Fredrik Westerlund

MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA–DNA triplex structures

Long noncoding RNAs (lncRNAs) regulate gene expression by association with chromatin, but how they target chromatin remains poorly understood. We have used chromatin RNA immunoprecipitation-coupled high-throughput sequencing to identify 276 lncRNAs enriched in repressive chromatin from breast cancer cells. Using one of the chromatin-interacting lncRNAs, MEG3, we explore the mechanisms by which lncRNAs target chromatin. Here we show that MEG3 and EZH2 share common target genes, including the TGF-β pathway genes. Genome-wide mapping of MEG3 binding sites reveals that MEG3 modulates the activity of TGF-β genes by binding to distal regulatory elements. MEG3 binding sites have GA-rich sequences, which guide MEG3 to the chromatin through RNA–DNA triplex formation. We have found that RNA–DNA triplex structures are widespread and are present over the MEG3 binding sites associated with the TGF-β pathway genes. Our findings suggest that RNA–DNA triplex formation could be a general characteristic of target gene recognition by the chromatin-interacting lncRNAs.

A hybrid G-quadruplex structure formed between RNA and DNA explains the extraordinary stability of the mitochondrial R-loop

In human mitochondria the transcription machinery generates the RNA primers needed for initiation of DNA replication. A critical feature of the leading-strand origin of mitochondrial DNA replication is a CG-rich element denoted conserved sequence block II (CSB II). During transcription of CSB II, a G-quadruplex structure forms in the nascent RNA, which stimulates transcription termination and primer formation. Previous studies have shown that the newly synthesized primers form a stable and persistent RNA–DNA hybrid, a R-loop, near the leading-strand origin of DNA replication. We here demonstrate that the unusual behavior of the RNA primer is explained by the formation of a stable G-quadruplex structure, involving the CSB II region in both the nascent RNA and the non-template DNA strand. Based on our data, we suggest that G-quadruplex formation between nascent RNA and the non-template DNA strand may be a regulated event, which decides the fate of RNA primers and ultimately the rate of initiation of DNA synthesis in human mitochondria.

Hydride formation thermodynamics and hysteresis in individual Pd nanocrystals with different size and shape

Physicochemical properties of nanoparticles may depend on their size and shape and are traditionally assessed in ensemble-level experiments, which accordingly may be plagued by averaging effects. These effects can be eliminated in single-nanoparticle experiments. Using plasmonic nanospectroscopy, we present a comprehensive study of hydride formation thermodynamics in individual Pd nanocrystals of different size and shape, and find corresponding enthalpies and entropies to be nearly size- and shape-independent. The hysteresis observed is significantly wider than in bulk, with details depending on the specifics of individual nanoparticles. Generally, the absorption branch of the hysteresis loop is size-dependent in the sub-30 nm regime, whereas desorption is size- and shape-independent. The former is consistent with a coherent phase transition during hydride formation, influenced kinetically by the specifics of nucleation, whereas the latter implies that hydride decomposition either occurs incoherently or via different kinetic pathways.

Lipid-Based Passivation in Nanofluidics

Stretching DNA in nanochannels is a useful tool for direct, visual studies of genomic DNA at the single molecule level. To facilitate the study of the interaction of linear DNA with proteins in nanochannels, we have implemented a highly effective passivation scheme based on lipid bilayers. We demonstrate virtually complete long-term passivation of nanochannel surfaces to a range of relevant reagents, including streptavidin-coated quantum dots, RecA proteins, and RecA–DNA complexes. We show that the performance of the lipid bilayer is significantly better than that of standard bovine serum albumin-based passivation. Finally, we show how the passivated devices allow us to monitor single DNA cleavage events during enzymatic degradation by DNase I. We expect that our approach will open up for detailed, systematic studies of a wide range of protein–DNA interactions with high spatial and temporal resolution.

Solution-Based Fabrication of Single-Crystalline Arrays of Organic Nanowires

Organic single-crystalline nanowire arrays, with a length of several hundreds of micrometers and controllable width, are grown on a substrate surface by vertically pulling the substrate out of an organic solution of the molecule of interest. Optical microscopy and atomic force microscopy show that the large-scale arrays are oriented parallel to the pulling direction and are well adhered to the substrate surface. Cross-polarized microscopy, polarized UV-vis absorption, and grazing incidence X-ray diffraction confirm that the arrays have high crystal quality. On the basis of this method, the fabrication of organic devices is realized in one step. The results presented here for three different small molecules show the promising potential of this facile solution-based process for the growth of high-quality organic semiconductors, the fabrication of high-density and high-performance devices, and the fabrication of controlled assemblies of nanoscale circuits for fundamental studies and future applications.

Self-Assembled Nanogaps via Seed-Mediated Growth of End-to-End Linked Gold Nanorods

Gold nanorods (AuNRs) are of interest for a wide range of applications, ranging from imaging to molecular electronics, and they have been studied extensively for the past decade. An important issue in AuNR applications is the ability to self-assemble the rods in predictable structures on the nanoscale. We here present a new way to end-to-end link AuNRs with a single or few linker molecules. Whereas methods reported in the literature so far rely on modification of the AuNRs after the synthesis, we here dimerize gold nanoparticle seeds with a water-soluble dithiol-functionalized polyethylene glycol linker and expose the linked seeds to growth conditions identical to the synthesis of unlinked AuNRs. Doing so, we obtain a large fraction of end-to-end linked rods, and transmission electron microscopy provides evidence of a 1-2 nm wide gap between the AuNRs. Flow linear dichroism demonstrates that a large fraction of the rods are flexible around the hinging molecule in solution, as expected for a molecularly linked nanogap. By using excess of gold nanoparticles relative to the linking dithiol molecule, this method can provide a high probability that a single molecule is connecting the two rods. In essence, our methods hence demonstrate the fabrication of a nanostructure with a molecule connected to two nanoelectrodes by bottom-up chemical assembly.

