| Atomic Force Microscopy Captures the Initiation of Methyl-Directed DNA Mismatch Repair |
2015 |
954 |
In Escherichia coli, errors in newly-replicated DNA, such as the incorporation of a nucleotide with a mis-paired base or an accidental insertion or deletion of nucleotides, are corrected by a methyl-directed mismatch repair (MMR) pathway. While the e... |
| Electric-field Dependent Conformations of DNA Molecules on a Model Biosensor Surface |
2012 |
188 |
Despite the variety of nucleic acid sensors developed, we still do not have definite answers to some questions that are important to the molecular binding and, ultimately, the sensitivity and reliability of the sensors. How do the DNA probes distribu... |
| Electrochemical Etching of Gold within Nanoshaved Self-Assembled Monolayers |
2013 |
895 |
Wet etching of metal substrates with patterned self-assembled monolayers (SAMs) is an inexpensive and convenient method to produce metal nanostructures. For this method to be relevant to the fabrication of high precision plasmonic structures, the kin... |
| Endonuclease-independent DNA Mismatch Repair Processes on the Lagging Strand |
2018 |
1141 |
DNA mismatch repair (MMR) pathways coordinate the excision and re-synthesis of newly-replicated DNA if a mismatched base-pair has been identified by protein MutS or MutS homologues (MSHs) after replication. DNA excision during MMR is initiated at sin... |
| Increasing the specificity of CRISPR systems with engineered RNA secondary structures |
2019 |
540 |
CRISPR (clustered regularly interspaced short palindromic repeat) systems have been broadly adopted for basic science, biotechnology, and gene and cell therapy. In some cases, these bacterial nucleases have demonstrated off-target activity. This crea... |
| Modular, Nondegenerate Polyprotein Scaffolds for Atomic Force Spectroscopy |
2016 |
1024 |
Atomic force spectroscopy (AFS) is a technique in which a cantilever probe of an atomic force microscope (AFM) is used to directly manipulate and pull on individual protein molecules. In an AFS experiment proteins of interest are deposited onto a sur... |
| Molecular Conformations of Targets Captured by DNA Nanoarrays |
2017 |
205 |
An open question in single molecule nanoarrays is how the chemical and morphological heterogeneities of the solid support affect the properties of biomacromolecules. We generated arrays that allowed individually-resolvable DNA molecules to interact w... |
| Nanografting Sodium Dodecyl Sulfate under Potential Control: new insights into tip-directed molecular assembly |
2013 |
952 |
We have demonstrated that under potential control, sodium dodecyl sulfate can form ordered and stable patterns within nanoscale regions of a pre-existing SAM where thiol molecules have been mechanically removed. The results offer novel insights into ... |
| Nanoscale Chemical Patterns on Gold Microplates |
2012 |
329 |
To generate nanoscale biochemical patterns for fundamental biophysical studies as well as practical biosensors, there remains a need for a high quality and versatile substrate. We show that chemically synthesized gold microplates on indium tin oxide ... |
| Nanoscale Positioning of Individual DNA Molecules by an Atomic Force Microscope |
2010 |
928 |
Here we report a method to assemble nanoscale DNA structures with single-molecule precision. This assembly is accomplished by performing nanografting in the presence of short, thiolated DNA strands that have been diluted by a positively charged alkan... |
| Nanoscale Spatial Distribution of Tethered DNA on Model Nucleic Acid Sensor Surfaces |
2013 |
373 |
The nanoscale arrangement of the DNA probe molecules on sensor surfaces has a profound impact on molecular recognition and signaling reactions on DNA biosensors and microarrays. Using electrochemical atomic force microscopy, we have directly determin... |
| A ‘Semi-Protected Oligonucleotide Recombination’ Assay for DNA Mismatch Repair in vivo Suggests Different Modes of Repair for Lagging Strand Mismatches |
2017 |
280 |
In Escherichia coli, a DNA mismatch repair (MMR) pathway corrects errors that occur during DNA replication by coordinating the excision and re-synthesis of a long tract of the newly-replicated DNA between an epigenetic signal (a hemi-methylated d(GAT... |
| A Single Molecule View of Conformational Switching of DNA Tethered to a Gold Electrode |
2012 |
1068 |
Surfaces that can actively regulate binding affinities or catalytic properties in response to external stimuli are a powerful means to probe and control the dynamic interactions between the cell and its microenvironment. Active surfaces also enable n... |
| Structure and Specificity of the RNA-guided Endonuclease Cas9 during DNA Interrogation, Target Binding, and Cleavage |
2015 |
1163 |
CRISPR-associated endonuclease Cas9 cuts DNA at variable target sites designated by a Cas9-bound RNA molecule. Cas9's ability to be directed by single ‘guide RNA’ molecules to target nearly any sequence has been recently exploited for a number of eme... |
| A Switchable Surface Enables Detection of Single DNA Hybridization Events with Atomic Force Microscopy |
2013 |
207 |
Here we describe a novel surface that enables direct visualization of the hybridization of single DNA molecules with an unprecedented resolution using atomic force microscopy. The surface consists of single-stranded DNA probes that are covalently anc... |