C. Joo

Point set registration for combining fluorescence microscopy methods

The paper introduces a three-step point set registration method for aligning microscopy datasets, demonstrating its use in combining fluorescence and sequencing data.

RNA-guided RNA silencing by an Asgard archaeal Argonaute

The paper identifies an Asgard archaeal Argonaute, HrAgo1, that performs RNA-guided RNA silencing, bridging the gap between prokaryotic and eukaryotic Argonaute mechanisms.

iMAX FRET (Information Maximized FRET) for multipoint single-molecule structural analysis

The paper introduces iMAX FRET, a single-molecule method for structural analysis that captures 3D biomolecular structures and conformational changes through FRET and geometrical reconstruction.

Full-Length Single-Molecule Protein Fingerprinting

This paper introduces a method to map amino acid positions and post-translational modifications in single protein molecules with sub-nanometer resolution using FRET-based single-molecule protein fingerprinting.

Evaluation of FRET X for Single-Molecule Protein Fingerprinting

The paper evaluates FRET X fingerprinting for single-molecule protein identification through simulations and experiments, achieving 95% accuracy in identifying proteins from a complex mixture.

Drift correction in localization microscopy using entropy minimization

This paper introduces an entropy minimization method to improve drift correction in localization microscopy, achieving 5x better precision than existing methods without fiducial markers.

High-Resolution Single-Molecule FRET via DNA eXchange (FRET X)

This paper introduces FRET X, a method to measure multiple FRET pairs in single molecules with sub-nanometer resolution by using DNA strand exchange.

Targeting G-quadruplex Forming Sequences with Cas9

This study investigates how G-quadruplex forming sequences affect CRISPR-Cas9 complex structure and dynamics using single molecule FRET.

FRETboard: semi-supervised classification of FRET traces

FRETboard is a semi-supervised tool for classifying FRET traces, improving efficiency and accuracy compared to manual methods and existing software.

Skipping and sliding to optimize target search on protein-bound DNA and RNA

The paper shows that skipping and sliding motions allow searchers to maintain search speed on crowded nucleic-acid substrates, as demonstrated by analyzing human and bacterial Argonaute proteins.

High-Speed Super-Resolution Imaging Using Protein-Assisted DNA-PAINT

This paper introduces Ago-PAINT, a method that accelerates DNA-PAINT imaging by using Argonaute protein to enhance imager strand binding, achieving 10x faster acquisition without compromising resolution.

Selective Prespacer Processing Ensures Precise CRISPR-Cas Adaptation

This study identifies how Cas1-Cas2 selects and processes prespacers for CRISPR-Cas adaptation using single-molecule fluorescence and DnaQ exonucleases.

Argonaute bypasses cellular obstacles without hindrance during target search

This study shows Argonaute proteins efficiently search for targets by gliding over secondary structures and bypassing protein barriers through lateral diffusion and intersegmental jumps.

Multiplex single-molecule DNA barcoding using an oligonucleotide ligation assay

This paper develops a sensitive and specific method for detecting DNA sequences using oligonucleotide ligation assay combined with multicolor single-molecule fluorescence.

CRISPR Cas9 searches for a protospacer adjacent motif by one-dimensional diffusion

This study uses smFRET to show Cas9 searches for PAM sequences via one-dimensional diffusion, competing with 3D diffusion for efficient target binding.

Single-Molecule Peptide Fingerprinting

This paper introduces a single-molecule FRET-based technique for protein fingerprinting using ClpXP to sequence peptides with high processivity and low sample requirements.

Repetitive DNA reeling by the Cascade-Cas3 complex in nucleotide unwinding steps

This study investigates the DNA unwinding mechanism of the Cascade-Cas3 complex using single-molecule FRET, revealing a spring-loaded reeling process that compensates for inefficient nicking.