Functional self-assembled DNA nanostructures for molecular recognition

Aptamers for Viral Detection and Inhibition

Recent times have experienced more than ever the impact of viral infections in humans. Viral infections are known to cause diseases not only in humans but also in plants and animals. Here, we have compiled the literature review of aptamers selected and used for detection and inhibition of viral infections in all three categories: humans, animals, and plants. This review gives an in-depth introduction to aptamers, different types of aptamer selection (SELEX) methodologies, the benefits of using aptamers over commonly used antibody-based strategies, and the structural and functional mechanism of aptasensors for viral detection and therapy. The review is organized based on the different characterization and read-out tools used to detect virus-aptasensor interactions with a detailed index of existing virus-targeting aptamers. Along with addressing recent developments, we also discuss a way forward with aptamers for DNA nanotechnology-based detection and treatment of viral diseases. Overall, this review will serve as a comprehensive resource for aptamer-based strategies in viral diagnostics and treatment.

Enhanced and synergistic downregulation of oncogenic miRNAs by self-assembled branched DNA

miRNAs, a group of small non-coding RNA molecules, regulate the expression of many genes involved in various cellular processes. Acute evidence suggests that one miRNA can regulate many genes as its targets, while one gene can be targeted by many miRNAs that co-operatively regulate the gene. Thus, targeting a single miRNA is not sufficient enough to rescue the disease phenotype but it is also essential to target multiple miRNAs simultaneously. This inspired us to design a novel DNA nanostructure that can concurrently downregulate multiple oncomiRNAs. Here we designed a programmable antimiR branched DNA (antimiR-bDNA) nanostructure having antimiRNAs for selective binding to oncomiRNAs miRNA-27a, 96 and 182 which collectively downregulate FOXO1a expression. The antimiR-bDNAs show enhanced stability compared to naked antimiRNAs in serum and are able to knockdown these miRNAs with up to ∼50% greater repression as compared to antimiRNAs. This synergistic miRNA repression leads to the restoration of FOXO1a protein levels which in turn inhibit G1-S traversion in cancer cells. To the best of our knowledge, this is the first study harnessing the ability of bDNA structures to silence multiple miRNAs simultaneously.

Ultrafast structural molecular dynamics investigated with 2D infrared spectroscopy methods

Ultrafast, multi-dimensional infrared (IR) spectroscopy has been advanced in recent years to a versatile analytical tool with a broad range of applications to elucidate molecular structure on ultrafast timescales, and it can be used for samples in a many different environments. Following a short and general introduction on the benefits of 2D IR spectroscopy, the first part of this chapter contains a brief discussion on basic descriptions and conceptual considerations of 2D IR spectroscopy. Outstanding classical applications of 2D IR are used afterwards to highlight the strengths and basic applicability of the method. This includes the identification of vibrational coupling in molecules, characterization of spectral diffusion dynamics, chemical exchange of chemical bond formation and breaking, as well as dynamics of intra- and intermolecular energy transfer for molecules in bulk solution and thin films. In the second part, several important, recently developed variants and new applications of 2D IR spectroscopy are introduced. These methods focus on (i) applications to molecules under two- and three-dimensional confinement, (ii) the combination of 2D IR with electrochemistry, (iii) ultrafast 2D IR in conjunction with diffraction-limited microscopy, (iv) several variants of non-equilibrium 2D IR spectroscopy such as transient 2D IR and 3D IR, and (v) extensions of the pump and probe spectral regions for multi-dimensional vibrational spectroscopy towards mixed vibrational-electronic spectroscopies. In light of these examples, the important open scientific and conceptual questions with regard to intra- and intermolecular dynamics are highlighted. Such questions can be tackled with the existing arsenal of experimental variants of 2D IR spectroscopy to promote the understanding of fundamentally new aspects in chemistry, biology and materials science. The final part of the chapter introduces several concepts of currently performed technical developments, which aim at exploiting 2D IR spectroscopy as an analytical tool. Such developments embrace the combination of 2D IR spectroscopy and plasmonic spectroscopy for ultrasensitive analytics, merging 2D IR spectroscopy with ultra-high-resolution microscopy (nanoscopy), future variants of transient 2D IR methods, or 2D IR in conjunction with microfluidics. It is expected that these techniques will allow for groundbreaking research in many new areas of natural sciences.

A highly versatile platform based on geometrically well-defined 3D DNA nanostructures for selective recognition and positioning of multiplex targets

We develop a versatile recognition system based on 3D triangular-shaped DNA nanotubes by integrating three different aptamer sequences along the three edges. This would allow multiple binding activities to be combined into a single system. The versatility of this nanotube platform can also provide a framework for spatial orientation and positioning of different aptamer-binding ligands in a 'pea-pod' architecture.

