Site-Specific Control of Distances between Gold Nanoparticles Using Phosphorothioate Anchors on DNA and a Short Bifunctional Molecular Fastener

Utilizing peptide-anchored DNA templates for novel programmable nanoparticle assemblies in biological macromolecules: A review

Biological macromolecules such as proteins and DNA are known to self-assemble into various structural moieties with distinct functions. While nucleic acids are the structural building blocks, peptides exemplify diversity as tailorable biochemical units. Thus, combining the scaffold properties of the biomacromolecule DNA and the functionality of peptides could evolve into a powerful method to obtain tailorable nano assemblies. In this review, we discuss the assembly of non-DNA-coated colloidal NPs on DNA/peptide templates using functional anchors. We begin with strategies for directly attaching metallic NPs to DNA templates to ascertain the functional role of DNA as a scaffold. Followed by methods to assemble peptides onto DNA templates to emphasize the functional versatility of biologically abundant DNA-binding peptides. Next, we focus on studies corroborating peptide self-assembling into macromolecular templates onto which NPs can attach to emphasize the properties of NP-binding peptides. Finally, we discuss the assembly of NPs on a DNA template with a focus on the bifunctional DNA-binding peptides with NP-binding affinity (peptide anchors). This review aims to highlight the immense potential of combining the functional power of DNA scaffolds and tailorable functionalities of peptides for NP assembly and the need to utilize them effectively to obtain tailorable hierarchical NP assemblies.

Ultrasmall ATP-Coated Gold Nanoparticles Specifically Bind to Non-Hybridized Regions in DNA

Here we report the synthesis of ultrasmall (2 nm in diameter) ATP-coated gold nanoparticles, ATP-NPs. ATP-NPs can be enlarged in a predictable manner by the surface-catalyzed reduction of gold ions with ascorbate, yielding uniform gold nanoparticles ranging in size from 2 to 5 nm in diameter. Using atomic force microscopy (AFM), we demonstrate that ATP-NPs can efficiently and selectively bind to a short non-hybridized 5A/5A region (composed of a 5A-nucleotide on each strand of the double helix) inserted into a circular double-stranded plasmid, Puc19. Neither small (1.4 nm in diameter) commercially available nanoparticles nor 5 nm citrate-protected ones are capable of binding to the plasmid. The unique ability to specifically target DNA regions characterized by local structural alterations of the double helix can pave the way for applications of the particles in the detection of genomic DNA regions containing mismatches and mutations that are common for cancer cells.

Gold Nanoparticles as Exquisite Colorimetric Transducers for Water Pollutant Detection

Gold nanoparticles (AuNPs) are useful nanomaterials as transducers for colorimetric sensors because of their high extinction coefficient and ability to change color depending on aggregation status. Therefore, over the past few decades, AuNP-based colorimetric sensors have been widely applied in several environmental and biological applications, including the detection of water pollutants. According to various studies, water pollutants are classified into heavy metals or cationic metal ions, toxins, and pesticides. Notably, many researchers have been interested in AuNP that detect water pollutants with high sensitivity and selectivity, while offering no adverse environmental issues in terms of AuNP use. This review provides a representative overview of AuNP-based colorimetric sensors for detecting several water pollutants. In particular, we emphasize the advantages of AuNP as colorimetric transducers for water pollutant detection in terms of their low toxicity, high stability, facile processability, and unique optical properties. Next, we discuss the status quo and future prospects of AuNP-based colorimetric sensors for the detection of water pollutants. We believe that this review will promote research and development of AuNP as next-generation colorimetric transducers for water pollutant detection.

Rapid, inexpensive, sequence-independent fluorescent labeling of phosphorothioate DNA

Fluorescently labeled oligonucleotides are powerful tools for characterizing DNA processes; however, their use is limited by the cost and sequence requirements of current labeling technologies. Here, we develop an easy, inexpensive, and sequence-independent method for site-specifically labeling DNA oligonucleotides. We utilize commercially synthesized oligonucleotides containing phosphorothioate diester(s) in which a nonbridging oxygen is replaced with a sulfur (PS-DNA). The increased nucleophilicity of the thiophosphoryl sulfur relative to the phosphoryl oxygen permits selective reactivity with iodoacetamide compounds. As such, we leverage a long-existing bifunctional linker, N,N'-bis(α-iodoacetyl)-2-2'-dithiobis(ethylamine) (BIDBE), that reacts with PS-DNAs to leave a free thiol, allowing conjugation of the wide variety of commercial maleimide-functionalized compounds. We optimized BIDBE synthesis and its attachment to PS-DNA and then fluorescently labeled the BIDBE-PS-DNA using standard protocols for labeling cysteines. We purified the individual epimers, and using single-molecule Förster resonance energy transfer (FRET), we show that the FRET efficiency is independent of the epimeric attachment. Subsequently, we demonstrate that an epimeric mixture of double-labeled Holliday junctions (HJs) can be used to characterize their conformational properties in the absence and presence of the structure-specific endonuclease Drosophila melanogaster Gen. Finally, we use a biochemical activity assay to show that this double-labeled HJ is functional for cleavage by Gen and that the double-labeled HJ allows multiple DNA species to be identified in a single experiment. In conclusion, our results indicate that dye-labeled BIDBE-PS-DNAs are comparable to commercially labeled DNAs at a significantly reduced cost. Notably, this technology could be applied to other maleimide-functionalized compounds, such as spin labels, biotin, and proteins. The sequence independence of labeling, coupled with its ease and low cost, enables unrestricted exploration of dye placement and choice, providing the potential for creation of differentially labeled DNA libraries and opening previously inaccessible experimental avenues.

