Reverse engineering DNA origami nanostructure designs from raw scaffold and staple sequence lists

Designs for scaffolded DNA origami nanostructures are commonly and minimally published as the list of DNA staple and scaffold sequences required. In nearly all cases, high-level editable design files (e.g. caDNAno) which generated the low-level sequences are not made available. This de facto 'raw sequence' exchange format allows published origami designs to be re-attempted in the laboratory by other groups, but effectively stops designs from being significantly modified or re-purposed for new future applications. To make the raw sequence exchange format more accessible to further design and engineering, in this work we propose the first algorithmic solution to the inverse problem of converting staple/scaffold sequences back to a 'guide schematic' resembling the original origami schematic. The guide schematic can be used to aid the manual re-input of an origami into a CAD tool like caDNAno, hence recovering a high-level editable design file. Creation of a guide schematic can also be used to double check that a list of staple strand sequences does not have errors and indeed does assemble into a desired origami nanostructure prior to costly laboratory experimentation. We tested our reverse algorithm on 36 diverse origami designs from the literature and found that 29 origamis (81 %) had a good quality guide schematic recovered from raw sequences. Our software is made available at https://revnano.readthedocs.io.

Mechanical DNA Origami to Investigate Biological Systems

The ability to self-assemble DNA nanodevices with programmed structural dynamics that can sense and respond to the local environment can enable transformative applications in fields including mechanobiology and nanomedicine. The responsive function of biomolecules is often driven by alterations in conformational distributions mediated by highly sensitive interactions with the local environment. In this review, the current state-of-the-art in constructing complex DNA geometries with dynamic and mechanical properties to enable a molecular scale force measurement is first summarized. Next, an overview of engineering modular DNA devices that interact with cell surfaces is highlighted detailing examples of mechanosensitive proteins and the force-induced dynamic molecular interaction on the downstream biochemical signaling. Finally, the challenges and an outlook on this promising class of DNA devices acting as nanomachines to operate at a low piconewton range suitable for a majority of biological effects or as hybrid materials to achieve higher tension exertion required for other biological investigations, are discussed.

Thickness determination in anisotropic media with plasmon waveguide resonance imaging

This paper describes a simple procedure to determine the local thickness of a thin anisotropic layer. It also discriminates between isotropic and anisotropic regions, provided a smoothness hypothesis on the refractive index distribution is satisfied. The procedure is based on the analysis of surface plasmon resonance (SPR) data acquired in an imaging mode. The general arrangement of the setup is the Kretschmann configuration. We show, on an azobenzene modified polymer layer, good agreement between atomic force microscopy and optical measurements of thickness variation.

Spectral dependence of plasmon-enhanced fluorescence in a hollow nanotriangle assembled by DNA origami: towards plasmon assisted energy transfer

The precise positioning of plasmonic nanoscale objects and organic molecules can significantly boost our ability to fabricate hybrid nanoarchitectures with specific target functionalities. In this work, we used a DNA origami structure to precisely localize three different fluorescent dyes close to the tips of hollow gold nanotriangles. A spectral dependence of plasmon-enhanced fluorescence is evidenced through co-localized AFM and fluorescence measurements. The experimental results match well with explanatory FDTD simulations. Our findings open the way to the bottom-up fabrication of plasmonic routers operating through plasmon energy transfer. They will allow one to actively control the direction of light propagation.

A tensegrity driven DNA nanopore

Control of transport across membranes, whether natural or synthetic, is fundamental in many biotechnology applications, including sensing and drug release. Mutations of naturally existing protein channels, such as hemolysin, have been explored in the past. More recently, DNA channels with conductivities in the nanosiemens range have been designed. Regulating transport across DNA channels in response to external stimuli remains an important challenge. Previous designs relied on steric hindrance to control the inner diameter of the channel, which resulted in unstable electric signatures. In this paper we introduce a new design to control electric channel conductance of a DNA nanopore. The tensegrity driven mechanism inhibits the flux of small analytes while keeping a tightly controlled ionic transport modulated by the addition of specific DNA sequences. Current signals are clearly defined, with no sign of gating, opening new perspectives in single molecule DNA sensing.

