Nanoparticle-Based, Fluorous-Tag-Driven DNA Detection

Gene Regulation Using Spherical Nucleic Acids to Treat Skin Disorders

Spherical nucleic acids (SNAs) are nanostructures consisting of nucleic acids in a spherical configuration, often around a nanoparticle core. SNAs are advantageous as gene-regulating agents compared to conventional gene therapy owing to their low toxicity, enhanced stability, uptake by virtually any cell, and ability to penetrate the epidermal barrier. In this review we: (i) describe the production, structure and properties of SNAs; (ii) detail the mechanism of SNA uptake in keratinocytes, regulated by scavenger receptors; and (iii) report how SNAs have been topically applied and intralesionally injected for skin disorders. Specialized SNAs called nanoflares can be topically applied for gene-based diagnosis (scar vs. normal tissue). Topical SNAs directed against TNFα and interleukin-17A receptor reversed psoriasis-like disease in mouse models and have been tested in Phase 1 human trials. Furthermore, SNAs targeting ganglioside GM3 synthase accelerate wound healing in diabetic mouse models. Most recently, SNAs targeting toll-like receptor 9 are being used in Phase 2 human trials via intratumoral injection to induce immune responses in Merkel cell and cutaneous squamous cell carcinoma. Overall, SNAs are a valuable tool in bench-top and clinical research, and their advantageous properties, including penetration into the epidermis after topical delivery, provide new opportunities for targeted therapies.

Synthesis and applications of theranostic oligonucleotides carrying multiple fluorine atoms

The use of various oligonucleotide (ON) syntheses and post-synthetic strategies for targeted chemical modification enables improving their efficacy as potent modulators of gene expression levels in eukaryotic cells. However, the search still continues for new approaches designed for increasing internalization, lysosomal escape, and tissue specific delivery of ON. In this review we emphasized all aspects related to the synthesis and properties of ON derivatives carrying multifluorinated (MF) groups. These MF groups have unique physico-chemical properties because of their simultaneous hydrophobicity and lipophobicity. Such unusual combination of properties results in the overall modification of ON mode of interaction with the cells and making multi-fluorination highly relevant to the goal of improving potency of ON as components of new therapies. The accumulated evidence so far is pointing to high potential of ON probes, RNAi components and ON imaging beacons carrying single or multiple MF groups for improving the stability, specificity of interaction with biological targets and delivery of ONs in vitro and potentially in vivo.

Plasmonic bimetallic nanodisk arrays for DNA conformation sensing

The integration of large-scale 2D bimetallic Ag/Au nanodisk arrays with gold nanoparticles is developed for sensing DNA conformation with the assistance of 3D finite-difference time-domain simulation. The optimized system comprising Ag/Au nanodisk arrays and gold nanoparticles offers a more than 6-fold enhancement in surface plasmon resonance shift, enabling the feasibility for sensitive DNA detection with a detection limit down to 100 femtomolar. Importantly, owing to the distance-dependent nature of the surface plasmon signal, sensitive differentiation of DNA conformations can be achieved with a conventional optical measurement. This platform could provide new exciting capabilities for a reliable, reproducible, and label-free assay analysis for investigating the conformations of DNA and other biological molecules.

Fluorocarbons Enhance Intracellular Delivery of Short STAT3-sensors and Enable Specific Imaging

Short oligonucleotide sequences are now being widely investigated for their potential therapeutic properties. The modification of oligonucleotide termini with short fluorinated residues is capable of drastically altering their behavior in complex in vitro and in vivo systems, and thus may serve to greatly enhance their therapeutic potential. The main goals of our work were to explore: 1) how modification of STAT3 transcription factor-binding oligodeoxynucleotide (ODN) duplexes (ODND) with one or two short fluorocarbon (FC)-based residues would change their properties in vitro and in vivo, and if so, how this would affect their intracellular uptake by cancer cells, and 2) the ability of such modified ODND to form non-covalent complexes with FC-modified carrier macromolecule. The latter has an inherent advantage of producing a ¹⁹F-specific magnetic resonance (MR) imaging signature. Thus, we also tested the ability of such copolymers to generate ¹⁹F-MR signals. Materials and Methods. Fluorinated nucleic acid residues were incorporated into ODN by using automated synthesis or via activated esters on ODN 5'-ends. To quantify ODND uptake by the cells and to track their stability, we covalently labeled ODN with fluorophores using internucleoside linker technology; the FC-modified carrier was synthesized by acylation of pegylated polylysine graft copolymer with perfluoroundecanoic acid (M5-gPLL-PFUDA). Results. ODN with a single FC group exhibited a tendency to form duplexes with higher melting points and with increased stability against degradation when compared to control non-modified ODNs. ODND carrying fluorinated residues showed complex formation with M5-gPLL-PFUDA as predicted by molecular dynamics simulations. Moreover, FC groups modulated the specificity of ODND binding to the STAT3 target. Finally, FC modification resulted in greater cell uptake (2 to 4 fold higher) when compared to the uptake of non-modified ODND as determined by quantitative confocal fluorescence imaging of A431 and INS-1 cells. Conclusion. ODND modification with FC residues enables fine-tuning of protein binding specificity to double-strand binding motifs and results in an increased internalization by A431 and INS-1 cells in culture. Our results show that modification of ODN termini with FC residues is both a feasible and powerful strategy for developing more efficient nucleic acid-based therapies with the added benefit of allowing for non-invasive MR imaging of ODND therapeutic targeting and response.

