A visual representation of a scientific method or workflow with a central glowing sphere, colorful elements, and a winding path. The image suggests a step-by-step process or experimental procedure.

Methods

/ Research / By

We continuously devise new methods and optimization protocols to improve performance and sensitivity.
Below are the publications that describe these advances for each specific approach.

Tethered Particle Microscopy:

  1. Qian J, Collette D, Finzi L, Dunlap D. Detecting DNA Loops Using Tethered Particle Motion. Methods in Molecular Biology (Clifton, N.J.). 2024; 2694:451-466. PubMed PMID: 37824017; DOI: 10.1007/978-1-0716-3377-9_21
  2. Laura Finzi and David Dunlap. The tethered particle motion and magnetic tweezer techniques: an introduction and some applications. Proceedings of the International School of Physics “Enrico Fermi”, Multimodal and Nanoscale Optical Microscopy, course 210, 2022.
  3. Wenxuan Xu, David Dunlap and Laura Finzi. Tethered Particle Microscopy. Encyclopedia of Biophysics, European Biophysical Societies’ Association (EBSA), 2021. DOI: 10.1007/978-3-642-35943-9_489-1
  4. Daniel T. Kovari, Yan Yan, Laura Finzi and David Dunlap. Tethered Particle Motion: an easy technique for probing DNA topology and interactions with transcription factors. Methods in Molecular Biology, vol 1665, 2018.
  5. Suleyman Ucuncuoglu et al. Multiplexed, tethered particle microscopy for studies of DNA-enzyme dynamics. Methods in Enzymology, 2016.
  6. Sandip Kumar et al. Enhanced Tether Particle Motion Analysis Reveals Viscous Effects. Biophysical Journal, 106(2):399–409, 2014.
  7. David D. Dunlap et al. Probing DNA topology with Tethered Particle Motion. Methods in Molecular Biology, 2011.
  8. C. Manzo and L. Finzi. Quantitative analysis of DNA looping kinetics. Methods in Enzymology, 2010.
  9. John F. Beausang et al. DNA Looping Kinetics Analysed Using Diffusive Hidden Markov Method Model. Biophys J., 2007.
  10. P. Nelson et al. Tethered Particle Motion as a Diagnostic of DNA Tether Length. J. Phys. Chem. B, 2006.
  11. E. Consoli et al. Diffusion of phosphorylated and non-phosphorylated LHCII. EMBO Reports, 2005.

Magnetic Tweezer method:

  1. Laura Finzi and David Dunlap. The tethered particle motion and magnetic tweezer techniques. Enrico Fermi School, 2022.
  2. Joe Piccolo et al. Force spectroscopy with electromagnetic tweezers. Journal of Applied Physics, 2021.
  3. Daniel T. Kovari et al. Model-free 3D localization. Optics Express, 2019.
  4. Sachin Goyal et al. Stretching DNA to quantify non-specific binding. PRE, 2012.
  5. Qing Shao et al. Physiological salt levels favor writhe. Macromolecules, 2012.

Atomic Force Microscopy method:

  1. Ning Gao et al. Purification of Bacteriophage Lambda Repressor. Protein Expression and Purification, 2013.
  2. Marta A. Mendes et al. MADS-domain transcription factor looping. Plant Cell, 2013.
  3. Haowei Wang et al. Single molecule analysis of DNA wrapping. Nucleic Acids Research, 2013.
  4. H. Wang et al. AFM studies of CI oligomers. Curr. Pharmaceutical Biotechnology, 2009.
  5. G. Lia et al. ATP-dependent looping of DNA by ISWI. J. Biophotonics, 2008.
  6. M. Podestà et al. Positively charged surfaces increase DNA flexibility. Biophys J., 2005.
  7. A. Podestà et al. Atomic Force Microscopy studies of DNA. Journal of Microscopy, 2004.

Complete List of Published Work in MyBibliography:

https://www.ncbi.nlm.nih.gov/myncbi/browse/collection/40647244/?sort=date&direction=descending