Encoding folding paths of RNA switches

RNA co-transcriptional folding has long been suspected to play an active role in helping proper native folding of ribozymes and structured regulatory motifs in mRNA untranslated regions. Yet, the underlying mechanisms and coding requirements for efficient co-transcriptional folding remain unclear. Traditional approaches have intrinsic limitations to dissect RNA folding paths, as they rely on sequence mutations or circular permutations that typically perturb both RNA folding paths and equilibrium structures. Here, we show that exploiting sequence symmetries instead of mutations can circumvent this problem by essentially decoupling folding paths from equilibrium structures of designed RNA sequences. Using bistable RNA switches with symmetrical helices conserved under sequence reversal, we demonstrate experimentally that native and transiently formed helices can guide efficient co-transcriptional folding into either long-lived structure of these RNA switches. Their folding path is controlled by the order of helix nucleations and subsequent exchanges during transcription, and may also be redirected by transient antisense interactions. Hence, transient intra- and intermolecular base pair interactions can effectively regulate the folding of nascent RNA molecules into different native structures, provided limited coding requirements, as discussed from an information theory perspective. This constitutive coupling between RNA synthesis and RNA folding regulation may have enabled the early emergence of autonomous RNA-based regulation networks.Comment: 9 pages, 6 figure

Probing complex RNA structures by mechanical force

RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpretated by solely invoking successive openings of native helices. Indeed, typical force-extension responses of complex RNA molecules are largely shaped by stretching-induced, long-lived intermediates including non-native helices. This is first shown for a set of generic structural motifs found in larger RNA structures, and then for Escherichia coli's 1540-base long 16S ribosomal RNA, which exhibits a surprisingly well-structured and reproducible unfolding pathway under mechanical stretching. Using out-of-equilibrium stochastic simulations, we demonstrate that these experimental results reflect the slow relaxation of RNA structural rearrangements. Hence, micromanipulations of single RNA molecules probe both their native structures and long-lived intermediates, so-called "kinetic traps", thereby capturing -at the single molecular level- the hallmark of RNA folding/unfolding dynamics.Comment: 9 pages, 9 figure

Single-molecule experiments in biological physics: methods and applications

I review single-molecule experiments (SME) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize individual molecules and measure microscopic forces. Using SME it is possible to: manipulate molecules one at a time and measure distributions describing molecular properties; characterize the kinetics of biomolecular reactions and; detect molecular intermediates. SME provide the additional information about thermodynamics and kinetics of biomolecular processes. This complements information obtained in traditional bulk assays. In SME it is also possible to measure small energies and detect large Brownian deviations in biomolecular reactions, thereby offering new methods and systems to scrutinize the basic foundations of statistical mechanics. This review is written at a very introductory level emphasizing the importance of SME to scientists interested in knowing the common playground of ideas and the interdisciplinary topics accessible by these techniques. The review discusses SME from an experimental perspective, first exposing the most common experimental methodologies and later presenting various molecular systems where such techniques have been applied. I briefly discuss experimental techniques such as atomic-force microscopy (AFM), laser optical tweezers (LOT), magnetic tweezers (MT), biomembrane force probe (BFP) and single-molecule fluorescence (SMF). I then present several applications of SME to the study of nucleic acids (DNA, RNA and DNA condensation), proteins (protein-protein interactions, protein folding and molecular motors). Finally, I discuss applications of SME to the study of the nonequilibrium thermodynamics of small systems and the experimental verification of fluctuation theorems. I conclude with a discussion of open questions and future perspectives.Comment: Latex, 60 pages, 12 figures, Topical Review for J. Phys. C (Cond. Matt

Design of Protein-Coated Carbon Nanotubes Loaded with Hydrophobic Drugs through Sacrificial Templating of Mesoporous Silica Shells

One key challenge in the fields of nanomedicine and tissue engineering is the design of theranostic nanoplatforms able to monitor their therapeutic effect by imaging. Among current developed nano-objects, carbon nanotubes (CNTs) were found suitable to combine imaging, photothermal therapy, and to be loaded with hydrophobic drugs. However, a main problem is their resulting low hydrophilicity. To face this problem, an innovative method is developed here, which consists in loading the surface of carbon nanotubes (CNTs) with drugs followed by a protein coating around them. The originality of this method relies on first covering CNTs with a sacrificial template mesoporous silica (MS) shell grafted with isobutyramide (IBAM) binders on which a protein nanofilm is strongly adhered through IBAM-mediated physical cross-linking. This concept is first demonstrated without drugs, and is further improved with the suitable loading of hydrophobic drugs, curcumin (CUR) and camptothecin (CPT), which are retained between the CNTs and human serum albumin (HSA) layer. Such novel nanocomposites with favorable photothermal properties are very promising for theranostic systems, drug delivery, and phototherapy applications