A label-free method for the detection of specific DNA sequences using gold nanoparticles bifunctionalized with a chemiluminescent reagent and a catalyst as signal reporters

Sensitive, specific, simple, fast, and low-cost DNA detection methods are extremely important in clinical diagnostics, gene therapy, and a variety of biomedical studies. In this work, we developed a general method for the detection of specific DNA sequences from Mycobacterium tuberculosis (TB), hepatitis B virus (HBV), and myelocytomatosis viral oncogene (v-myc) using gold nanoparticles bifunctionalized with both a chemiluminescent (CL) reagent and a catalytic metal complex as signal reporters and a DNA strand complementary to the target as the capture probe. In this CL method, a biotinylated single-strand DNA capture probe was immobilized in a streptavidin-coated microwell. Upon the addition of the target single-strand DNA, the capture probe hybridized with the target DNA. After adding the bifunctionalized gold nanoparticles and H₂O₂, a well-defined CL signal was obtained, and the CL intensity was observed to change as the target DNA concentration was increased. It was possible to determine the concentration of the target TB single-strand DNA in the range 1.0 × 10^-13-1.0 × 10^-8 M with a detection limit of 4.8 × 10^-14 M. HBV single-strand DNA and v-myc single-strand DNA could also be determined in the range 1.0 × 10^-11-1.0 × 10^-8 M with detection limits of 5.9 × 10^-12 M and 8.0 × 10^-12 M, respectively, using this CL technique. The method reported in this paper is the first label-free CL method for the determination of specific DNA sequences to utilize gold nanoparticles bifunctionalized with both a CL reagent and a catalytic metal complex. The sensitivity of this CL method is superior to those of most previously reported label-free methods. Compared with methods that use polymerase chain reaction amplification, this label-free CL method is much simpler, faster, and more economic. This work has thus demonstrated a simple and fast scanning strategy for the detection of specific DNA sequences related to diseases. Graphical Abstract Schematic illustration of label-free CL method for detection of specific DNA sequences.

Surface-initiated controlled radical polymerizations from silica nanoparticles, gold nanocrystals, and bionanoparticles

This review summarizes recent progress in surface-initiated controlled radical polymerizations from silica nanoparticles, gold nanocrystals, and bionanoparticles.

Salt-enabled visual detection of DNA

We report herein a label-free, salt-enabled visual detection strategy for DNA, based on the alteration of surface adhesion properties of salt solution, which can translate to the change in the size of the salt residue upon drying, with self-assembled DNA nanostructures. This environmentally friendly array assay protocol enables the achievement of a detection sensitivity comparable to classic colorimetric methods, single-base mismatch differentiation selectivity, multiple-target detection capability, RNA target detection, and a ligase chain reaction-rolling circle amplification implementation format.

Multiplexed DNA detection based on positional encoding/decoding with self-assembled DNA nanostructures

A multiplexed DNA detection strategy with fast hybridization kinetics based on positional encoding/decoding with self-assembled DNA nanostructures has been developed.

Current multiplexed analysis methods suffer from either slow reaction kinetics (planar arrays) or complicated encoding/decoding procedures (suspension arrays). We report herein a multiplexed DNA detection strategy that addresses these issues, based on positional encoding/decoding with self-assembled DNA nanostructures. The strategy enables the acquisition of high-resolution, consistent, and quantitative assay results in a single round of a transmission electron microscopy imaging operation. Applications in polymerase chain reaction-free settings and assays of other structurally distinct targets can be anticipated through the implementation of the strategy with miniaturized femtoliter/attoliter dispensing technology and readily accessible DNA conjugate structures.

