Benjamin Ambrose
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View article: Herpes simplex virus type 1 origin binding protein UL9 tethers and loops origin- and non-origin-DNA intra- and intermolecularly
Herpes simplex virus type 1 origin binding protein UL9 tethers and loops origin- and non-origin-DNA intra- and intermolecularly Open
Herpesviruses are ubiquitous human pathogens, which are the causative agent of mild to severe symptoms ranging from cold sore to nasopharyngeal carcinoma. Even though replication of the linear dsDNA genome has been studied for decades, we …
View article: The transitional kinetics between open and closed Rep structures can be tuned by salt via two intermediate states
The transitional kinetics between open and closed Rep structures can be tuned by salt via two intermediate states Open
DNA helicases undergo conformational changes; however, their structural dynamics are poorly understood. Here, we study single molecules of superfamily 1A DNA helicase Rep, which undergo conformational transitions during bacterial DNA repli…
View article: A new twist on PIFE: photoisomerisation-related fluorescence enhancement
A new twist on PIFE: photoisomerisation-related fluorescence enhancement Open
PIFE was first used as an acronym for protein-induced fluorescence enhancement, which refers to the increase in fluorescence observed upon the interaction of a fluorophore, such as a cyanine, with a protein. This fluorescence enhancement i…
View article: A new twist on PIFE: photoisomerisation-related fluorescence enhancement
A new twist on PIFE: photoisomerisation-related fluorescence enhancement Open
PIFE was first used as an acronym for protein-induced fluorescence enhancement, which refers to the increase in fluorescence observed upon the interaction of a fluorophore, such as a cyanine, with a protein. This fluorescence enhancement i…
View article: Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins
Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins Open
Single-molecule FRET (smFRET) has become an established tool to study biomolecular structure and dynamics in vitro and in live cells. We performed a worldwide blind study involving 19 labs to assess the uncertainty of FRET experiments for …
View article: An Open-source, Cost-Efficient Excitation Module for Single-molecule Microscopy
An Open-source, Cost-Efficient Excitation Module for Single-molecule Microscopy Open
In fluorescence microscopy, scientific-grade laser diodes are key components and contribute a considerable expense to the total cost of the microscope setup. Existing open-source laser excitation modules are mainly designed for super-resol…
View article: Making Precise and Accurate Single-Molecule FRET Measurements using the Open-Source smfBox
Making Precise and Accurate Single-Molecule FRET Measurements using the Open-Source smfBox Open
The smfBox is a recently developed cost-effective, open-source instrument for single-molecule Förster Resonance Energy Transfer (smFRET), which makes measurements on freely diffusing biomolecules more accessible. This overview includes a s…
View article: FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices
FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices Open
Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in s…
View article: CHARMM-DYES: Parameterization of Fluorescent Dyes for Use with the CHARMM Force Field
CHARMM-DYES: Parameterization of Fluorescent Dyes for Use with the CHARMM Force Field Open
We present CHARMM-compatible force field parameters for a series of fluorescent dyes from the Alexa, Atto, and Cy families, commonly used in Förster resonance energy transfer (FRET) experiments. These dyes are routinely used in experiments…
View article: The smfBox is an open-source platform for single-molecule FRET
The smfBox is an open-source platform for single-molecule FRET Open
Single-molecule Förster Resonance Energy Transfer (smFRET) is a powerful technique capable of resolving both relative and absolute distances within and between structurally dynamic biomolecules. High instrument costs, and a lack of open-so…
View article: CHARMM-DYES: Parameterization of Fluorescent Dyes for Use with the CHARMM Forcefield
CHARMM-DYES: Parameterization of Fluorescent Dyes for Use with the CHARMM Forcefield Open
We present CHARMM-compatible forcefield parameters for a series of fluorescent dyes from the Alexa, Atto and Cy families, commonly used in F¨orster resonance energy transfer (FRET) experiments. These dyes are routinely used in experiments …
View article: CHARMM-DYES: Parameterization of Fluorescent Dyes for Use with the CHARMM Forcefield
CHARMM-DYES: Parameterization of Fluorescent Dyes for Use with the CHARMM Forcefield Open
We present CHARMM-compatible forcefield parameters for a series of fluorescent dyes from the Alexa, Atto and Cy families, commonly used in F¨orster resonance energy transfer (FRET) experiments. These dyes are routinely used in experiments …
View article: The FRET-based structural dynamics challenge -- community contributions to consistent and open science practices
The FRET-based structural dynamics challenge -- community contributions to consistent and open science practices Open
Single-molecule Förster resonance energy transfer (smFRET) has become a mainstream technique for probing biomolecular structural dynamics. The rapid and wide adoption of the technique by an ever-increasing number of groups has generated ma…
View article: The smfBox: an open-source platform for single-molecule FRET
The smfBox: an open-source platform for single-molecule FRET Open
Single-molecule Förster Resonance Energy Transfer (smFRET) is a powerful technique capable of resolving both relative and absolute distances within and between structurally dynamic biomolecules. High instrument costs, and a lack of open-so…
View article: Regional conformational flexibility couples substrate specificity and scissile phosphate diester selectivity in human flap endonuclease 1
Regional conformational flexibility couples substrate specificity and scissile phosphate diester selectivity in human flap endonuclease 1 Open
Human flap endonuclease-1 (hFEN1) catalyzes the divalent metal ion-dependent removal of single-stranded DNA protrusions known as flaps during DNA replication and repair. Substrate selectivity involves passage of the 5'-terminus/flap throug…