High-resolution-scanning waveguide microscopy: spatial refractive index and topography quantification

We report on a high-resolution metal-clad waveguide scanning microscopic method with a diffraction-limited resolution. This microscope can be operated in both TM and TE waveguide modes with radially and azimuthally polarized beams, respectively, and allows both refractive index and topography of dielectric objects to be evaluated at high resolution and sensitivity. We emphasize the performance of this microscopic method from calibrated 3D polymer microstructures with rectangular, disk, and ring shapes.

Time-lapse scanning surface plasmon microscopy of living adherent cells with a radially polarized beam

We report on a fibered high-resolution scanning surface plasmon microscope for long term imaging of living adherent cells. The coupling of a high numerical aperture objective lens and a fibered heterodyne interferometer enhances both the sensitivity and the long term stability of this microscope, allowing for time-lapse recording over several days. The diffraction limit is reached with a radially polarized illumination beam. Adherence and motility of living C2C12 myoblast cells are followed for 50 h, revealing that the dynamics of these cells change after 10 h. This plasmon enhanced evanescent wave microscopy is particularly suited for investigating cell adhesion, since it can not only be performed without staining of the sample but it can also capture in real time the exchange of extracellular matrix elements between the substrate and the cells.

G-Quadruplexes Light up Localized DNA Circuits

DNA circuits tethered to nanoplatforms can perform cascade reactions for signal amplification. One DNA single strand activates a strand-displacement cascade generating numerous outputs, and therefore amplifying the signal. These localized circuits present, however, an important limitation: the spontaneous activation of the cascade reaction. Current methods to stabilize these circuits employ combination of protective DNA strands, which need to be removed to activate the device. This protection-deprotection process generates an important amount of unwanted side reactions. This is indeed an important limitation for the large potential application of these amplification circuits. In the present work, G-quadruplex DNA structures were used to stabilize localized DNA circuits. This new protocol generates nanoplatforms that no longer requires protective-deprotective systems and is therefore completely neutral to the sample. In addition, cations such as Pb(2+) or Ca(2+) can be also employed to activate the device enlarging the potential applications from biosensors devices to metal detector sensors.

Spectroscopic data for the G-quadruplex DNA to duplex DNA reaction

This article describes additional data related to a research article entitled “Kinetics of Quadruplex to Duplex Conversion” (Mendoza et al. 2015 [1]). We followed the opening reaction of a series of intramolecular G-quadruplex structures by the addition of their corresponding complementary strand. Fluorolabeled complementary strands allowed to monitor the reaction in real-time. An adapted kinetic model was then applied in order to obtain the kinetic parameters of this reaction.

We present a series of kinetic traces providing raw data of the G4 opening reaction and the fitting model applied in every case. In addition CD spectra and UV melting data is also provided to confirm the stability of all the DNA structures considered (G-quadruplex and duplex DNA).

Deciphering the internal complexity of living cells with quantitative phase microscopy: a multiscale approach

The distribution of refractive indices (RIs) of a living cell contributes in a nonintuitive manner to its optical phase image and quite rarely can be inverted to recover its internal structure. The interpretation of the quantitative phase images of living cells remains a difficult task because (1) we still have very little knowledge on the impact of its internal macromolecular complexes on the local RI and (2) phase changes produced by light propagation through the sample are mixed with diffraction effects by the internal cell bodies. We propose to implement a two-dimensional wavelet-based contour chain detection method to distinguish internal boundaries based on their greatest optical path difference gradients. These contour chains correspond to the highest image phase contrast and follow the local RI inhomogeneities linked to the intracellular structural intricacy. Their statistics and spatial distribution are the morphological indicators suited for comparing cells of different origins and/or to follow their transformation in pathologic situations. We use this method to compare nonadherent blood cells from primary and laboratory culture origins and to assess the internal transformation of hematopoietic stem cells by the transduction of the BCR-ABL oncogene responsible for the chronic myelogenous leukemia.