A Versatile Self-Assembly Strategy for the Synthesis of Shape-Selected Colloidal Noble Metal Nanoparticle Heterodimers

The self-assembly of individual nanoparticles into dimers—so-called heterodimers—is relevant for a broad range of applications, in particular in the vibrant field of nanoplasmonics and nanooptics. In this paper we report the synthesis and characterization of material- and shape-selected nanoparticle heterodimers assembled from individual particles via electrostatic interaction. The versatility of the synthetic strategy is shown by assembling combinations of metal particles of different shapes, sizes, and metal compositions like a gold sphere (90 nm) with either a gold cube (35 nm), gold rhombic dodecahedron (50 nm), palladium truncated cube (120 nm), palladium rhombic dodecahedron (110 nm), palladium octahedron (130 nm), or palladium cubes (25 and 70 nm) as well as a silver sphere (90 nm) with palladium cubes (25 and 70 nm). The obtained heterodimer combinations are characterized by transmission electron microscopy (TEM), scanning electron microscopy (SEM), scanning transmission electron microscopy–energy dispersive X-ray spectroscopy (STEM-EDX), dynamic light scattering (DLS), and zeta-potential measurements. We describe the optimal experimental conditions to achieve the highest yield of heterodimers compared to other aggregates. The experimental results have been rationalized using theoretical modeling. A proof-of-principle experiment where individual Au–Pd heterodimers are exploited for indirect plasmonic sensing of hydrogen finally illustrates the potential of these structures to probe catalytic processes at the single particle level.

Steady-state and time-resolved Thioflavin-T fluorescence can report on morphological differences in amyloid fibrils formed by Aβ(1-40) and Aβ(1-42)

Thioflavin-T (ThT) is one of the most commonly used dyes for amyloid detection, but the origin of its fluorescence enhancement is not fully understood. Herein we have characterised the ThT fluorescence response upon binding to the Aβ(1-40) and Aβ(1-42) variants of the Alzheimers-related peptide amyloid-β, in order to explore how the photophysical properties of this dye relates to structural and morphological properties of two amyloid fibril types formed by peptides with a high degree of sequence homology. We show that the steady-state ThT fluorescence is 1.7 times more intense with Aβ(1-40) compared to Aβ(1-42) fibrils in concentration matched samples prepared under quiescent conditions. By measuring the excited state lifetime of bound ThT, we also demonstrate a distinct difference between the two fibril isoforms, with Aβ(1-42) fibrils producing a longer ThT fluorescence lifetime compared to Aβ(1-40). The substantial steady-state intensity difference is therefore not explained by differences in fluorescence quantum yield. Further, we find that the ThT fluorescence intensity, but not the fluorescence lifetime, is dependent on the fibril preparation method (quiescent versus agitated conditions). We therefore propose that the fluorescence lifetime is inherent to each isoform and sensitively reports on fibril microstructure in the protofilament whereas the total fluorescence intensity relates to the amount of exposed β-sheet in the mature Aβ fibrils and hence to differences in their morphology. Our results highlight the complexity of ThT fluorescence, and demonstrate its extended use in amyloid fibril characterisation.

A single-step competitive binding assay for mapping of single DNA molecules

Optical mapping of genomic DNA is of relevance for a plethora of applications such as scaffolding for sequencing and detection of structural variations as well as identification of pathogens like bacteria and viruses. For future clinical applications it is desirable to have a fast and robust mapping method based on as few steps as possible. We here demonstrate a single-step method to obtain a DNA barcode that is directly visualized using nanofluidic devices and fluorescence microscopy. Using a mixture of YOYO-1, a bright DNA dye, and netropsin, a natural antibiotic with very high AT specificity, we obtain a DNA map with a fluorescence intensity profile along the DNA that reflects the underlying sequence. The netropsin binds to AT-tetrads and blocks these binding sites from YOYO-1 binding which results in lower fluorescence intensity from AT-rich regions of the DNA. We thus obtain a DNA barcode that is dark in AT-rich regions and bright in GC-rich regions with kilobasepair resolution. We demonstrate the versatility of the method by obtaining a barcode on DNA from the phage T4 that captures its circular permutation and agrees well with its known sequence.

Mechanically Manipulating the DNA Threading Intercalation Rate

The dumbbell shaped binuclear ruthenium complex DeltaDelta-P requires transiently melted DNA in order to thread through the DNA bases and intercalate DNA. Because such fluctuations are rare at room temperature, the binding rates are extremely low in bulk experiments. Here, single DNA molecule stretching is used to lower the barrier to DNA melting, resulting in direct mechanical manipulation of the barrier to DNA binding by the ligand. The rate of DNA threading depends exponentially on force, consistent with theoretical predictions. From the observed force dependence of the binding rate, we demonstrate that only one base pair must be transiently melted for DNA threading to occur.