A5090791975- DNA and Nucleic Acid Chemistry
- Advanced biosensing and bioanalysis techniques
- Nanopore and Nanochannel Transport Studies
- RNA Interference and Gene Delivery
- Antibiotic Resistance in Bacteria
- Metal complexes synthesis and properties
- Microfluidic and Capillary Electrophoresis Applications
- Bacteriophages and microbial interactions
- Microfluidic and Bio-sensing Technologies
- Ferrocene Chemistry and Applications
- RNA and protein synthesis mechanisms
- Gold and Silver Nanoparticles Synthesis and Applications
- Biosensors and Analytical Detection
- Electrostatics and Colloid Interactions
- DNA Repair Mechanisms
- Bacterial Identification and Susceptibility Testing
- Genomics and Phylogenetic Studies
- Molecular Junctions and Nanostructures
- Antibiotics Pharmacokinetics and Efficacy
- Bacterial biofilms and quorum sensing
- Lipid Membrane Structure and Behavior
- Click Chemistry and Applications
- Advanced Fluorescence Microscopy Techniques
- Alzheimer's disease research and treatments
- Bacterial Genetics and Biotechnology
Chalmers University of Technology
2016-2025
University of Gothenburg
2010-2024
In-Q-Tel
2017
Swedish Defence Research Agency
2009-2016
University of Copenhagen
2008-2013
Uppsala University
2013
University of Miami
2013
Max Planck Innovation
2012
Max Planck Society
2012
Suez University
2008
Abstract Long noncoding RNAs (lncRNAs) regulate gene expression by association with chromatin, but how they target chromatin remains poorly understood. We have used RNA immunoprecipitation-coupled high-throughput sequencing to identify 276 lncRNAs enriched in repressive from breast cancer cells. Using one of the chromatin-interacting lncRNAs, MEG3 , we explore mechanisms which chromatin. Here show that and EZH2 share common genes, including TGF-β pathway genes. Genome-wide mapping binding...
Abstract Copper compounds with artificial metallo-nuclease (AMN) activity are mechanistically unique compared to established metallodrugs. Here, we describe the development of a new dinuclear copper AMN, Cu2-BPL-C6 (BPL-C6 = bis-1,10-phenanthroline-carbon-6), prepared using click chemistry that demonstrates site-specific DNA recognition low micromolar cleavage activity. The BPL-C6 ligand was designed force two redox-active centres—central for enhancing AMN activity—to bind DNA, via...
In human mitochondria the transcription machinery generates RNA primers needed for initiation of DNA replication. A critical feature leading-strand origin mitochondrial replication is a CG-rich element denoted conserved sequence block II (CSB II). During CSB II, G-quadruplex structure forms in nascent RNA, which stimulates termination and primer formation. Previous studies have shown that newly synthesized form stable persistent RNA–DNA hybrid, R-loop, near We here demonstrate unusual...
Significance The main stabilizer of the DNA double helix is not base-pair hydrogen bonds but coin-pile stacking base pairs, whose hydrophobic cohesion, requiring abundant water, indirectly makes interior dry so that can exert full recognition power. We report certain semihydrophobic agents depress energy (measurable in single-molecule experiments), leading to transiently occurring holes stack (monitorable via binding threading intercalators). Similar structures observed complexes with RecA...
Thioflavin-T (ThT) is one of the most commonly used dyes for amyloid detection, but origin its fluorescence enhancement not fully understood. Herein we have characterised ThT response upon binding to Aβ(1-40) and Aβ(1-42) variants Alzheimer's-related peptide amyloid-β, in order explore how photophysical properties this dye relates structural morphological two fibril types formed by peptides with a high degree sequence homology. We show that steady-state 1.7 times more intense compared...
Extracellular polymeric substances (EPS) produced by bacteria form a matrix supporting the complex three-dimensional architecture of biofilms. This EPS is primarily composed polysaccharides, proteins and extracellular DNA. In addition to community structure, protects bacterial biofilms from environment. Specifically, it shields cells inside biofilm, preventing antimicrobial agents getting in contact with them, thereby reducing their killing effect. New strategies for disrupting formation can...
Abstract The key first step in developing bacterial infections related to implants and medical devices is the attachment of planktonic cells, subsequent formation biofilms. Herein, it reported that graphene, a 2D carbon‐based material, can be effectively used prevent attachment. parameter for this effect orientation graphene with respect coated surface. Chemical vapor deposition (CVD) deposited horizontally on surface, exhibits no antibacterial effect. By contrast, an array flakes grown...
