Nucleic acid conjugated nanomaterials for enhanced molecular recognition

Improving the fluorescence detection limit with positively charged carbon nanostructures as a low background signal platform

We have demonstrated a new strategy to improve the fluorescence detection limit by enhancing the energy transfer efficiency between carbon structures and fluorescent dyes using polyimidazolium-functionalized carbon nanostructures as a low background signal platform.

Structural insights into DNA replication without hydrogen bonds

The genetic alphabet is composed of two base pairs, and the development of a third, unnatural base pair would increase the genetic and chemical potential of DNA. d5SICS-dNaM is one of the most efficiently replicated unnatural base pairs identified to date, but its pairing is mediated by only hydrophobic and packing forces, and in free duplex DNA it forms a cross-strand intercalated structure that makes its efficient replication difficult to understand. Recent studies of the KlenTaq DNA polymerase revealed that the insertion of d5SICSTP opposite dNaM proceeds via a mutually induced-fit mechanism, where the presence of the triphosphate induces the polymerase to form the catalytically competent closed structure, which in turn induces the pairing nucleotides of the developing unnatural base pair to adopt a planar Watson-Crick-like structure. To understand the remaining steps of replication, we now report the characterization of the prechemistry complexes corresponding to the insertion of dNaMTP opposite d5SICS, as well as multiple postchemistry complexes in which the already formed unnatural base pair is positioned at the postinsertion site. Unlike with the insertion of d5SICSTP opposite dNaM, addition of dNaMTP does not fully induce the formation of the catalytically competent closed state. The data also reveal that once synthesized and translocated to the postinsertion position, the unnatural nucleobases again intercalate. Two modes of intercalation are observed, depending on the nature of the flanking nucleotides, and are each stabilized by different interactions with the polymerase, and each appear to reduce the affinity with which the next correct triphosphate binds. Thus, continued primer extension is limited by deintercalation and rearrangements with the polymerase active site that are required to populate the catalytically active, triphosphate bound conformation.

Building a multifunctional aptamer-based DNA nanoassembly for targeted cancer therapy

The ability to self-assemble one-dimensional DNA building blocks into two- and three-dimensional nanostructures via DNA/RNA nanotechnology has led to broad applications in bioimaging, basic biological mechanism studies, disease diagnosis, and drug delivery. However, the cellular uptake of most nucleic acid nanostructures is dependent on passive delivery or the enhanced permeability and retention effect, which may not be suitable for certain types of cancers, especially for treatment in vivo. To meet this need, we have constructed a multifunctional aptamer-based DNA nanoassembly (AptNA) for targeted cancer therapy. In particular, we first designed various Y-shaped functional DNA domains through predesigned base pair hybridization, including targeting aptamers, intercalated anticancer drugs, and therapeutic antisense oligonucleotides. Then these functional DNA domains were linked to an X-shaped DNA core connector, termed a building unit, through the complementary sequences in the arms of functional domains and connector. Finally, hundreds (~100-200) of these basic building units with 5'-modification of acrydite groups were further photo-cross-linked into a multifunctional and programmable aptamer-based nanoassembly structure able to take advantage of facile modular design and assembly, high programmability, excellent biostability and biocompatibility, as well as selective recognition and transportation. With these properties, AptNAs were demonstrated to have specific cytotoxic effect against leukemia cells. Moreover, the incorporation of therapeutic antisense oligonucleotides resulted in the inhibition of P-gp expression (a drug efflux pump to increase excretion of anticancer drugs) as well as a decrease in drug resistance. Therefore, these multifunctional and programmable aptamer-based DNA nanoassemblies show promise as candidates for targeted drug delivery and cancer therapy.

Spectroscopic and microscopic analyses of rod-shaped gold nanoparticles interacting with single-stranded DNA oligonucleotides

The application of rod-shaped gold nanoparticles as probes and carriers in biological systems have recently attracted great interest. UV-vis spectroscopy, circular dichroism, Fourier transform infrared spectroscopy, scanning electron microscopy and atomic force microscopy were used to study optical and structural properties of rod-shaped gold nanoparticles when interacting with DNA oligomers in phosphate sodium salt buffer. The morphological transformation process of rod-shaped gold nanoparticles resulting from the interaction with single-stranded DNA (ssDNA) showed the role of hexadecyltrimethylammonium bromide (CTAB) in nanostructures as the main interacting agent. The obtained results confirmed that the CTAB coat of rod-shaped gold nanoparticles have powerful positive charges for conjugations with surface negative charges of phosphate groups on ssDNA oligomers. The CTAB also inhibit the formation of covalent sulphide bonds between the gold core of rod-shaped nanoparticles and alkanethiol oligonucleotides. The authors found that when the nanorods were exposed to ssDNA oligonucleotides, the gold nanorods changed their shapes and sizes, and exposed some microscopic malformations which could be used in the development of colorimetric assays of nucleic acids.