Connecting localized DNA strand displacement reactions

Logic circuits based on DNA strand displacement reactions have been shown to be versatile enough to compute the square root of four-bit numbers. The implementation of these circuits as a set of bulk reactions faces difficulties which include leaky reactions and intrinsically slow, diffusion-limited reaction rates. In this paper, we consider simple examples of these circuits when they are attached to platforms (DNA origamis). As expected, constraining distances between DNA strands leads to faster reaction rates. However, it also induces side-effects that are not detectable in the solution-phase version of this circuitry. Appropriate design of the system, including protection and asymmetry between input and fuel strands, leads to a reproducible behaviour, at least one order of magnitude faster than the one observed under bulk conditions.

Diffraction phase microscopy: retrieving phase contours on living cells with a wavelet-based space-scale analysis

We propose a two-dimensional (2-D) space-scale analysis of fringe patterns collected from a diffraction phase microscope based on the 2-D Morlet wavelet transform. We show that the adaptation of a ridge detection method with anisotropic 2-D Morlet mother wavelets is more efficient for analyzing cellular and high refractive index contrast objects than Fourier filtering methods since it can separate phase from intensity modulations. We compare the performance of this ridge detection method on theoretical and experimental images of polymer microbeads and experimental images collected from living myoblasts.

Plasmon-based tomographic microscopy

The imaging principle of the scanning surface plasmon microscope (SSPM) springs from the high sensitivity of surface plasmons to modifications of material properties near the dielectric-metal interface. In this paper, we show that tomographic techniques can be applied to SSPM imaging of dielectric objects to reach resolutions beyond the diffraction-limited half-wavelength scale. Furthermore, this high resolution is not limited to the multiple scattering regime. Finally, we conclude that SSPM is less sensitive to noise because it provides higher contrast ratio than other far-field microscopies.

Guided wave microscopy: mastering the inverse problem

Surface plasmon microscopy is widely recognized for its high sensitivity to nanoscale dielectric or metallic structures confined in a close neighborhood of a gold surface. Recently, its coupling to high-numerical-aperture objective lenses pushed its resolution down to the diffraction limit. Here, we show that the same microscope configuration can be used to excite standing guided waves in asymmetric slabs, which definitely extends the range of applications of this type of microscopy from nano- to microscale structure imaging. We demonstrate experimentally on PPMA films that the V(Z) response of a scanning surface plasmon microscope can be Fourier inverted in order to obtain the reflectivity curve R(ν). When the guided waves are excited, R(ν) shows a finite number of sharp peaks corresponding to quantified guiding modes from which one can extract both the refractive index (RI) and the thickness of the layer at the point focused by the microscope. This device can thus be used to reconstruct RI and thickness contours of dielectric samples with a high spatial resolution.

Cooperativity in the annealing of DNA origamis

DNA based nanostructures built on a long single stranded DNA scaffold, known as DNA origamis, offer the possibility to organize various molecules at the nanometer scale in one pot experiments. The folding of the scaffold is guaranteed by the presence of short, single stranded DNA sequences (staples), that hold together separate regions of the scaffold. In this paper, we modelize the annealing-melting properties of these DNA constructions. The model captures important features such as the hysteresis between melting and annealing, as well as the dependence upon the topology of the scaffold. We show that cooperativity between staples is critical to quantitatively explain the folding process of DNA origamis.

Wavelet-based decomposition of high resolution surface plasmon microscopy V(Z) curves at visible and near infrared wavelengths

Surface plasmon resonance is conventionally conducted in the visible range and, during the past decades, it has proved its efficiency in probing molecular scale interactions. Here we elaborate on the first implementation of a high resolution surface plasmon microscope that operates at near infrared (IR) wavelength for the specific purpose of living matter imaging. We analyze the characteristic angular and spatial frequencies of plasmon resonance in visible and near IR lights and how these combined quantities contribute to the V(Z) response of a scanning surface plasmon microscope (SSPM). Using a space-frequency wavelet decomposition, we show that the V(Z) response of the SSPM for red (632.8 nm) and near IR (1550 nm) lights includes the frequential response of plasmon resonance together with additional parasitic frequencies induced by the objective pupil. Because the objective lens pupil profile is often unknown, this space-frequency decomposition turns out to be very useful to decipher the characteristic frequencies of the experimental V(Z) curves. Comparing the visible and near IR light responses of the SSPM, we show that our objective lens, primarily designed for visible light microscopy, is still operating very efficiently in near IR light. Actually, despite their loss in resolution, the SSPM images obtained with near IR light remain contrasted for a wider range of defocus values from negative to positive Z values. We illustrate our theoretical modeling with a preliminary experimental application to blood cell imaging.