Abstract Label-free characterization of single biomolecules aims to complement fluorescence microscopy in situations where labeling compromises data interpretation, is technically challenging or even impossible. However, existing methods require the investigated species bind a surface be visible, thereby leaving large fraction analytes undetected. Here, we present nanofluidic scattering (NSM), which overcomes these limitations by enabling label-free, real-time imaging diffusing inside...
Amyloid fibrils are protein polymers noncovalently assembled through β-strands arranged in a cross-β structure. Biological amyloids were considered chemically inert until we and others recently demonstrated their ability to catalyze chemical reactions vitro. To further explore the functional repertoire of amyloids, here probe if α-synuclein (αS) display reactivity toward DNA. We demonstrate that αS bind DNA at micromolar concentrations Using activity repair enzymes as proxy for damage,...
We here report a remarkably slow rearrangement of binding modes for binuclear ruthenium(II) complex upon interaction with DNA. It has been previously shown that Delta,Delta-[mu-(11,11'-bidppz)(phen)4Ru2]4+ binds to DNA in one the grooves. However, we find this is only an initial, metastable, mode, which extremely slowly reorganized into intercalative geometry. The and dissociation, revealed by flow linear dichroism fluorescence spectroscopy, are concluded be result from being threaded...
Stretching DNA in nanochannels is a useful tool for direct, visual studies of genomic at the single molecule level. To facilitate study interaction linear with proteins nanochannels, we have implemented highly effective passivation scheme based on lipid bilayers. We demonstrate virtually complete long-term nanochannel surfaces to range relevant reagents, including streptavidin-coated quantum dots, RecA proteins, and RecA–DNA complexes. show that performance bilayer significantly better than...
The self-assembly of individual nanoparticles into dimers-so-called heterodimers-is relevant for a broad range applications, in particular the vibrant field nanoplasmonics and nanooptics. In this paper we report synthesis characterization material- shape-selected nanoparticle heterodimers assembled from particles via electrostatic interaction. versatility synthetic strategy is shown by assembling combinations metal different shapes, sizes, compositions like gold sphere (90 nm) with either...
A nano flow cytometer to quantify lipid vesicles and analyse fluorescence intensity on a single vesicle level is presented.
Abstract We demonstrate a single DNA molecule optical mapping assay able to resolve specific Escherichia coli strain from other strains. The is based on competitive binding of the fluorescent dye YOYO-1 and AT-specific antibiotic netropsin. map visualized by stretching molecules in nanofluidic channels. optimize experimental conditions obtain reproducible barcodes containing as much information possible. implement multi-ligand transfer matrix method for calculating theoretical known...
Rapid characterization of unknown biological samples is under the focus many current studies. Here we report a method for screening by optical mapping their DNA. We use novel, one-step chemo-enzymatic reaction to covalently bind fluorophores DNA at four-base recognition sites methyltransferase. Due diffraction limit light, dense distribution labels results in continuous fluorescent signal along The amplitude modulations (AM) fluorescence intensity stretched molecules exhibit unique molecular...
Abstract Bacterial plasmids are extensively involved in the rapid global spread of antibiotic resistance. We here present an assay, based on optical DNA mapping single nanofluidic channels, which provides detailed information about a bacterial isolate. In experiment, we obtain number different sample, size each plasmid, barcode that can be used to identify and trace plasmid interest carries specific resistance gene. Gene identification is done using CRISPR/Cas9 loaded with guide-RNA (gRNA)...
Thioflavin-T binds to and detects amyloid fibrils via fluorescence enhancement. Using a combination of linear dichroism spectroscopies, we report that the relation between emission intensity binding thioflavin-T insulin is nonlinear discuss this in its use kinetic assays. We demonstrate, from lifetime recordings, nonlinearity due being sensitive self-quenching. In addition, can induce fibril compaction but not alter structure. Our work underscores photophysical complexity necessity...
A smartphone-based fluorescence microscope for detection of bacteria in complex samples using a species-specific peptide nucleic acid probe.
Optical genome mapping in nanochannels is a powerful genetic analysis method, complementary to deoxyribonucleic acid (DNA) sequencing. The method based on detecting pattern of fluorescent labels attached along individual DNA molecules. When such molecules are extended nanochannels, the create barcode that used for molecule its genomic locus and identifying large-scale variation from reference. Mapping resolution currently limited by two main factors: optical diffraction limit thermal...