Strategies for optimizing DNA hybridization on surfaces

Specific and predictable hybridization of the polynucleotide sequences to their complementary counterparts plays a fundamental role in the rational design of new nucleic acid nanodevices. Generally, nucleic acid hybridization can be performed using two major strategies, namely hybridization of DNA or RNA targets to surface-tethered oligonucleotide probes (solid-phase hybridization) and hybridization of the target nucleic acids to randomly distributed probes in solution (solution-phase hybridization). Investigations into thermodynamic and kinetic parameters of these two strategies showed that hybridization on surfaces is less favorable than that of the same sequence in solution. Indeed, the efficiency of DNA hybridization on surfaces suffers from three constraints: (1) electrostatic repulsion between DNA strands on the surface, (2) steric hindrance between tethered DNA probes, and (3) nonspecific adsorption of the attached oligonucleotides to the solid surface. During recent years, several strategies have been developed to overcome the problems associated with DNA hybridization on surfaces. Optimizing the probe surface density, application of a linker between the solid surface and the DNA-recognizing sequence, optimizing the pH of DNA hybridization solutions, application of thiol reagents, and incorporation of a polyadenine block into the terminal end of the recognizing sequence are among the most important strategies for enhancing DNA hybridization on surfaces.

Site-specifically arraying small molecules or proteins on DNA using an expanded genetic alphabet

A class of replicable unnatural DNA base pairs formed between d5SICS and either dMMO2, dDMO, or dNaM were developed. To explore the use of these pairs to produce site-specifically labeled DNA, the synthesis of a variety of derivatives bearing propynyl groups, an analysis of their polymerase-mediated replication, and subsequent site-specific modification of the amplified DNA by Click chemistry is reported. With the d5SICS scaffold a propynyl ether linker is accommodated better than its aliphatic analogue, but not as well as the protected propargyl amine linker explored previously. It was also found that with the dMMO2 and dDMO analogues, the dMMO2 position para to the glycosidic linkage is best suited for linker attachment and that although aliphatic and ether-based linkers are similarly accommodated, the direct attachment of an ethynyl group to the nucleobase core is most well tolerated. To demonstrate the utility of these analogues, a variety of them were used to site-selectively attach a biotin tag to the amplified DNA. Finally, we use d5SICS(CO) -dNaM to couple one or two proteins to amplified DNA, with the double labeled product visualized by atomic force microscopy. The ability to encode the spatial relationships of arrayed molecules in PCR amplifiable DNA should have important applications, ranging from SELEX with functionalities not naturally present in DNA to the production, and perhaps "evolution" of nanomaterials.

Selective FL quenching or enhancing of diimine ligands by guanine

Diimine ligand (DL) 1 significantly exhibited the fluorescence quenching upon binding to guanine. Changing at the para-substituent of the phenyl ring from the hydroxyl to bromo groups reversely enhanced the fluorescence in the presence of guanine. The reverse in the fluorescence selectivity indicated the profound effect of the substituent at the para-position of the phenyl ring. The simple synthesis of DL 1 and DL 2 with good selectivity for guanine offers these DLs as promising compounds for chemosensors of other guanine derivatives.

Multivalent DNA nanospheres for enhanced capture of cancer cells in microfluidic devices