Phosphorothioate-Based Site-Specific Labeling of Large RNAs for Structural and Dynamic Studies

Pulsed electron-electron double resonance (PELDOR) spectroscopy, X-ray scattering interferometry (XSI), and single-molecule Förster resonance energy transfer (smFRET) are molecular rulers that provide inter- or intramolecular pair-wise distance distributions in the nanometer range, thus being ideally suitable for structural and dynamic studies of biomolecules including RNAs. The prerequisite for such applications requires site-specific labeling of biomolecules with spin labels, gold nanoparticles, and fluorescent tags, respectively. Recently, site-specific labeling of large RNAs has been achieved by a combination of transcription of an expanded genetic alphabet containing A-T/G-C base pairs and NaM-TPT3 unnatural base pair (UBP) with post-transcriptional modifications at UBP bases by click chemistry or amine-NHS ester reactions. However, due to the bulky sizes of functional groups or labeling probes used, such strategies might cause structural perturbation and decrease the accuracy of distance measurements. Here, we synthesize an α-thiophosphorylated variant of rTPT3TP (rTPT3αS), which allows for post-transcriptional site-specific labeling of large RNAs at the internal α-phosphate backbone via maleimide-modified probes. Subsequent PELDOR, XSI, and smFRET measurements result in narrower distance distributions than labeling at the TPT3 base. The presented strategy provides a new route to empower the molecular rulers for structural and dynamic studies of large RNA and its complex.

Wavelength-Selective Activation of Photocaged DNAzymes for Metal Ion Sensing in Live Cells

RNA-cleaving DNAzymes are widely applied as sensors for detecting metal ions in environmental samples owing to their high sensitivity and selectivity, but their use for sensing biological metal ions in live cells is challenging because constitutive sensors fail to report the spatiotemporal heterogeneity of biological processes. Photocaged DNAzymes can be activated by light for sensing purposes that need spatial and temporal resolution. Studying complex biological processes requires logic photocontrol, but unfortunately all the literature-reported photocaged DNAzymes working in live cells cannot be selectively controlled by light irradiation at different wavelengths. In this work, we developed photocaged DNAzymes responsive to UV and visible light using a general synthetic method based on phosphorothioate chemistry. Taking the Zn²⁺-dependent DNAzyme sensor as a model, we achieved wavelength-selective activation of photocaged DNAzymes in live human cells by UV and visible light, laying the groundwork for the logic activation of DNAzyme-based sensors in biological systems.

Chemical synthesis of stimuli-responsive guide RNA for conditional control of CRISPR-Cas9 gene editing

CRISPR-Cas9 promotes changes in identity or abundance of nucleic acids in live cells and is a programmable modality of broad biotechnological and therapeutic interest. To reduce off-target effects, tools for conditional control of CRISPR-Cas9 functions are under active research, such as stimuli-responsive guide RNA (gRNA). However, the types of physiologically relevant stimuli that can trigger gRNA are largely limited due to the lack of a versatile synthetic approach in chemistry to introduce diverse labile modifications into gRNA. In this work, we developed such a general method to prepare stimuli-responsive gRNA based on site-specific derivatization of 2′-O-methylribonucleotide phosphorothioate (PS-2′-OMe). We demonstrated CRISPR-Cas9-mediated gene editing in human cells triggered by oxidative stress and visible light, respectively. Our study tackles the synthetic challenge and paves the way for chemically modified RNA to play more active roles in gene therapy.

Conditional control of CRISPR-Cas9 activity by reactive oxygen species and visible light is achieved using stimuli-responsive guide RNA synthesized by a general method based on RNA 2′-O-methylribonucleotide phosphorothioate.

