools and microscopic force transducers. Quantitative measurements require the accurate calibration of the trap stiffness of the optical trap and the diffusion constant of the optically trapped particle. This is typically done by statistical estimators constructed from the position signal of the particle, which is recorded by a digital camera or a quadrant photodiode. The finite integration time and sampling frequency of the detector need to be properly taken into account. Here, we present a general approach based on the joint probability density function of the sampled trajectory that corrects exactly the biases due to the detector's finite integration time and limited sampling frequency, providing theoretical formulas for the most widely employed calibration methods: equipartition, mean squared displacement, autocorrelation, power spectral density, and force reconstruction via maximum-likelihood-estimator analysis (FORMA). Our results, tested with experiments and Monte Carlo simulations, will permit users of OT to confidently estimate the trap stiffness and diffusion constant, extending their use to a broader set of experimental conditions.
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Affiliation(s)
- Laura Pérez-García
- Department of Physics, University of Gothenburg, 41296 Gothenburg, Sweden
| | - Martin Selin
- Department of Physics, University of Gothenburg, 41296 Gothenburg, Sweden
| | - Antonio Ciarlo
- Department of Physics, University of Gothenburg, 41296 Gothenburg, Sweden
- Department of Physics E. Pancini, University of Naples Federico II, Complesso Universitario Monte Sant’Angelo, Via Cintia, I- 80126, Naples, Italy
| | - Alessandro Magazzù
- Department of Physics, University of Gothenburg, 41296 Gothenburg, Sweden
| | - Giuseppe Pesce
- Department of Physics, University of Gothenburg, 41296 Gothenburg, Sweden
- Department of Physics E. Pancini, University of Naples Federico II, Complesso Universitario Monte Sant’Angelo, Via Cintia, I- 80126, Naples, Italy
| | - Antonio Sasso
- Department of Physics E. Pancini, University of Naples Federico II, Complesso Universitario Monte Sant’Angelo, Via Cintia, I- 80126, Naples, Italy
| | - Giovanni Volpe
- Department of Physics, University of Gothenburg, 41296 Gothenburg, Sweden
| | - Isaac Pérez Castillo
- Departamento de Física, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Ciudad de México 09340, Mexico
| | - Alejandro V. Arzola
- Departamento de Física Cuántica y Fotónica, Instituto de Física, Universidad Nacional Autónoma de México, C.P. 04510, Cd. de México, Mexico
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Price RM, Budzyński MA, Kundra S, Teves SS. Advances in visualizing transcription factor - DNA interactions. Genome 2020; 64:449-466. [PMID: 33113335 DOI: 10.1139/gen-2020-0086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
At the heart of the transcription process is the specific interaction between transcription factors (TFs) and their target DNA sequences. Decades of molecular biology research have led to unprecedented insights into how TFs access the genome to regulate transcription. In the last 20 years, advances in microscopy have enabled scientists to add imaging as a powerful tool in probing two specific aspects of TF-DNA interactions: structure and dynamics. In this review, we examine how applications of diverse imaging technologies can provide structural and dynamic information that complements insights gained from molecular biology assays. As a case study, we discuss how applications of advanced imaging techniques have reshaped our understanding of TF behavior across the cell cycle, leading to a rethinking in the field of mitotic bookmarking.
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Affiliation(s)
- Rachel M Price
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.,Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Marek A Budzyński
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.,Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Shivani Kundra
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.,Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Sheila S Teves
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.,Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
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