Isolation of circulating tumor cells (CTCs) from peripheral blood or cancer cells from bone marrow has significant applications in cancer diagnosis, therapy monitoring, and drug development. CTCs are cancer cells shed from primary tumors; they circulate in the bloodstream, leading to metastasis. The extraordinary rarity of CTCs in the bloodstream makes their isolation a significant technological challenge. Herein, we report the development of a platform combining multivalent DNA aptamer nanospheres with microfluidic devices for efficient isolation of cancer cells from blood. Gold nanoparticles (AuNPs) were used as an efficient platform for assembling a number of aptamers for high-efficiency cell capture. Up to 95 aptamers were attached onto each AuNP, resulting in enhanced molecular recognition capability. An increase of 39-fold in binding affinity was confirmed by flow cytometry for AuNP-aptamer conjugates (AuNP-aptamer) when compared with aptamer alone. With a laminar flow flat channel microfluidic device, the capture efficiency of human acute leukemia cells from a cell mixture in buffer increased from 49% using aptamer alone to 92% using AuNP-aptamer. We also employed AuNP-aptamer in a microfluidic device with herringbone mixing microstructures for isolation of leukemia cells in whole blood. The cell capture efficiency was also significantly increased with the AuNP-aptamer over aptamer alone, especially at high flow rates. Our results show that the platform combining DNA nanostructures with microfluidics has a great potential for sensitive isolation of CTCs and is promising for cancer diagnosis and prognosis.

Supramolecular self-assemblies as functional nanomaterials

In this review, we survey the diversity of structures and functions which are encountered in advanced self-assembled nanomaterials. We highlight their flourishing implementations in three active domains of applications: biomedical sciences, information technologies, and environmental sciences. Our main objective is to provide the reader with a concise and straightforward entry to this broad field by selecting the most recent and important research articles, supported by some more comprehensive reviews to introduce each topic. Overall, this compilation illustrates how, based on the rules of supramolecular chemistry, the bottom-up approach to design functional objects at the nanoscale is currently producing highly sophisticated materials oriented towards a growing number of applications with high societal impact.

Attaching DNA to nanoceria: regulating oxidase activity and fluorescence quenching

Cerium oxide nanoparticles (nanoceria) have recently emerged as a nanozyme with oxidase activity. In this work, we present a few important interfacial properties of nanoceria. First, the surface charge of nanoceria can be controlled not only by adjusting pH but also by adsorption of simple inorganic anions. Adsorption of phosphate and citrate gives negatively charged surface over a broad pH range. Second, nanoceria adsorbs DNA via the DNA phosphate backbone in a sequence-independent manner; DNA adsorption inhibits its oxidase activity. Other anionic polymers display much weaker inhibition effects. Adsorption of simple inorganic phosphate does not have the inhibition effect. Third, nanoceria is a quencher for many fluorophores. These discoveries provide an important understanding for further use of nanoceria in biosensor development, materials science, and nanotechnology.

Library approach for reliable synthesis and properties of DNA-gold nanorod conjugates

We developed a library-based approach to chemically stabilize cetyltrimethylammonium bromide (CTAB)-coated gold nanorods for the synthesis of polyvalent DNA-gold nanorod conjugates (DNA-AuNRs). Eleven chemical reagents were carefully chosen to constitute an additive library and screened by UV-vis spectroscopy to evaluate their stabilizing capability for the CTAB-coated AuNRs. Interestingly, 5-bromosalicylic acid (5-BrSA) was determined to most significantly stabilize the AuNRs by inducing additional adsorption of CTAB on the rod. Importantly, these stabilized AuNRs with 5-BrSA were conjugated with thiol DNA in an exceptionally reproducible and reliable method, which led to the systematic investigation of their cooperative assembly and disassembly properties under various conditions, including different types and lengths of the DNA sequences.

Aptamer-conjugated gold nanoparticles for bioanalysis

Aptamers are single-stranded oligonucleotides synthesized through an in vitro selection and amplification process that involves systematic evolution of ligands by exponential enrichment. Based on their high binding affinity and specificity towards other molecules, aptamers generated during the final rounds of selection can be utilized in applications ranging from biosensing to diagnostics and therapeutics. Meanwhile, advances in nanotechnology have led to new and improved materials for biomedical applications. Specifically, nanoparticles can readily interact with both intra- and extra-cellular biomolecules to yield improved signal amplification and target recognition. By combining both technologies, aptamer-conjugated nanoparticles, especially gold nanoparticles (Apt–AuNPs), offer great promise for applications in bioanalysis and biomedicine, including early diagnosis and drug delivery. This review summarizes recent methodologies that have increased the application of Apt–AuNPs in biomedicine, and discusses the potential of Apt–AuNPs in bioanalysis.