Designing of peptide aptamer targeting the receptor-binding domain of spike protein of SARS-CoV-2: an in silico study

Short synthetic peptide molecules which bind to a specific target protein with a high affinity to exert its function are known as peptide aptamers. The high specificity of aptamers with small-molecule targets (metal ions, dyes and theophylline; ATP) is within 1 pM and 1 μM range, whereas with the proteins (thrombin, CD4 and antibodies) it is in the nanomolar range (which is equivalent to monoclonal antibodies). The recently identified coronavirus (SARS-CoV-2) genome encodes for various proteins, such as envelope, membrane, nucleocapsid, and spike protein. Among these, the protein necessary for the virus to enter inside the host cell is spike protein. The work focuses on designing peptide aptamer targeting the spike receptor-binding domain of SARS-CoV-2. The peptide aptamer has been designed by using bacterial Thioredoxin A as the scaffold protein and an 18-residue-long peptide. The tertiary structure of the peptide aptamer is modeled and docked to spike receptor-binding domain of SARS CoV2. Molecular dynamic simulation has been done to check the stability of the aptamer and receptor-binding domain complex. It was observed that the aptamer binds to spike receptor-binding domain of SARS-CoV-2 in a similar pattern as that of ACE2. The aptamer-receptor-binding domain complex was found to be stable in a 100 ns molecular dynamic simulation. The aptamer is also predicted to be non-antigenic, non-allergenic, non-hemolytic, non-inflammatory, water-soluble with high affinity toward ACE2 than serum albumin. Thus, peptide aptamer can be a novel approach for the therapeutic treatment for SARS-CoV-2.

Multifunctional Heterogeneous Carbon Nanotube Nanocomposites Assembled by DNA-Binding Peptide Anchors

Although carbon nanotubes (CNTs) are remarkable materials with many exceptional characteristics, their poor chemical functionality limits their potential applications. Herein, a strategy is proposed for functionalizing CNTs, which can be achieved with any functional group (FG) without degrading their intrinsic structure by using a deoxyribonucleic acid (DNA)-binding peptide (DBP) anchor. By employing a DBP tagged with a certain FG, such as thiol, biotin, and carboxyl acid, it is possible to introduce any FG with a controlled density on DNA-wrapped CNTs. Additionally, different types of FGs can be introduced on CNTs simultaneously, using DBPs tagged with different FGs. This method can be used to prepare CNT nanocomposites containing different types of nanoparticles (NPs), such as Au NPs, magnetic NPs, and quantum dots. The CNT nanocomposites decorated with these NPs can be used as reusable catalase-like nanocomposites with exceptional catalytic activities, owing to the synergistic effects of all the components. Additionally, the unique DBP-DNA interaction allows the on-demand detachment of the NPs attached to the CNT surface; further, it facilitates a CNT chirality-specific NP attachment and separation using the sequence-specific programmable characteristics of oligonucleotides. The proposed method provides a novel chemistry platform for constructing new functional CNTs suitable for diverse applications.

A palindromic-based strategy for colorimetric detection of HIV-1 nucleic acid: Single-component assembly of gold nanoparticle-core spherical nucleic acids

Gold nanoparticle-core spherical nucleic acids (AuNP core-SNAs), by virtue of the programmable nature of oligonucleotides, have yielded access to the innovative strategies for targeted biodiagnostics. Here, DNA-directed self-assembly of AuNP core-SNAs has been used to design a colorimetric method to sense HIV-1 viral nucleic acid. This strategy utilizes an oligonucleotide with sequence of 5'-untranslated region (5' UTR) of the HIV-1 RNA genome anchored on the surface of AuNPs and a complementary linker strand with a palindromic sequence tail. In the absence of HIV-1 target nucleic acid the complementary linker induces self-assembly of SNAs based on sequence symmetry in the free palindromic tail which can bridge two DNA double helices. While in the presence of the target DNA, due to linker-target duplex formation, the colloidal stability and the red color of the SNAs solution are preserved. Picomole amounts of target DNA can easily be detected with the naked eyes. A 95-mer synthetic DNA strand with the same sequence of HIV-1 viral RNA was utilized for positive control of HIV-1 RNA. The selectivity of the selected linker was satisfactory up to 90% match.

Multiply Modified Repeating DNA Templates for Production of Novel DNA-Based Nanomaterial

Here, we report synthesis of long (thousands of base pairs), uniform double-stranded (ds) DNA comprising short (6-15 base pairs) tandem repeats. The synthesis method is based on self-assembly of short (6-15 bases) half-complementary 5'-end phosphorylated single-stranded oligonucleotides into long ds polymer molecules and covalent association of the oligonucleotide fragments in the polymer by DNA ligase to yield complete non-nicked ds DNA. The method is very flexible in regard to the sequence of the oligonucleotides and their length. Human telomeric DNA comprising thousands of base pairs as well as methylated, mismatched, and fluorescent dye-modified uniform dsDNA molecules can be synthesized. We have demonstrated by high resolution frequency-modulation atomic force microscopy that the structure of DNA containing mismatches is strongly different from that of the non-mismatched one. The DNA molecules comprising groups capable of anchoring metal particles and other redox active elements along the whole length of the nucleic acid polymer should find use as wires or transistors in future nanoelectronic applications.