Cell viscosity influences hematogenous dissemination and metastatic extravasation of tumor cells

Metastases arise from a multi-step process during which tumor cells change their mechanics in response to microenvironmental cues. While such mechanical adaptability could influence metastatic success, how tumor cell mechanics directly impacts intravascular behavior of circulating tumor cells (CTCs) remains poorly understood. In the present study, we demonstrate how the deformability of CTCs affects hematogenous dissemination and identify the mechanical profiles that favor metastatic extravasation. Combining intravital microscopy with CTC-mimicking elastic beads and mechanically-tuned tumor cells, we demonstrate that the inherent properties of circulating objects dictate their ability to enter constraining vessels. We identify cellular viscosity as the key property that governs CTC circulation and arrest patterns. We further demonstrate that cellular viscosity is required for efficient extravasation and find that properties that favor extravasation and subsequent metastatic outgrowth can be opposite. Altogether, we identify CTC viscosity as a key biomechanical parameter that shapes several steps of metastasis

N-Heterocyclic Carbene-Platinum Complexes Featuring an Anthracenyl Moiety: Anti-Cancer Activity and DNA Interaction

A platinum (II) complex stabilized by a pyridine and an N-heterocyclic carbene ligand featuring an anthracenyl moiety was prepared. The compound was fully characterized and its molecular structure was determined by single-crystal X-ray diffraction. The compound demonstrated high in vitro antiproliferative activities against cancer cell lines with IC50 ranging from 10 to 80 nM. The presence of the anthracenyl moiety on the N-heterocyclic carbene (NHC) Pt complex was used as a luminescent tag to probe the metal interaction with the nucleobases of the DNA through a pyridine-nucleobase ligand exchange. Such interaction of the platinum complex with DNA was corroborated by optical tweezers techniques and liquid phase atomic force microscopy (AFM). The results revealed a two-state interaction between the platinum complex and the DNA strands. This two-state behavior was quantified from the different experiments due to contour length variations. At 24 h incubation, the stretching curves revealed multiple structural breakages, and AFM imaging revealed a highly compact and dense structure of platinum complexes bridging the DNA strands

Wrapped stellate silica nanocomposites as biocompatible luminescent nanoplatforms assessed in vivo

The engineering of luminescent nanoplatforms for biomedical applications displaying ability for scaling-up, good colloidal stability in aqueous solutions, biocompatibility, and providing an easy detection in vivo by fluorescence methods while offering high potential of functionalities, is currently a challenge. The original strategy proposed here involves the use of large pore (ca. 15 nm) mesoporous silica (MS) nanoparticles (NPs) having a stellate morphology (denoted STMS) on which fluorescent InP/ZnS quantum dots (QDs) are covalently grafted with a high yield (>= 90%). These nanoplatforms are after that further coated to avoid a potential QDs release. To protect the QDs from potential release or dissolution, two wrapping methods are developed: (i) a further coating with a silica shell having small pores (<= 2 nm) or (ii) a tight polysaccharide shell deposited on the surface of these STMS@QDs particles via an original isobutyramide (IBAM)-mediated method. Both wrapping approaches yield to novel luminescent nanoplatforms displaying a highly controlled structure, a high size monodispersity (ca. 200 and 100 nm respectively) and colloidal stability in aqueous solutions. Among both methods, the IBAM-polysaccharide coating approach is shown the most suitable to ensure QDs protection and to avoid metal cation release over three months. Furthermore, these original STMS@QDs@polysaccharide luminescent nanoplatforms are shown biocompatible in vitro with murine cancer cells and in vivo after injections within zebrafish (ZF) translucent embryos where no sign of toxicity is observed during their development over several days. As assessed by in vivo confocal microscopy imaging, these nanoplatforms are shown to rapidly extravasate from blood circulation to settle in neighboring tissues, ensuring a remanent fluorescent labelling of ZF tissues in vivo. Such fluorescent and hybrid STMS composites are envisioned as novel luminescent nanoplatforms for in vivo fluorescence tracking applications and offer a versatile degree of additional functionalities (drug delivery, incorporation of magnetic/plasmonic core). (C) 2019 Elsevier Inc. All rights reserved

Effect of the size and shape of dendronized iron oxide nanoparticles bearing a targeting ligand on MRI, magnetic hyperthermia, and photothermia properties - from suspension to in vitro studie

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