One-pot synthesized aptamer-functionalized CdTe:Zn2+ quantum dots for tumor-targeted fluorescence imaging in vitro and in vivo

High quality and facile DNA functionalized quantum dots (QDs) as efficient fluorescence nanomaterials are of great significance for bioimaging both in vitro and in vivo applications. Herein, we offer a strategy to synthesize DNA-functionalized Zn(2+) doped CdTe QDs (DNA-QDs) through a facile one-pot hydrothermal route. DNA is directly attached to the surface of QDs. The as-prepared QDs exhibit small size (3.85 ± 0.53 nm), high quantum yield (up to 80.5%), and excellent photostability. In addition, the toxicity of QDs has dropped considerably because of the Zn-doping and the existence of DNA. Furthermore, DNA has been designed as an aptamer specific for mucin 1 overexpressed in many cancer cells including lung adenocarcinoma. The aptamer-functionalized Zn(2+) doped CdTe QDs (aptamer-QDs) have been successfully applied in active tumor-targeted imaging in vitro and in vivo. A universal design of DNA for synthesis of Zn(2+) doped CdTe QDs could be extended to other target sequences. Owing to the abilities of specific recognition and the simple synthesis route, the applications of QDs will potentially be extended to biosensing and bioimaging.

Dissecting colloidal stabilization factors in crowded polymer solutions by forming self-assembled monolayers on gold nanoparticles

An ideal colloidal system should be highly stable in a diverse range of buffer conditions while still retaining its surface accessibility. We recently reported that dispersing citrate-capped gold nanoparticles (AuNPs) in polymers, such as polyethylene glycol (PEG), can achieve such a goal because of contributions from depletion stabilization. Because AuNPs can weakly adsorb PEG to exert steric stabilization and the remaining citrate can impart charge stabilization, the extent of the contribution of depletion stabilization is unclear. In this work, we aim to dissect the contribution of each stabilizing factor. This is achieved by coating AuNPs with a layer of thiolated compound, which inhibits the adsorption of PEG and also allows for the control of surface charge. We found that depletion stabilization alone was insufficient to stabilize AuNPs at room temperature. However, when working together with other stabilization mechanisms, ultrahigh stability can be achieved. The size of both AuNPs and PEG was systematically varied, and the trends were compared to theoretical calculations. Finally, we report the importance of the surface chemistry of commercial AuNPs.

Polarity control for nonthiolated DNA adsorption onto gold nanoparticles

Gold nanoparticles (AuNPs) functionalized with thiolated DNA have enabled many studies in nanoscience. The strong thiol/gold affinity and the nanoscale curvature of AuNPs allow the attached DNA to adapt an upright conformation favorable for hybridization. Recently, it has been shown that nonthiolated DNA can also be attached via DNA base adsorption. Without a thiol label, both ends of the DNA and even internal bases could be adsorbed, decreasing the specificity of subsequent molecular recognition reactions. In this work, we employed a modular sequence design approach to systematically study the effect of DNA sequence on adsorption polarity. A block of poly adenine (poly-A) could be used to achieve a high density of DNA attachment. When the poly-A block length is short (e.g., below 5-7), the loading was independent of the block length, and the conjugate cannot hybridize to its cDNA effectively, suggesting a random attachment controlled by adsorption kinetics. Increasing the block length leads to reduced capacity but improved hybridization, suggesting that more DNA with the desired conformation was adsorbed due to the thermodynamic effects of poly-A binding. The design can be further improved by including capping sequences rich in T or G. Finally, a more general double-stranded DNA approach was described to be suitable for DNA that cannot satisfy the above-mentioned design requirements.

Surface-enhanced Raman scattering molecular sentinel nanoprobes for viral infection diagnostics

In this paper, we describe a surface-enhanced Raman scattering (SERS)-based detection approach, referred to as "molecular sentinel" (MS) plasmonic nanoprobes, to detect an RNA target related to viral infection. The MS method is essentially a label-free technique incorporating the SERS effect modulation scheme associated with silver nanoparticles and Raman dye-labeled DNA hairpin probes. Hybridization with target sequences opens the hairpin and spatially separates the Raman label from the silver surface thus reducing the SERS signal of the label. Herein, we have developed a MS nanoprobe to detect the human radical S-adenosyl methionine domain containing 2 (RSAD2) RNA target as a model system for method demonstration. The human RSAD2 gene has recently emerged as a novel host-response biomarker for diagnosis of respiratory infections. Our results showed that the RSAD2 MS nanoprobes exhibits high specificity and can detect as low as 1 nM target sequences. With the use of a portable Raman spectrometer and total RNA samples, we have also demonstrated for the first time the potential of the MS nanoprobe technology for detection of host-response RNA biomarkers for infectious disease diagnostics.