Evidence for cardiolipin binding sites on the membrane-exposed surface of the cytochrome bc1

The respiratory chain is located in the inner membrane of mitochondria and produces the major part of the ATP used by a cell. Cardiolipin (CL), a double charged phospholipid composing ~10-20% of the mitochondrial membrane, plays an important role in the function and supramolecular organization of the respiratory chain complexes. We present an extensive set of coarse-grain molecular dynamics (CGMD) simulations aiming at the determination of the preferential interfaces of CLs on the respiratory chain complex III (cytochrome bc(1), CIII). Six CL binding sites are identified, including the CL binding sites known from earlier structural studies and buried into protein cavities. The simulations revealed the importance of two subunits of CIII (G and K in bovine heart) for the structural integrity of these internal CL binding sites. In addition, new binding sites are found on the membrane-exposed protein surface. The reproducibility of these binding sites over two species (bovine heart and yeast mitochondria) points to an important role for the function of the respiratory chain. Interestingly the membrane-exposed CL binding sites are located on the matrix side of CIII in the inner membrane and thus may provide localized sources of proton ready for uptake by CIII. Furthermore, we found that CLs bound to those membrane-exposed sites bridge the proteins during their assembly into supercomplexes by sharing the binding sites.

Modeling the mechanical properties of DNA nanostructures

We discuss generalizations of a previously published coarse-grained description [Mergell et al., Phys. Rev. E 68, 021911 (2003)] of double stranded DNA (dsDNA). The model is defined at the base-pair level and includes the electrostatic repulsion between neighbor helices. We show that the model reproduces mechanical and elastic properties of several DNA nanostructures (DNA origamis). We also show that electrostatic interactions are necessary to reproduce atomic force microscopy measurements on planar DNA origamis.

Stability and structure of protein-lipoamino acid colloidal particles: toward nasal delivery of pharmaceutically active proteins

To circumvent the painful intravenous injection of proteins in the treatment of children with growth deficiency, anemia, and calcium insufficiency, we investigated the stability and structure of protein-lipoamino acid complexes that could be nasally sprayed. Preparations that ensure a colloidal and structural stability of recombinant human growth hormone (rhGH), recombinant human erythropoietin (rhEPO), and salmon calcitonin (sCT) mixed with lauroyl proline (LP) were established. Protein structure was controlled by circular dichroism, and very small sizes of ca. 5 nm were determined by dynamic light scattering. The colloidal preparations could be sprayed with a droplet size of 20-30 μm. The molecular structure of aggregates was investigated by all-atom molecular dynamics. Whereas a lauroyl proline capping of globular proteins rhGH and rhEPO with preservation of their active structure was observed, a mixed micelle of sCT and lipoamino acids was formed. In the latter, aggregated LP constitutes the inner core and the surface is covered with calcitonins that acquire a marked α-helix character. Hydrophobic/philic interaction balance between proteins and LP drives the particles' stability. Passage through nasal cells grown at confluence was markedly increased by the colloidal preparations and could reach a 20 times increase in the case of EPO. Biological implications of such colloidal preparations are discussed in terms of furtiveness.

Amplitude and phase images of cellular structures with a scanning surface plasmon microscope

Imaging cellular internal structure at nanometer scale axial resolution with non invasive microscopy techniques has been a major technical challenge since the nineties. We propose here a complement to fluorescence based microscopies with no need of staining the biological samples, based on a Scanning Surface Plasmon Microscope (SSPM). We describe the advantages of this microscope, namely the possibility of both amplitude and phase imaging and, due to evanescent field enhancement by the surface plasmon resonance, a very high resolution in Z scanning (Z being the axis normal to the sample). We show for fibroblast cells (IMR90) that SSPM offers an enhanced detection of index gradient regions, and we conclude it is very well suited to discriminate regions of variable density in biological media such as cell compartments, nucleus, nucleoli and membranes.