Phosphorothioate DNA Mediated Sequence-Insensitive Etching and Ripening of Silver Nanoparticles

Many DNA-functionalized nanomaterials and biosensors have been reported, but most have ignored the influence of DNA on the stability of nanoparticles. We observed that cytosine-rich DNA oligonucleotides can etch silver nanoparticles (AgNPs). In this work, we showed that phosphorothioate (PS)-modified DNA (PS-DNA) can etch AgNPs independently of DNA sequence, suggesting that the thio-modifications are playing the major role in etching. Compared to unmodified DNA (e.g., poly-cytosine DNA), the concentration of required PS DNA decreases sharply, and the reaction rate increases. Furthermore, etching by PS-DNA occurs quite independent of pH, which is also different from unmodified DNA. The PS-DNA mediated etching could also be controlled well by varying DNA length and conformation, and the number and location of PS modifications. With a higher activity of PS-DNA, the process of etching, ripening, and further etching was taken place sequentially. The etching ability is inhibited by forming duplex DNA and thus etching can be used to measure the concentration of complementary DNA.

Aptamer-assisted novel technologies for detecting bacterial pathogens

Nowadays, all people are at risk of infectious diseases that are mainly caused by bacteria causing infection. There is a permanent demand for an appropriate detection method that is affordable, practical, careful, rapid, sensitive, efficient and economical. Aptamers are single stranded DNA or RNA oligonucleotides, which can be recognized specifically and bind to their target molecules and also, be exploited in diagnostic applications. Recently, aptamer-based systems have offered great potentials in applications for the recognition of several important bacterial pathogens from clinical and food specimens. There are several reports appraising the diagnostic applicability of aptamer-based systems for the detection of pathogens. As for its excellent sensitivity, as well as its rapid and efficient detectability, this technique may be practical to indicate bacterial targets with less sample size and may consume less time than traditional methods These systems offer a promising approach for the sensitive and quick detection of food-borne and clinical agents. This review provides an overview of aptamer-based methods as a novel approach for detecting bacterial pathogens.

DNA Binding Peptide Directed Synthesis of Continuous DNA Nanowires for Analysis of Large DNA Molecules by Scanning Electron Microscope

Synthesis of smooth and continuous DNA nanowires, preserving the original structure of native DNA, and allowing its analysis by scanning electron microscope (SEM), is demonstrated. Gold nanoparticles densely assembled on the DNA backbone via thiol-tagged DNA binding peptides work as seeds for metallization of DNA. This method allows whole analysis of DNA molecules with entangled 3D features.

Quantum dots-DNA bioconjugates: synthesis to applications

Semiconductor nanoparticles particularly quantum dots (QDs) are interesting alternatives to organic fluorophores for a range of applications such as biosensing, imaging and therapeutics. Addition of a programmable scaffold such as DNA to QDs further expands the scope and applicability of these hybrid nanomaterials in biology. In this review, the most important stages of preparation of QD-DNA conjugates for specific applications in biology are discussed. Special emphasis is laid on (i) the most successful strategies to disperse QDs in aqueous media, (ii) the range of different conjugation with detailed discussion about specific merits and demerits in each case, and (iii) typical applications of these conjugates in the context of biology.

DNA-Mediated Morphological Control of Silver Nanoparticles

It is demonstrated that DNA can be used to control the synthesis of silver nanoplates with different morphologies using spherical silver seeds. UV-vis spectroscopy, transmission electron microscopy, scanning electron microscopy, X-ray photoelectron spectroscopy, and Raman spectroscopy are used to characterize the synthesized nanoparticles. Silver nanoprisms are encoded by poly C and poly G, while silver flower bouquets and silver nanodiscs are synthesized using poly A and poly T, respectively. The length of DNA is found to have little effect on the morphology of silver nanoparticles. Moreover, the synthesized silver nanoplates are found to have high surface enhanced Raman scattering enhancement ability, good antibacterial activity, and good biocompatibility. These discoveries will broaden the application of DNA in nanoscience and will provide a new platform to investigate the interaction between DNA sequences and silver nanoparticles.