An exceptionally simple strategy for DNA-functionalized up-conversion nanoparticles as biocompatible agents for nanoassembly, DNA delivery, and imaging

Lanthanide-doped up-conversion nanoparticles (UCNPs) have shown promise in biomedical applications. However, as the UCNPs are normally capped with hydrophobic ligands, it remains challenging to prepare biocompatible UCNPs with specific molecular recognition capabilities. We herein report an exceptionally simple strategy to prepare uniform DNA-modified UCNPs as versatile bioprobes. The approach can directly convert as-prepared hydrophobic UCNPs into water-soluble DNA-UCNPs without any chemical modification of UCNPs or oligonucleotides. Furthermore, DNA molecules on the DNA-UCNPs retain their biorecognition ability, allowing programmable assembly of hybrid nanostructures. More importantly, we show that these DNA-UCNPs are capable of crossing cell membranes without the need of transfection agents, and their use as agents for bioimaging and DNA delivery are also demonstrated. Finally, DNA aptamer-conjugated UCNPs can be readily used for targeted imaging of cancer cells.

Fast pH-assisted functionalization of silver nanoparticles with monothiolated DNA

Attaching monothiolated DNA to silver nanoparticles has been achieved at pH 3.0 in 30 minutes and difficulties associated with DNA attachment to AgNPs at neutral pH have been revealed by studying DNA adsorption kinetics.

Aptamer-conjugated multifunctional nanoflowers as a platform for targeting, capture, and detection in laser desorption ionization mass spectrometry

Although many different nanomaterials have been tested as substrates for laser desorption and ionization mass spectrometry (LDI-MS), this emerging field still requires more efficient multifuncional nanomaterials for targeting, enrichment, and detection. Here, we report the use of gold manganese oxide (Au@MnO) hybrid nanoflowers as an efficient matrix for LDI-MS. The nanoflowers were also functionalized with two different aptamers to target cancer cells and capture adenosine triphosphate (ATP). These nanoflowers were successfully used for metabolite extraction from cancer cell lysates. Thus, in one system, our multifunctional nanoflowers can (1) act as an ionization substrate for mass spectrometry, (2) target cancer cells, and (3) detect and analyze metabolites from cancer cells.

DNAzyme-functionalized gold nanoparticles for biosensing

Recent progress in using DNAzyme-functionalized gold nanoparticles (AuNPs) for biosensing is summarized in this chapter. A variety of methods, including those for attaching DNA on AuNPs, detecting metal ions and small molecules by DNAzyme-functionalized AuNPs, and intracellular applications of DNAzyme-functionalized AuNPs are discussed. DNAzyme-functionalized AuNPs will increasingly play more important roles in biosensing and many other multidisciplinary applications. This chapter covers the recent advancement in biosensing applications of DNAzyme-functionalized gold nanoparticles, including the detection of metal ions, small molecules, and intracellular imaging.

Expanding DNAzyme Functionality through Enzyme Cascades with Applications in Single Nucleotide Repair and Tunable DNA-Directed Assembly of Nanomaterials

Many biological functions require two or more enzymes working together in cascades. While many examples of protein and RNA enzyme cascades are known, few enzyme cascades containing solely DNAzymes have been reported. Herein we demonstrate the combination of an 8-17 DNAzyme with RNA cleavage activity and an E47 DNAzyme with DNA ligation activity to achieve a new function of single ribonucleotide repair in DNA while maintaining the integrity of the original DNA sequence, which is difficult for a single DNAzyme to achieve. In addition, this method is applied to modify the sequences of DNA strands immobilized on the surface of nanoparticles to control the DNA-directed assembly selectively and sequentially. Such an approach can be applied to other DNAzymes with different activities to expand the functions of DNAzymes and the scope of their applications.