Fluorous methods for the synthesis of peptides and oligonucleotides

The non-covalent affinity of a perfluoro chain towards similar has been exploited by many to separate fluorous tagged compounds from non-fluorous compounds by F-SPE or F-LLE. This purification strategy found its application across diverse fields including peptide and oligonucleotide synthesis where even slight inefficient couplings result in deletion sequences that are often difficult to remove from the target sequence. Two commonly employed strategies to address this problem involve end-tagging the target sequence or capping the deletion sequences with fluorous tags. Solution phase syntheses using soluble fluorous supports are easier and quicker. These approaches are reviewed here in detail.

Ultrasensitive colorimetric DNA detection using a combination of rolling circle amplification and nicking endonuclease-assisted nanoparticle amplification (NEANA)

A combination of rolling circle amplification and nicking endonuclease-assisted nanoparticle amplification (NEANA) is used for the rapid, colorimetric detection of DNA. The integration of rolling circle amplification into the NEANA approach allows for detection of oligonucleotides with arbitrary sequences at ultralow concentrations.

Ultrafast kinetic DNA hybridization assay based on the visualization of threshold turbidity

We report herein the development of an ultrafast kinetic DNA hybridization assay system based on the visualization of threshold turbidity associated with the assembly of polystyrene nanospheres. Initial testing of our diagnostic protocol on a sequence associated with the anthrax lethal factor indicates that a visually identifiable, turbidity-definitive, and kinetic threshold state could be reached at a time as short as 1 min. The assay scheme allows for both target concentration quantification and differentiation of single base mismatches through registry of the threshold turbidity onset time. The positively charged environment on nanospheres not only contributes to expedited signal generation but also imparts cooperative DNA binding properties. The kinetic visual protocol complements conventionally used thermodynamic strategies and provides an entry point for the circumvention of assay issues associated with ill-defined thermodynamic end points.

Using commercially available personal glucose meters for portable quantification of DNA

DNA detection is commonly used in molecular biology, pathogen analysis, genetic disorder diagnosis, and forensic tests. While traditional methods for DNA detection such as polymerase chain reaction (PCR) and DNA microarrays have been well developed, they require sophisticated equipment and operations, and thus it is still challenging to develop a portable and quantitative DNA detection method for the public use at home or in the field. Although many other techniques and devices have been reported to make the DNA detection simple and portable, very few of them are currently accessible to the public for quantitative DNA detection because of either the requirement of laboratory-based instrument or lack of quantitative detection. Herein we report application of personal glucose meters (PGMs), which are widely available, low cost, and simple to use, for quantitative detection of DNA, including a hepatitis B virus DNA fragment. The quantification is based on target-dependent binding of cDNA-invertase conjugate with the analyte DNA, thereby transforming the concentration of DNA in the sample into glucose through invertase-catalyzed hydrolysis of sucrose. Instead of amplifying DNA strands through PCR, which is vulnerable to contaminations commonly encountered for home and field usage, we demonstrate here signal amplifications based on enzymatic turnovers, making it possible to detect 40 pM DNA using PGM that can detect glucose only at the mM level. The method also shows excellent selectivity toward single nucleotide mismatches.

A coordination complex system for generic, ultrafast, and sensitive multimode fluorescent staining of biomolecules

Gel electrophoresis staining methodologies documented thus far are largely utilized in a biomolecule context-dependent manner. We report herein the development of a generic, ultrafast, and sensitive multimode fluorescent system for the efficient identification of DNA, RNA, and proteins. Interaction between a positively charged, planar ligand-based coordination complex with partner biomolecule leads to aggregation-induced fluorescence quenching and allows for the image contrast generation within one minute. Alternatively, successive reactions of the biomolecule-loaded gel with cation and ligand, in either order of sequence, provide an equally effective staining efficacy. Image contrast reversal is accomplished through a facile washing or photobleaching procedure. The versatility in the applicable target species and signal generation modes provides a hint at the design of novel staining structures and potentially enables the high-throughput readout of biomolecules.