An Ultrasensitive Light-up Cu(2+) Biosensor Using a New DNAzyme Cleaving a Phosphorothioate-Modified Substrate

Cu(2+) is a very important metal ion in biology, environmental science, and industry. Developing biosensors for Cu(2+) is a key topic in analytical chemistry. DNAzyme-based sensors are highly attractive for their excellent sensitivity, stability, and programmability. In the past decade, a few Cu(2+) biosensors were reported using DNAzymes with DNA cleavage or DNA ligation activity. However, they require unstable ascorbate or imidazole activation. So far, no RNA-cleaving DNAzymes specific for Cu(2+) are known. In this work, a phosphorothioate (PS) RNA-containing library was used for in vitro selection, and a few new Cu(2+)-specific RNA-cleaving DNAzymes were isolated. Among them, a DNAzyme named PSCu10 was studied further. It has only eight nucleotides in the enzyme loop with a cleavage rate of 0.1 min(-1) in the presence of 1 μM Cu(2+) at pH 6.0 (its optimal pH). Between the two diastereomers of the PS RNA chiral center, the R(p) isomer is 37 times more active than the S(p) one. Among the other divalent metal ions, only Hg(2+) can cleave the substrate due to its extremely high thiophilicity. A catalytic beacon sensor was designed with a detection limit of 1.6 nM Cu(2+) and extremely high selectivity. PSCu10 is specific for Cu(2+), and it has no cleavage in the presence of ascorbate, which reduces Cu(2+) to Cu(+).

Desulfurization Activated Phosphorothioate DNAzyme for the Detection of Thallium

Thallium (Tl) is a highly toxic heavy metal situated between mercury and lead in the periodic table. While its neighbors have been thoroughly studied for DNA-based sensing, little is known about thallium detection. In this work, in vitro selection of RNA-cleaving DNAzymes is carried out using Tl(3+) as the target metal cofactor. Both normal DNA and phosphorothioate (PS)-modified DNA are tested for this purpose. While no Tl(3+)-dependent DNAzymes are obtained, a DNA oligonucleotide containing a single PS-modified RNA nucleotide is found to cleave by ∼7% by Tl(3+) at the RNA position. The remaining 93% are desulfurized. By hybridization of this PS-modified oligonucleotide with the Tm7 DNAzyme, the cleavage yield increases to ∼40% in the presence of Tl(3+) and Er(3+). Tm7 is an Er(3+)-dependent RNA-cleaving DNAzyme. It cleaves only the normal substrate but is completely inactive using the PS-modified substrate. Tl(3+) desulfurizes the PS substrate to the normal substrate to be cleaved by Tm7 and Er(3+). This system is engineered into a catalytic beacon for Tl(3+) with a detection limit of 1.5 nM, which is below its maximal contamination limit defined by the U.S. Environmental Protection Agency (10 nM).

Overcoming the Coupling Dilemma in DNA-Programmable Nanoparticle Assemblies by "Ag+ Soldering"

Strong coupling between nanoparticles is critical for facilitating charge and energy transfers. Despite the great success of DNA-programmable nanoparticle assemblies, the very weak interparticle coupling represents a key barrier to various applications. Here, an extremely simple, fast, and highly efficient process combining DNA-programming and molecular/ionic bonding is developed to address this challenge, which exhibits a seamless fusion with DNA nanotechnology.

Phosphorothioate DNA Stabilized Fluorescent Gold and Silver Nanoclusters

Unmodified single-stranded DNA has recently gained popularity for the templated synthesis of fluorescent noble metal nanoclusters (NCs). Bright, stable, and biocompatible clusters have been developed primarily through optimization of DNA sequence. However, DNA backbone modifications have not yet been investigated. In this work, phosphorothioate (PS) DNAs are evaluated in the synthesis of Au and Ag nanoclusters, and are employed to successfully template a novel emitter using T₁₅ DNA at neutral pH. Mechanistic studies indicate a distinct UV-dependent formation mechanism that does not occur through the previously reported thymine N3. The positions of PS substitution have been optimized. This is the first reported use of a T₁₅ template at physiological pH for AgNCs.

Rational evolution of Cd2+-specific DNAzymes with phosphorothioate modified cleavage junction and Cd2+ sensing

In vitro selection of RNA-cleaving DNAzymes is a powerful method for isolating metal-specific DNA. A few successful examples are known, but it is still difficult to target some thiophilic metals such as Cd²⁺ due to limited functional groups in DNA. While using modified bases expands the chemical functionality of DNA, a single phosphorothioate modification might boost its affinity for thiophilic metals without complicating the selection process or using bases that are not commercially available. In this work, the first such in vitro selection for Cd²⁺ is reported. After using a blocking DNA and negative selections to rationally direct the library outcome, a highly specific DNAzyme with only 12 nucleotides in the catalytic loop is isolated. This DNAzyme has a cleavage rate of 0.12 min⁻¹ with 10 μM Cd²⁺ at pH 6.0. The R_p form of the substrate is cleaved ∼100-fold faster than the S_p form. The DNAzyme is most active with Cd²⁺ and its selectivity against Zn²⁺ is over 100 000-fold. Its application in detecting Cd²⁺ is also demonstrated. The idea of introducing single modifications in the fixed region expands the scope of DNA/metal interactions with minimal perturbation of DNA structure and property.