Effects of polyethylene glycol on DNA adsorption and hybridization on gold nanoparticles and graphene oxide

Understanding the interface between DNA and nanomaterials is crucial for rational design and optimization of biosensors and drug delivery systems. For detection and delivery into cells, where high concentrations of cellular proteins are present, another layer of complexity is added. In this context, we employ polyethylene glycol (PEG) as a model polymer to mimic the excluded volume effect of cellular proteins and to test its effects on DNA adsorption and hybridization on gold nanoparticles (AuNPs) and graphene oxide (GO), both of which show great promise for designing intracellular biosensors and drug delivery systems. We show that PEG 20000 (e.g., 4%) accelerates DNA hybridization to DNA-functionalized AuNPs by 50-100%, but this enhanced hybridization kinetics has not been observed with free DNA. Therefore, this rate enhancement is attributed to the surface blocking effect by PEG instead of the macromolecular crowding effect. On the other hand, DNA adsorption on citrate-capped AuNP surfaces is impeded even in the presence of a trace level (i.e., parts per billion) of PEG, confirming PEG competes with DNA for surface binding sites. Additional insights have been obtained by studying the adsorption of a thiolated DNA and a peptide nucleic acid. In these cases, the steric effects of PEG to impede adsorption are observed. Similar observations have also been made with GO. Therefore, PEG may be used as an effective blocking agent for both hydrophilic AuNP and for GO that also contains hydrophobic domains.

Amino acid ionic liquid modified mesoporous carbon: a tailor-made nanostructure biosensing platform

A novel nanocomposite based on ordered graphitized mesoporous carbon (GMC) and amino acid ionic liquids (AAIL) is obtained through controlled surface modification of GMC with hydrophilic AAILs (1-ethyl-3-methylimidazolium alanine, EMIM[Ala]), which is used as a platform for a tyrosinase biosensor to detect phenol. The GMC-AAIL nanocomposite possesses a better biocompatibility and improved aqueous-phase dispersion than hydrophobic GMC alone, owing to the introduction of hydrophilic and biocompatible AAILs. Comparative studies revealed that the catalytic activity of tyrosinase for phenol in phosphate buffer solution (PBS) containing EMIM[Ala] was about ten times higher than that in pure PBS. By entrapping tyrosinase molecules into the mesopores of GMC, making use of the synergy effect of GMC and AAIL (the "interspace confinement effect", the anti-fouling ability, and the biocompatible microenvironment), the GMC-AAIL-based biosensors display superior analytical performance to GMC-based ones in terms of signal-to-noise ratio, stability, repeatability, and working life. After 21-day storage, the electrode retained more than 90% of its initial response, indicating that surface modification of GMC with hydrophilic and biocompatible AAILs could significantly prolong the life of tyrosinase in vitro. The GMC10-EMIM[Ala]-based biosensor demonstrates a linear response for phenol concentrations from 0.1 to 10 µmol L(-1) with a low detection limit of 20 nmol L(-1) and sensitivity of 1385 mA cm(-2) M(-1). The GMC-AAIL nanocomposite proves to be a promising platform for enzyme-based biosensors and biocatalysis.

Highly sensitive optical biosensor for thrombin based on structure switching aptamer-luminescent silica nanoparticles

We describe here the construction of a sensitive and selective optical sensor system for the detection of human α-thrombin. The surface functionalized luminescent [Ru(dpsphen)(3)](4-) (dpsphen-4,7-diphenyl-1,10-phenanthroline disulfonate) ion doped silica nanoparticles (SiNPs) with a size ~70 nm have been prepared. The DABCYL (2-(4-dimethylaminophenyl)diazenyl-benzoic acid) quencher labeled thrombin binding aptamer is conjugated to the surface of SiNPs using BS(3) (bis(sulfosuccinimidyl) suberate) as a cross-linker, resulting in the conformational change of aptamer to form G-quadruplex structure upon the addition of thrombin. The binding event is translated into a change in the luminescence intensity of Ru(II) complex via FRET mechanism, due to the close proximity of DABCYL quencher with SiNPs. The selective detection of thrombin using the SiNPs-aptamer system up to 4 nM is confirmed by comparing its sensitivity towards other proteins. This work demonstrates the application of simple aptamer-SiNPs conjugate as a highly sensitive system for the detection of thrombin and also it is highly sensitive towards thrombin in the presence of other proteins and complex medium such as BSA.

