The McCluskey Lab

The McCluskey Lab at Pomona College

This site is under construction!

Some working notes for this landing screen: a sidebar with announcements wouldn’t fit, but can I have scrolling announcements below the splash image? Also, use a group picture as the splash, not a research one.

Building exterior in Toronto, Canada

About

Here is a paragraph about the lab, probably some cool images. This section doesn’t have links to other pages, though it should probably have a Home button (or the buttons should scroll with it) so visitors don’t have to scroll all the way back up.

Teaching

PHYS101 FA2024

  • This will link to a different page
  • Syllabus? Resources? Password-protected link to Canvas?
  • It would be a great place for inclusivity resources.
  • I need to get rid of these silly check mark bullet points.
Tourist taking photo of a building
Windows of a building in Nuremberg, Germany

PHYS 042 Lab FA 2024

  • Obviously there will be spring courses too.
  • Past courses should be in a more modest list at the bottom, without the images (textbook covers?)

Research Projects

Single-molecule fluorescence microscopy

These images (and a “click here” link at the end of the text) will go to separate pages for each project.

Figure out how to turn images and “go to” blocks into links without the address appearing under them.

Go to TIRF microscopy ->

Tourist taking photo of a building

Replace with a cool 3D render of the objective, stage, and micromirrors with a zoom to the evanescent field region

Use a combo of eDrawings and Illustrator (or BioRender)

Windows of a building in Nuremberg, Germany

Replace this with a real picture of our MT, maybe a redraw of the schematics and zooms in the one ND lab uses.

Probably do this in Illustrator or BioRender.

Force spectroscopy with magnetic tweezers

As above, a brief description will go here, linking to a new page.

Go to magnetic tweezers ->

Folding of the viral Frameshift Element (FSE)

These images (and a “click here” link at the end of the text) will go to separate pages for each project.

Go to FSE folding ->

Tourist taking photo of a building

Replace with a 2D structure cartoon, maybe a virology diagram

Windows of a building in Nuremberg, Germany

Replace with a schematic optical path (eDrawings or Illustrator, probably) and an SLM pattern (doesn’t have to be a meaningful one)

Spectral TIRF (spTIRF)

TIRF microscopy requires a separate detection channel for each wavelength of interest, which adds cost and complexity while keeping the spectral range limited. Learn how we are using phase-based light shaping to build spectral sensitivity directly into our microscopy images, and how that will make TIRF more flexible and powerful for a wide range of applications.

Go to spTIRF ->

Current Lab Members

Kaley McCluskey

Role: PI

Research interests: RNA folding, RNA-protein interactions, single-molecule microscopy

Riley Foard

3/2 Class of 2027

Major: engineering

Project: folding of the viral FSE

Jacob Zhang

Class of 2027

Major: physics

Project: spectral TIRF

(Gabriel, Nhi, Isabel)

Previous Group Members

Yaru Luo ’24. Thesis: “Building a micromirror total internal reflection fluorescence microscope (mmTIRFM).” Currently a grad student at UC Boulder.

Publications

  • Liu et al. A biophysics toolbox for reliable data acquisition and processing in integrated force-confocal fluorescence microscopy. Submitted, 2023.
  • K. McCluskey and N.H. Dekker. Principles and best practices of optimizing a micromirror-based multicolor TIRF microscopy system. Opt. Comms. 2023, DOI: https://doi.org/10.1016/j.optcom.2023.129474.
  • K. McCluskey et al. Global correction of optical distortions in multicolor single-molecule microscopy using Zernike polynomial gradients. Optics Express, vol 29, issue 25, pp. 42251-42264, 2021. DOI: 10.1364/OE.445230.
  • H. Sánchez, K. McCluskey et al. DNA replication origins retain mobile licensing proteins. Nat. Comms., vol. 12, art. 1908, 2021.
  • K. McCluskey et al.  Unprecedented tunability of riboswitch structure and regulatory function by sub-millimolar variations in physiological Mg2+. NAR, vol. 47, issue 12, pp. 6478-6487, 2019. DOI: 10.1093/nar/gkz316.
  • J. Nylk, K. McCluskey, et. al. Light-sheet microscopy with attenuation-compensated propagation-invariant beams. Science Advances, vol. 4, issue 4, eaar4817, 2018.
  • K. McCluskey and J.C. Penedo. An integrated perspective on RNA aptamer-ligand recognition mechanisms: clearing muddy waters. PCCP, vol. 19, pp. 6921-6932, 2017.
  • J. Nylk, K. McCluskey, et al.  Enhancement of image quality and imaging depth with Airy light-sheet microscopy in cleared and non-cleared neural tissue.  Biomedical Optics Express vol. 7, issue 10, pp. 4021-4033, 2016.
  • E. Shaw, K. McCluskey, et al.  Using smFRET and denaturants to reveal folding landscapes.  Methods in Enzymology, vol. 549, pp. 313-341, 2014.
  • P. St.-Pierre, K. McCluskey, et al.  Fluorescence tools to investigate riboswitch structural dynamics.  BBA: Gene Regulatory Mechanisms.  DOI: 10.1016/j.bbargm.2014.05.015, 2014.
  • K. McCluskey, E. Shaw, D.A. Lafontaine, and J.C. Penedo.  Single-molecule fluorescence of nucleic acids, in: Yves Engelborghs and Antonie J.W.G. Visser (eds.), Fluorescence Spectroscopy and Microscopy: Methods and Protocols, Methods in Molecular Biology, vol. 1076, 2013.

Contact Information

kaley.mccluskey@pomona.edu
(909) 621-8729
Estella Laboratory 1283