Search results for "fluorescence [detector]"

Identifying three-way DNA junction-specific small-molecules

2012

Three-way junction DNA (TWJ-DNA, also known as 3WJ-DNA) is an alternative secondary DNA structure comprised of three duplex-DNAs that converge towards a single point, termed the branch point. This point is characterized by unique geometrical properties that make its specific targeting by synthetic small-molecules possible. Such a targeting has already been demonstrated in the solid state but not thoroughly biophysically investigated in solution. Herein, a set of simple biophysical assays has been developed to identify TWJ-specific small-molecule ligands; these assays, inspired by the considerable body of work that has been reported to characterize the interactions between small-molecules an…

Single-Molecule FRET Reveals a Cooperative Effect of Two Methyl Group Modifications in the Folding of Human Mitochondrial tRNALys

2011

Summary Using a combination of advanced RNA synthesis techniques and single molecule spectroscopy, the deconvolution of individual contributions of posttranscriptional modifications to the overall folding and stabilization of human mitochondrial tRNA Lys is described. An unexpected destabilizing effect of two pseudouridines on the native tRNA folding was evidenced. Furthermore, the presence of m 2 G10 alone does not facilitate the folding of tRNA Lys , but a stabilization of the biologically functional cloverleaf shape in conjunction with the principal stabilizing component m 1 A9 exceeds the contribution of m 1 A alone. This constitutes an unprecedented cooperative effect of two nucleotide…

Glutamate 270 plays an essential role in K+-activation and domain closure ofThermus thermophilusisopropylmalate dehydrogenase

2014

The mutant E270A of Thermus thermophilus 3-isopropylmalate dehydrogenase exhibits largely reduced (∼1%) catalytic activity and negligible activation by K(+) compared to the wild-type enzyme. A 3-4 kcal/mol increase in the activation energy of the catalysed reaction upon this mutation could also be predicted by QM/MM calculations. In the X-ray structure of the E270A mutant a water molecule was observed to take the place of K(+). SAXS and FRET experiments revealed the essential role of E270 in stabilisation of the active domain-closed conformation of the enzyme. In addition, E270 seems to position K(+) into close proximity of the nicotinamide ring of NAD(+) and the electron-withdrawing effect…

Structure, interdomain dynamics, and pH-dependent autoactivation of pro-rhodesain, the main lysosomal cysteine protease from African trypanosomes

2021

AbstractRhodesain is the lysosomal cathepsin L-like cysteine protease ofT. brucei rhodesiense, the causative agent of Human African Trypanosomiasis. The enzyme is essential for the proliferation and pathogenicity of the parasite as well as its ability to overcome the blood-brain barrier of the host. Lysosomal cathepsins are expressed as zymogens with an inactivating pro-domain that is cleaved under acidic conditions. A structure of the uncleaved maturation intermediate from a trypanosomal cathepsin L-like protease is currently not available. We thus established the heterologous expression ofT. brucei rhodesiensepro-rhodesain inE. coliand determined its crystal structure. The trypanosomal pr…

When two become one: Integrating FRET and EPR into one structural model

2021

On the Mechanism of Gold/NHC Compounds Binding to DNA G-Quadruplexes: Combined Metadynamics and Biophysical Methods

2018

The binding modes and free-energy landscape of two AuI /N-heterocyclic carbene complexes interacting with G-quadruplexes, namely a human telomeric (hTelo) and a promoter sequence (C-KIT1), are studied here for the first time by metadynamics. The theoretical results are validated by FRET DNA melting assays and provide an accurate estimate of the absolute gold complex/DNA binding free energy. This advanced in silico approach is valuable to achieve rational drug design of selective G4 binders.

Fluorescence Lifetime of a Single Molecule as an Observable of Meta-Basin Dynamics in Fluids Near the Glass Transition

2006

Using single molecule spectroscopy, we show that the fluorescence lifetime trajectories of single probe molecules embedded in a glass-forming polymer melt exhibit strong fluctuations of a hopping character. Using molecular dynamics simulations targeted to explain these experimental observations, we show that the lifetime fluctuations correlate strongly with the average square displacement function of the matrix particles. The latter observable is a direct probe of the meta-basin transitions in the potential energy landscape of glass-forming liquids. We thus show here that single molecule experiments can provide detailed microscopic information on system properties that hitherto have been ac…

Boolean operations mediated by an ion-pair receptor of a multi-readout molecular logic gate

2013

A heteroditopic BODIPY dye that performs all basic Boolean operations with a cation (K+) and an anion (F-) as inputs and absorption, transmission and fluorescence as outputs is described. The molecular logic gate can also act as a digital comparator between the inputs.

Inside a Shell—Organometallic Catalysis Inside Encapsulin Nanoreactors

2021

Abstract Compartmentalization of chemical reactions inside cells are a fundamental requirement for life. Encapsulins are self‐assembling protein‐based nanocompartments from the prokaryotic repertoire that present a highly attractive platform for intracellular compartmentalization of chemical reactions by design. Using single‐molecule Förster resonance energy transfer and 3D‐MINFLUX analysis, we analyze fluorescently labeled encapsulins on a single‐molecule basis. Furthermore, by equipping these capsules with a synthetic ruthenium catalyst via covalent attachment to a non‐native host protein, we are able to perform in vitro catalysis and go on to show that engineered encapsulins can be used …

FRET based ratiometric Ca(2+) imaging to investigate immune-mediated neuronal and axonal damage processes in experimental autoimmune encephalomyeliti…

2015

Abstract Background Irreversible axonal and neuronal damage are the correlate of disability in patients suffering from multiple sclerosis (MS). A sustained increase of cytoplasmic free [Ca2+] is a common upstream event of many neuronal and axonal damage processes and could represent an early and potentially reversible step. New method We propose a method to specifically analyze the neurodegenerative aspects of experimental autoimmune encephalomyelitis by Forster Resonance Energy Transfer (FRET) imaging of neuronal and axonal Ca2+ dynamics by two-photon laser scanning microscopy (TPLSM). Results Using the genetically encoded Ca2+ sensor TN-XXL expressed in neurons and their corresponding axo…