Allison Squires

Neubauer Family Assistant Professor
Pritzker School of Molecular Engineering
The University of Chicago

asquires@uchicago.edu

Project Description

DNA-FRET nanostructures for imaging and biomarker detection

Researchers in the Squires group will undertake design and characterization of DNA-fluorophore constructs engineered to generate distinct spectroscopic signatures for applications related to imaging and/or biomarker detection. Example of specific research project possibilities (to be undertaken with the guidance of the PI and a graduate student mentor) include:

(1) DNA tetrahedron–based FRET energy-transfer matrix (single-molecule)
Build tiny, self-assembled 3D DNA tetrahedra and place fluorescent dyes at selected edges to create controlled donor–acceptor pairs. The student will measure how efficiently energy moves between different dye positions (a “transfer matrix”) and how this depends on distance and geometry. We’ll use single-molecule fluorescence to read out FRET efficiencies and other spectroscopic properties.

(2) DNA-PAINT on DNA origami for imager-strand characterization
Perform super-resolution microscopy on DNA nanostructures. The student will test how different “imager” strands behave in a super-resolution imaging technique known as DNA-PAINT by binding them to defined docking sites on DNA origami immobilized on a surface in a flow cell. On/off rates, brightness, background, and localization precision will be quantified to conditions that give clean, reliable imaging.

(3) Spectroscopy of FRET-based DNA tags: surface vs. solution
Do single-molecule FRET constructs behave the same when stuck to a surface as they do free in solution? In this project you’ll compare key spectroscopic properties such as FRET efficiency distributions, photostability, blinking, and brightness, for DNA/protein FRET constructs measured in solution and on surfaces. The student will characterize the differences between the two systems and interpret what these differences might mean for single-molecule biophysical studies.

(4) Photoswitchable FRET-based DNA tags
Design and test DNA tags whose FRET signal can be toggled with light. The student place donor/acceptor dyes on short DNA scaffolds alongside a photoswitchable element (a dye that can be reversibly driven between dark and bright states) to create tags with controllable on/off FRET contrast. Using single-molecule microscopy, the student will quantify activation/deactivation kinetics and FRET state consistency, and explore an example application of this system.

Requirement

Basic understanding of: DNA structure, fluorophores and fluorescence, physicaland analytical chemistry; statistics of stochastic processes.

Essential skills: Basic wet lab biochemical technique (pipetting, hybridization, sample purification and quantification); moderate coding experience in any standard language including Python, Matlab, Java, etc.

Helpful but not strictly required: Previous optics or microscopy experience; information theory and/or advanced statistical characterization; experimental physical chemistry / photophysics / FRET experience; DNA origami or other related research experience.