Methods | Erie Lab

Analytical Chemistry & Biophysics
- Atomic Force Microscopy (AFM)
  - Dual Resonance Frequency Enhanced Electrostatic Microscopy (DREEM)
- Single molecule Total Internal Reflection Fluorescence (TIRF) Microscopy
- Capillary Electrophoresis (CE)
- In vivo fluorescence imaging
Physical Chemistry
- Pre steady-state Kinetics
- Thermodynamics
- Computational molecular modeling
- Optics
Organic Chemistry
- Surface chemistry
- Fluorophore conjugation chemistry
Biological Chemistry
- Cloning and DNA purification
- PCR and mutagenesis
- Protein expression and purification
- DNA and RNA foot-printing
- Electrophoresis and western blots
- In vivo fluorescence imaging

Erie lab publications

Single-Molecule FRET to Measure Conformational Dynamics of DNA Mismatch Repair Proteins October 30, 2016
Single-molecule FRET measurements have a unique sensitivity to protein conformational dynamics. The FRET signals can either be interpreted quantitatively to provide estimates of absolute distance in a molecule configuration or can be qualitatively interpreted as distinct states, from which quantitative kinetic schemes for conformational transitions can be deduced. Here we describe methods utilizing single-molecule FRET […]
J W Gauer
Hemi-methylated DNA regulates DNA methylation inheritance through allosteric activation of H3 ubiquitylation by UHRF1 September 7, 2016
The epigenetic inheritance of DNA methylation requires UHRF1, a histone- and DNA-binding RING E3 ubiquitin ligase that recruits DNMT1 to sites of newly replicated DNA through ubiquitylation of histone H3. UHRF1 binds DNA with selectivity towards hemi-methylated CpGs (HeDNA); however, the contribution of HeDNA sensing to UHRF1 function remains elusive. Here, we reveal that the […]
Joseph S Harrison
Enhanced electrostatic force microscopy reveals higher-order DNA looping mediated by the telomeric protein TRF2 February 10, 2016
Shelterin protein TRF2 modulates telomere structures by promoting dsDNA compaction and T-loop formation. Advancement of our understanding of the mechanism underlying TRF2-mediated DNA compaction requires additional information regarding DNA paths in TRF2-DNA complexes. To uncover the location of DNA inside protein-DNA complexes, we recently developed the Dual-Resonance-frequency-Enhanced Electrostatic force Microscopy (DREEM) imaging technique. DREEM imaging […]
Parminder Kaur
Visualizing the Path of DNA through Proteins Using DREEM Imaging January 18, 2016
Many cellular functions require the assembly of multiprotein-DNA complexes. A growing area of structural biology aims to characterize these dynamic structures by combining atomic-resolution crystal structures with lower-resolution data from techniques that provide distributions of species, such as small-angle X-ray scattering, electron microscopy, and atomic force microscopy (AFM). A significant limitation in these combinatorial methods […]
Dong Wu
Corrigendum: Transcription errors induce proteotoxic stress and shorten cellular lifespan October 15, 2015
No abstract
Marc Vermulst
Eukaryotic Mismatch Repair in Relation to DNA Replication October 6, 2015
Three processes act in series to accurately replicate the eukaryotic nuclear genome. The major replicative DNA polymerases strongly prevent mismatch formation, occasional mismatches that do form are proofread during replication, and rare mismatches that escape proofreading are corrected by mismatch repair (MMR). This review focuses on MMR in light of increasing knowledge about nuclear DNA […]
Thomas A Kunkel
Transcription errors induce proteotoxic stress and shorten cellular lifespan August 26, 2015
Transcription errors occur in all living cells; however, it is unknown how these errors affect cellular health. To answer this question, we monitor yeast cells that are genetically engineered to display error-prone transcription. We discover that these cells suffer from a profound loss in proteostasis, which sensitizes them to the expression of genes that are […]
Marc Vermulst
MutL traps MutS at a DNA mismatch August 19, 2015
DNA mismatch repair (MMR) identifies and corrects errors made during replication. In all organisms except those expressing MutH, interactions between a DNA mismatch, MutS, MutL, and the replication processivity factor (β-clamp or PCNA) activate the latent MutL endonuclease to nick the error-containing daughter strand. This nick provides an entry point for downstream repair proteins. Despite […]
Ruoyi Qiu
Single molecule studies of DNA mismatch repair April 22, 2014
DNA mismatch repair, which involves is a widely conserved set of proteins, is essential to limit genetic drift in all organisms. The same system of proteins plays key roles in many cancer related cellular transactions in humans. Although the basic process has been reconstituted in vitro using purified components, many fundamental aspects of DNA mismatch […]
Dorothy A Erie
Dynamics of MutS-mismatched DNA complexes are predictive of their repair phenotypes March 5, 2014
MutS recognizes base-base mismatches and base insertions/deletions (IDLs) in newly replicated DNA. Specific interactions between MutS and these errors trigger a cascade of protein-protein interactions that ultimately lead to their repair. The inability to explain why different DNA errors are repaired with widely varying efficiencies in vivo remains an outstanding example of our limited knowledge […]
Vanessa C DeRocco