Diversified nanoparticle assembly pathways: materials architecture control beyond the amphiphilicity paradigm

The functional versatility of a chemical system is ultimately dictated by the availability of distinctly accessible architectures. The generation of a diverse array of assembled constructs from a single type of nanoscale building block is a promising yet largely elusive goal. We report herein the utility of a monolayer-modified nanoparticle for the creation of a broad range of architectures. The versatile modes of assembly complement the conventionally used, amphiphilicity-driven strategy. We demonstrate that one can vary the nanoparticle assembly pathways within the confines of solvent media through the modulation of interactions and partitioning of nanoparticles. Merging of the molecular-scale design and higher-ordered arrangement enables diversified assembly through the manipulation of experimental parameters such as solvent, pH, affinity molecule, and temperature. Microfluidics provides an effective channel to control the monodispersity and size on all the architectures attainable in the bulk solution phase. These observations could be further explored for an understanding of diversified matter organization and order generation beyond the amphiphilicity paradigm.

Colorimetric detection of DNA by modulation of thrombin activity on gold nanoparticles

A colorimetric, non-cross-linking aggregation-based gold-nanoparticle (AuNP) probe has been developed for the detection of DNA and the analysis of single-nucleotide polymorphism (SNP). The probe acts by modulating the enzyme activity of thrombin relative to fibrinogen. A thrombin-binding aptamer with a 29-base-long oligonucleotide (TBA(29)) assembled on the nanoparticles (TBA(29)-AuNPs) through sandwich DNA hybridization was found to possess ultra-high anticoagulant potency. The enzyme inhibition of thrombin was determined by thrombin-induced aggregation of fibrinogen-functionalized 56 nm AuNPs (Fib-AuNPs). The potency of the inhibition of TBA(29)-AuNPs relative to thrombin--and thus the degree of aggregation of the Fib-AuNPs--is highly dependent on the concentration of perfectly matched DNA (DNA(pm)). Under optimal conditions [Tris-HCl (20 mM, pH 7.4), KCl (5 mM), MgCl(2) (1 mM), CaCl(2) (1 mM), NaCl (150 mM), thrombin (10 pM), and TBA(29)-AuNPs (20 pM)], the new TBA(29)-AuNP/Fib-AuNP probe shows linear sensitivity to DNA(pm) in the concentration range 20-500 pM with a correlation coefficient of 0.96. The limit of detection for DNA(pm) was experimentally determined to be 12 pM, based on a signal-to-noise ratio (S/N) of 3. The new probe was successfully applied to the analysis of an SNP that is responsible for sickle cell anemia. Relative to conventional molecular-beacon-based probes, the new probe offers the advantages of higher sensitivity and selectivity towards DNA and lower cost, showing its great potential for practical studies of SNPs.

Sequence-specific detection of short-length DNA via template-dependent surface-hybridization events

Short-length DNA and RNA, such as mature small RNA, which contains only 17-25 nucleotides, are always a problem in hybridization-based detection assays. In this paper, we report a proof-of-concept for a new short-length DNA detection technology which encompasses a design strategy whereby capture and reporter probes that do not hybridize to each other at 20 degrees C can be made to anneal to each other in the presence of a template via the formation of a stable three-component complex. The thermodynamics of this magnetic bead-based DNA biosensor was then investigated in detail by monitoring chemiluminescence (CL) changes in the absence and presence of targets over a temperature profile. The data show that this new biosensor offers the possibility of highly selective and sensitive detection of the short-length target DNA. In view of these advantages, this template-dependent surface-hybridization assay, as a new CL strategy, might create a universal technology for developing simple biosensors in sensitive and selective detection of short-length DNA and RNA.

Well-defined DNA nanoparticles templated by self-assembled M(12)L(24) molecular spheres and binding of complementary oligonucleotides

Perfectly monodisperse DNA nanoparticles were prepared via the self-assembly of 12 Pd(II) ions and 24 bidentate ligands functionalized with oligonucleotides of varying length (n = 1-3). The DNA nanoparticles formed hydrogen bonds with cDNA strands and an insoluble aggregate formed only with matching trimeric nucleotide strands (tri-A).

Biomineralization-assisted ultrasensitive detection of DNA

The development of instrument-free, PCR-less, ultrasensitive and selective DNA detection methods is highly desired in chemical and life sciences. Herein we report on the utility of a biomineralization-assisted amplification methodology for the identification of DNA. Significantly, the diagnostic strategy has allowed the target detection at a concentration as low as 50 aM, equivalent to approximately 180 copies in the entire 6 microL sample. In addition, the DNA sequence with a single-base mismatch can be differentiated from the perfect target through a facile salt-based stringency wash. Substitution of the DNA structures with other recognition moieties should allow the translation of the strategy to the assay of different targets of interest. The visual readout format provides a sound basis for the broad applicability of the proposed strategy, especially in resource-poor settings.