Sequence Design for a Test Tube of Interacting Nucleic Acid Strands

We describe an algorithm for designing the equilibrium base-pairing properties of a test tube of interacting nucleic acid strands. A target test tube is specified as a set of desired "on-target" complexes, each with a target secondary structure and target concentration, and a set of undesired "off-target" complexes, each with vanishing target concentration. Sequence design is performed by optimizing the test tube ensemble defect, corresponding to the concentration of incorrectly paired nucleotides at equilibrium evaluated over the ensemble of the test tube. To reduce the computational cost of accepting or rejecting mutations to a random initial sequence, the structural ensemble of each on-target complex is hierarchically decomposed into a tree of conditional subensembles, yielding a forest of decomposition trees. Candidate sequences are evaluated efficiently at the leaf level of the decomposition forest by estimating the test tube ensemble defect from conditional physical properties calculated over the leaf subensembles. As optimized subsequences are merged toward the root level of the forest, any emergent defects are eliminated via ensemble redecomposition and sequence reoptimization. After successfully merging subsequences to the root level, the exact test tube ensemble defect is calculated for the first time, explicitly checking for the effect of the previously neglected off-target complexes. Any off-target complexes that form at appreciable concentration are hierarchically decomposed, added to the decomposition forest, and actively destabilized during subsequent forest reoptimization. For target test tubes representative of design challenges in the molecular programming and synthetic biology communities, our test tube design algorithm typically succeeds in achieving a normalized test tube ensemble defect ≤1% at a design cost within an order of magnitude of the cost of test tube analysis.

Structural Characterization of Single-Stranded DNA Monolayers Using Two-Dimensional Sum Frequency Generation Spectroscopy

DNA-covered materials are important in technological applications such as biosensors and microarrays, but obtaining structural information on surface-bound biomolecules is experimentally challenging. In this paper, we structurally characterize single-stranded DNA monolayers of poly(thymine) from 10 to 25 bases in length with an emerging surface technique called two-dimensional sum frequency generation (2D SFG) spectroscopy. These experiments are carried out by adding a mid-IR pulse shaper to a femtosecond broad-band SFG spectrometer. Cross peaks and 2D line shapes in the 2D SFG spectra provide information about structure and dynamics. Because the 2D SFG spectra are heterodyne detected, the monolayer spectra can be directly compared to 2D infrared (2D IR) spectra of poly(thymine) in solution, which aids interpretation. We simulate the 2D SFG spectra using DFT calculations and an excitonic Hamiltonian that relates the molecular geometry to the vibrational coupling. Intrabase cross peaks help define the orientation of the bases and interbase cross peaks, created by coupling between bases, and resolves features not observed in 1D SFG spectra that constrain the relative geometries of stacked bases. We present a structure for the poly(T) oligomer that is consistent with the 2D SFG data. These experiments provide insight into the DNA monolayer structure and set precedent for studying complex biomolecules on surfaces with 2D SFG spectroscopy.

Backbone-branched DNA building blocks for facile angular control in nanostructures

Nanotechnology based on the highly specific pairing of nucleobases in DNA has been used to generate a wide variety of well-defined two- and three-dimensional assemblies, both static and dynamic. However, control over the junction angles to achieve them has been limited. To achieve higher order assemblies, the strands of the DNA duplex are typically made to deviate at junctions with configurations based on crossovers or non-DNA moieties. Such strand crossovers tend to be intrinsically unstructured with the overall structural rigidity determined by the architecture of the nanoassembly, rather than the junction itself. Specific approaches to define nanoassembly junction angles are based either on the cooperative twist- and strain-promoted tuning of DNA persistence length leading to bent DNA rods for fairly large nano-objects, or de novo synthesis of individual junction inserts that are typically non-DNA and based on small organic molecules or metal-coordinating ligand moieties. Here, we describe a general strategy for direct control of junction angles in DNA nanostructures that are completely tunable about the DNA helix. This approach is used to define angular vertices through readily accessible backbone-branched DNAs (bbDNAs). We demonstrate how such bbDNAs can be used as a new building block in DNA nanoconstruction to obtain well-defined nanostructures. Angular control through readily accessible bbDNA building block provides a general and versatile approach for incorporating well-defined junctions in nanoconstructs and expands the toolkit toward achieving strain free, highly size- and shape-tunable DNA based architectures.

A locked nucleic acid-based nanocrawler: designed and reversible movement detected by multicolor fluorescence

Herein we introduce a novel fluorescent LNA/DNA machine, a nanocrawler, which reversibly moves along a directionally polar complementary road controlled by affinity-enhancing locked nucleic acid (LNA) monomers and additional regulatory strands. Polyaromatic hydrocarbon (PAH) dyes attached to 2'-amino-LNA monomers are incorporated at four stations of the system, enabling simple detection of the position of the nanocrawler via a step-specific color signal. The sensing is provided by highly sensitive, chemically stable, and photostable PAH LNA interstrand communication systems, including pyrene excimer formation and pyrene-perylene interstrand Förster resonance energy transfer. We furthermore demonstrate that the nanocrawler selectively and reversibly moves along the road, followed by a bright and consistent fluorescence response for up to 10 cycles without any loss of signal.

Highly efficient remote controlled release system based on light-driven DNA nanomachine functionalized mesoporous silica

An intelligent photoswitchable single-molecule nanomachine with DNA hairpin-loop structure was designed by the incorporation of azobenzene groups in DNA sequences, which was studied by fluorescence resonance energy transfer (FRET) and attached onto the surface of mesoporous silica. Based on the photo-induced conformational transformation of DNA, highly efficient controlled release was realized.