Regiospecific Hetero-Assembly of DNA-Functionalized Plasmonic Upconversion Superstructures

We report a novel strategy for regiospecific hetero-assembly of DNA-modified gold nanoparticles (DNA-AuNPs) onto upconversion nanoparticles (UCNPs) into hybrid lab-on-a-particle systems. The DNA-AuNPs have been assembled onto the hexagonal plate-like UCNPs with well-regulated stoichiometry and controlled organization onto the different facets of UCNP, forming various addressable superstructures. The fine-tuning of stoichiometry and organization is realized by biorecognition specificity of DNA toward specific crystal facets of UCNPs. Such a hetero-assembled DNA-AuNP/UCNP system maintains both plasmonic resonance of AuNPs and fluorescent properties of UCNPs, allowing targeted dual-modality imaging of cancer cells using an aptamer.

Aptamers as a novel tool for diagnostics and therapy

Aptamers are short single-stranded DNA or RNA oligonucleotides that are capable of binding small molecules, proteins, or nucleotides with high specificity. They show a stable conformation and high binding affinity for their target molecules. There are numerous applications for aptamers in biotechnology, molecular diagnostics and targeted therapy of diseases. Their production is cheap, and they generally display lower immunogenicity than monoclonal antibodies. In the present review, we give an introduction to the preparation of aptamers and provide examples for their use in biotechnology, diagnostics and therapy of diseases.

Applications of synchrotron-based spectroscopic techniques in studying nucleic acids and nucleic acid-functionalized nanomaterials

In this review, we summarize recent progress in the application of synchrotron-based spectroscopic techniques for nucleic acid research that takes advantage of high-flux and high-brilliance electromagnetic radiation from synchrotron sources. The first section of the review focuses on the characterization of the structure and folding processes of nucleic acids using different types of synchrotron-based spectroscopies, such as X-ray absorption spectroscopy, X-ray emission spectroscopy, X-ray photoelectron spectroscopy, synchrotron radiation circular dichroism, X-ray footprinting and small-angle X-ray scattering. In the second section, the characterization of nucleic acid-based nanostructures, nucleic acid-functionalized nanomaterials and nucleic acid-lipid interactions using these spectroscopic techniques is summarized. Insights gained from these studies are described and future directions of this field are also discussed.

Tandem phosphorothioate modifications for DNA adsorption strength and polarity control on gold nanoparticles

Unmodified DNA was recently used to functionalize gold nanoparticles via DNA base adsorption. Compared to thiolated DNA, however, the application of unmodified DNA is limited by the lack of sequence generality, adsorption polarity control and poor adsorption stability. We report that these problems can be solved using phosphorothioate (PS) DNA. PS DNA binds to gold mainly via the sulfur atom and is thus less sequence dependent. The adsorption affinity is ranked to be thiol > PS > adenine > thymine. Tandem PS improves adsorption strength, allows tunable DNA density, and the resulting conjugates are functional at a low cost.

DNA as a powerful tool for morphology control, spatial positioning, and dynamic assembly of nanoparticles

Several properties of nanomaterials, such as morphologies (e.g., shapes and surface structures) and distance dependent properties (e.g., plasmonic and quantum confinement effects), make nanomaterials uniquely qualified as potential choices for future applications from catalysis to biomedicine. To realize the full potential of these nanomaterials, it is important to demonstrate fine control of the morphology of individual nanoparticles, as well as precise spatial control of the position, orientation, and distances between multiple nanoparticles. In addition, dynamic control of nanomaterial assembly in response to multiple stimuli, with minimal or no error, and the reversibility of the assemblies are also required. In this Account, we summarize recent progress of using DNA as a powerful programmable tool to realize the above goals. First, inspired by the discovery of genetic codes in biology, we have discovered DNA sequence combinations to control different morphologies of nanoparticles during their growth process and have shown that these effects are synergistic or competitive, depending on the sequence combination. The DNA, which guides the growth of the nanomaterial, is stable and retains its biorecognition ability. Second, by taking advantage of different reactivities of phosphorothioate and phosphodiester backbone, we have placed phosphorothioate at selective positions on different DNA nanostructures including DNA tetrahedrons. Bifunctional linkers have been used to conjugate phosphorothioate on one end and bind nanoparticles or proteins on the other end. In doing so, precise control of distances between two or more nanoparticles or proteins with nanometer resolution can be achieved. Furthermore, by developing facile methods to functionalize two hemispheres of Janus nanoparticles with two different DNA sequences regioselectively, we have demonstrated directional control of nanomaterial assembly, where DNA strands with specific hybridization serve as orthogonal linkers. Third, by using functional DNA that includes DNAzyme, aptamer, and aptazyme, dynamic control of assemblies of gold nanoparticles, quantum dots, carbon nanotubes, and iron oxide nanoparticles in response to one or more stimuli cooperatively have been achieved, resulting in colorimetric, fluorescent, electrochemical, and magnetic resonance signals for a wide range of targets, such as metal ions, small molecules, proteins, and intact cells. Fourth, by mimicking biology, we have employed DNAzymes as proofreading units to remove errors in nanoparticle assembly and further used DNAzyme cascade reactions to modify or repair DNA sequences involved in the assembly. Finally, by taking advantage of different affinities of biotin and desthiobiotin toward streptavidin, we have demonstrated reversible assembly of proteins on DNA origami.