Modeling of the scanning surface plasmon microscope

We propose a family of exact solutions of Maxwell's equations to model some aspects of the imaging process involved in the scanning surface plasmon microscope (SSPM). More precisely, we compute the SSPM response of a spherical nanoparticle immobilized close to a thin gold layer and illuminated by a tightly focused spot. We discuss the influence of parameters such as the defocus and the width of the gold layer on the image contrast. We show that this microscopy combines a subwavelength spatial resolution together with high sensitivity to small changes in dielectric properties on the nanoparticle.

High-resolution surface-plasmon imaging in air and in water: V(z) curve and operating conditions

We present what are believed to be the first images obtained with a far-field high-resolution scanning surface-plasmon microscope in an aqueous medium. Measurements of V(z), the output response of the microscope, versus defocus z give a signature of the surface-plasmon propagation. V(z) is strongly conditioned by the laser beam diameter and the objective's numerical aperture, and we show how the operating mode (in air and in water) must be chosen to maximize the surface-plasmon field and to minimize diffraction (edge) effects.

Selection rules for the tip-splitting instability

The local destabilization of a Saffman-Taylor viscous finger occurs by a splitting of its tip and results in the formation of two branches separated by a fjord. The accumulation of such instabilities leads to complex patterns. In this paper we present a detailed analysis of a dynamical model that accounts for the selection of both the width and the orientation of the fjords growing in a wedge of angle theta(0). It is shown that the selection rules have a dynamical origin and are related to the existence of attracting sets that disappear in the absence of surface tension. We also infer the existence of a critical angle theta(c)=60 degrees such that if theta(0)<theta(c), the symmetric tip-splitting becomes unstable.

Exploring the natural conformational changes of the C-terminal domain of calmodulin

Several experimental results suggest that the Ca2+-loaded C-terminal domain of calmodulin (or some of its mutants) exhibits conformational changes triggered solely by thermal fluctuations. The time scales involved are in the 10(-6)-10(-3) s range. Here we develop a theoretical method to explore this type of motions based on a modified version of molecular dynamics algorithm where the secondary structure motifs are held fixed. In this version, increasing the temperature enhances the sampling of conformations with locally fixed secondary structures. From the temperature dependence of the transition rate between various conformational states, we obtain characteristic times that are consistent with those observed experimentally.

Internal structure of dense electrodeposits

We report experimental investigations of the structure of dense patterns obtained during electrochemical deposition of copper in thin cells. The deposit correlation function reveals the periodic structuration of the patterns but shows that the primary spacing is not steady during the growth and that moreover it is not simply related to the diffusion length. Another measurable quantity is the occupancy ratio of the fingers in the cell. Its variation as a function of the experimental parameters is interpreted from specific properties of electrochemical growth. The results are discussed with respect to the well-known behavior of cellular solidification fronts.

Dense branching morphology in electrodeposition experiments: characterization and mean-field modeling

Dense branching morphologies (DBM) obtained in thin gap electrodeposition cells are characterized by a dense array of branches behind a flat advancing envelope. In this Letter, we show the existence in DBM of a new (porous) phase, qualitatively different from a (compact) metal deposit. The local porosity inside the branches is found to be much more robust than geometric characteristics such as the width or the distance between branches. This fact seems to be unreported in previous modeling of DBM. A mean-field model is proposed that displays overall features observed in the experiments, such as concentration profiles, front velocity, and branched internal structure.

Modeling large-scale dynamics of proteins

We study a dynamical model for the large-scale motions of bovine pancreatic trypsin inhibitor in vacuum. The model is obtained by projecting Newton equations onto some set of anharmonic modes. We compare the statistics of the so-obtained trajectories with those obtained by standard techniques, and conclude that our dynamical model is able to reproduce fairly well the average properties of the large-scale motions of this protein. Moreover, it allows for time steps one order of magnitude larger than the standard ones.