Sensing parts-per-trillion Cd(2+), Hg(2+), and Pb(2+) collectively and individually using phosphorothioate DNAzymes

Cadmium, mercury, and lead are collectively banned by many countries and regions in electronic devices due to their extremely high toxicity. To date, no sensing method can detect them as a group and also individually with sufficient sensitivity and selectivity. An RNA-cleaving DNAzyme (Ce13d) was recently reported to be active with trivalent lanthanides, which are hard Lewis acids. In this work, phosphorothioate (PS) modifications were systematically made on Ce13d. A single PS modification at the substrate cleavage site shifts the activity from being dependent on lanthanides to soft thiophilic metals. By incorporating the PS modification to another DNAzyme, a sensor array was prepared to detect each metal. Individual sensors have excellent sensitivity (limit of detection = 4.8 nM Cd(2+), 2.0 nM Hg(2+), and 0.1 nM Pb(2+)). This study provides a new route to obtain metal-specific DNAzymes by atomic replacement and also offers important mechanistic insights into metal binding and DNAzyme catalysis.

Asymmetric hetero-assembly of colloidal nanoparticles through "crash reaction" in a centrifugal field

Asymmetric hetero-assembly of two kinds of colloidal nanoparticles (NPs) was achieved by "crash reaction" in a density gradient centrifugation system using Au NPs as an example. Centrifugal force was applied to overcome the Brownian motion effect and cause NPs' directional movements. A water-oil interface was introduced to increase the effective collision probability.

Dumbbells, trikes and quads: organic-inorganic hybrid nanoarchitectures based on "clicked" gold nanoparticles

The controlled assembly of gold nanoparticles in terms of the spatial arrangement and number of particles is essential for many future applications like electronic devices, sensors and labeling. Here an approach is presented to build up oligomers of mono functionalized gold nanoparticles by the use of 1,3-bipolar azide alkyne cycloaddition click chemistry. The gold nanoparticles of 1.3 nm diameter are stabilized by one dendritic thioether ligand comprising an alkyne function. Together with di-, tri- and tetra-azide linker molecules the gold nanoparticle can be covalently coupled by a wet chemical protocol. The reaction is tracked with IR and UV-vis spectroscopy and the yielded organic-inorganic hybrid structures are analyzed by transmission electron microscopy. To evaluate the success of this click chemistry reaction statistical analysis of the formed oligomers is performed. The geometric and spatial arrangements of the found oligomers match perfectly the calculated values for the used linker molecules. Dimers, trimers and tetramers could be identified after the reaction with the corresponding linker molecule. The results of this model reaction suggest that the used click chemistry protocol is working well with mono functionalized gold nanoparticles.

Surfactant-free nanoparticle–DNA complexes with ultrahigh stability against salt for environmental and biological sensing

A AuNP–DNA complex highly stable in extremely high ionic strength media, such as seawater, was obtained by inserting a few thymine bases into the DNA strands.

Facile and efficient preparation of anisotropic DNA-functionalized gold nanoparticles and their regioselective assembly

Anisotropic nanoparticles can provide considerable opportunities for assembly of nanomaterials with unique structures and properties. However, most reported anisotropic nanoparticles are either difficult to prepare or to functionalize. Here we report a facile one-step solution-based method to prepare anisotropic DNA-functionalized gold nanoparticles (a-DNA-AuNP) with 96% yield and with high DNA density (120 ± 20 strands on the gold hemisphere). The method is based on the competition between a thiolated hydrophilic DNA and a thiolated hydrophobic phospholipid and has been applied to prepare a-DNA-AuNPs of different sizes and with a variety of DNA sequences. In addition, DNA strands on the a-DNA-AuNPs can be exchanged with other DNA strands with a different sequence. The anisotropic nature of the a-DNA-AuNPs allows regioselective hetero- and homonuclear assembly with high monodispersity, as well as regioselective functionalization of two different DNA strands for more diverse applications.

Hierarchically built hetero-superstructure arrays with structurally controlled material compositions

Hierarchical assemblies are repeatedly encountered in nature, and when replicated in synthetic patterns and materials, can enhance their functionality or impart multifunctionality. In order to assemble a hierarchical superstructure that consists of components made up of multiple nanostructures, control over placement and stoichiometry is desirable. Macroscopic arrays that present up to three levels of hierarchy are demonstrated here and are achieved using the self-assembly of soft, collapsible block copolymer nanospheres for the first two levels, followed by directed self-assembly of metal nanospheres for the third. The fabrication approach combines advantages of soft sphere self-assembly to yield non-close-packed and variable array pitch values, with the inherent chemical functionality presented by the polymer-based soft spheres; these assemblies can then be transformed into a range of different materials, including metal or semiconductor nanostructures, or further tailored with an additional level of complexity. Structural investigation shows the superstructure formation to be governed by generic design rules that can be extended across different material combinations.

Imparting the unique properties of DNA into complex material architectures and functions

While the remarkable chemical and biological properties of DNA have been known for decades, these properties have only been imparted into materials with unprecedented function much more recently. The inimitable ability of DNA to form programmable, complex assemblies through stable, specific, and reversible molecular recognition has allowed the creation of new materials through DNA's ability to control a material's architecture and properties. In this review we discuss recent progress in how DNA has brought unmatched function to materials, focusing specifically on new advances in delivery agents, devices, and sensors.

Correct spectral conversion between surface-enhanced raman and plasmon resonance scattering from nanoparticle dimers for single-molecule detection

Simultaneous measurement of surface-enhanced Raman scattering (SERS) and localized surface plasmon resonance (LSPR) in nanoparticle dimers presents outstanding opportunities in molecular identification and in the elucidation of physical properties, such as the size, distance, and deformation of target species. SERS-LSPR instrumentation exists and has been used under limited conditions, but the extraction of SERS and LSPR readouts from a single measurement is still a challenge. Herein, the extraction of LSPR spectra from SERS signals is reported and a tool for measuring the interparticle distance from Raman enhancement data by the standardization of the SERS signal is proposed. The SERS nanoruler mechanism incorporates two important aspects (the LSPR scattering peak shift and the Raman shift for measuring interparticle distance), and signifies their exact one-to-one correspondence after spectral correction. The developed methodology is applied to calculate the interparticle distance between nanoparticle dimers from SERS signals, to detect and quantify DNA at the single-molecule level in a base-pair-specific manner. It is also shown that the SERS nanoruler concept can be used in structural analysis for the specific detection of the interaction of immunoglobulin G (IgG) with its target from bianalyte Raman signals with identical shaping at single-molecule resolution. The SERS profile shaping approach not only offers a new detection mechanism for single molecules, but also has excellent potential for studying protein interactions and the intracellular detection of mRNA.

Nano-encrypted Morse code: a versatile approach to programmable and reversible nanoscale assembly and disassembly

While much work has been devoted to nanoscale assembly of functional materials, selective reversible assembly of components in the nanoscale pattern at selective sites has received much less attention. Exerting such a reversible control of the assembly process will make it possible to fine-tune the functional properties of the assembly and to realize more complex designs. Herein, by taking advantage of different binding affinities of biotin and desthiobiotin toward streptavidin, we demonstrate selective and reversible decoration of DNA origami tiles with streptavidin, including revealing an encrypted Morse code "NANO" and reversible exchange of uppercase letter "I" with lowercase "i". The yields of the conjugations are high (>90%), and the process is reversible. We expect this versatile conjugation technique to be widely applicable with different nanomaterials and templates.

Switchable nanodumbbell probes for analyte detection

Nanodumbbell gold nanoparticle (AuNP) dimers connected by DNA show significant change in interparticle distance in the presence of a specific analyte, ATP. The nanodumbbell begins in an extended state, but after the addition of the analyte, the DNA connecting the AuNPs forms a stable hairpin, which causes a large decrease in the interparticle distance.

Discovery of the DNA "genetic code" for abiological gold nanoparticle morphologies

DNA is in control: Different combinations of DNA nucleotides can control the shape and surface roughness of gold nanoparticles during their synthesis. These nanoparticles were synthesized in the presence of either homogenous oligonucleotides or mixed-base oligonucleotides using gold nanoprisms as seeds. The effect of the individual DNA bases and their combinations on shape control are shown in the figure.