Specific binding of anionic porphyrin and phthalocyanine to the G-quadruplex with a variety of in vitro and in vivo applications

The G-quadruplex, a four-stranded DNA structure with stacked guanine tetrads (G-quartets), has recently been attracting attention because of its critical roles in vitro and in vivo. In particular, the G-quadruplex functions as ligands for metal ions and aptamers for various molecules. Interestingly, the G-quadruplex can show peroxidase-like activity with an anionic porphyrin, iron (III) protoporphyrin IX (hemin). Importantly, hemin binds to G-quadruplexes with high selectivity over single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA), which is attributable to an electrostatic repulsion of phosphate groups in ssDNA and dsDNA. The G-quadruplex and hemin-G-quadruplex complex allow development of sensing techniques to detect DNA, metal ions and proteins. In addition to hemin, anionic phthalocyanines also bind to the G-quadruplex formed by human telomere DNA, specifically over ssDNA and dsDNA. Since the binding of anionic phthalocyanines to the G-quadruplex causes an inhibition of telomerase activity, which plays a role in the immortal growth of cancer cells, anionic phthalocyanines are promising as novel anticancer drug candidates. This review focuses on the specific binding of hemin and anionic phthalocyanines to G-quadruplexes and the applications in vitro and in vivo of this binding property.

Graphene enhanced electron transfer at aptamer modified electrode and its application in biosensing

Graphene (GN), a two-dimensional and one-atom thick carbon sheet, is showing exciting applications because of its unique morphology and properties. In this work, a new electrochemical biosensing platform by taking advantage of the ultrahigh electron transfer ability of GN and its unique GN/ssDNA interaction was reported. Adenosine triphosphate binding aptamer (ABA) immobilized on Au electrode could strongly adsorb GN due to the strong π-π interaction and resulted in a large decrease of the charge transfer resistance (R(ct)) of the electrode. However, the binding reaction between ABA and its target adenosine triphosphate (ATP) inhibited the adsorption of GN, and R(ct) could not be decreased. On the basis of this, we developed a new GN-based biosensing platform for the detection of small molecule ATP. The experimental results confirmed that the electrochemical aptasensor we developed possessed a good sensitivity and high selectivity for ATP. The detection range for ATP was from 15 × 10(-9) to 4 × 10(-3) M. The method here was label-free and sensitive and did not require sophisticated fabrication. Furthermore, we can generalize this strategy to detect Hg(2+) using a thymine (T)-rich, mercury-specific oligonucleotide. Therefore, we expected that this method may offer a promising approach for designing high-performance electrochemical aptasensors for the sensitive and selective detection of a spectrum of targets.

Assembly of aptamer switch probes and photosensitizer on gold nanorods for targeted photothermal and photodynamic cancer therapy

An aptamer switch probe (ASP) linking chlorin e6 (Ce6), a photosensitizer molecule, to the surface of gold nanorods (AuNRs) was used to target cancer cells for photodynamic therapy (PDT) and photothermal therapy (PTT). In the presence of target cancer cells, the ASP changes conformation to drive Ce6 away from the gold surface, thereby producing singlet oxygen for PDT upon light irradiation. Since each AuNR is modified with many ASP-Ce6 molecules, the AuNR-ASP-Ce6 conjugate yields enhanced binding and therapeutic effect by the added ability to carry many photosensitizers. In addition, absorption of radiation by the gold nanorods enables further cell destruction by the photothermal effect. Consequently, this multimodal AuNR-ASP-Ce6 conjugate offers a remarkably improved and synergistic therapeutic effect compared to PTT or PDT alone, providing high specificity and therapeutic efficiency, which can be generalized to other types of cancer therapies.

Nanotechnology advances in upper gastrointestinal, liver and pancreatic cancer

Cancers of the upper GI tract, liver and pancreas have some of the poorest prognoses of any malignancies. Advances in diagnosis and treatment are sorely needed to improve the outcomes of patients. Nanotechnology offers the potential for constructing tailor-made therapies capable of targeting specific cancers. The particles themselves may be endowed with multifunctional properties that can be exploited for both diagnosis and treatment. Although development of therapies is still in the early stages, the use of nanoparticles (NPs) is widespread in diagnostic applications and will probably involve all areas of medicine in the future. Research into NPs is ongoing for upper gastrointestinal, liver and pancreatic cancers, and their use is becoming increasingly popular as contrast media for radiological investigations. Although more sophisticated technologies capable of active targeting are still in the early stages of assessment for clinical use, a small number of NP-based therapies are in clinical use.

DNA surface modified gadolinium phosphate nanoparticles as MRI contrast agents

Oligonucleotide modified gadolinium phosphate nanoparticles have been prepared and their magnetic resonance relaxivity properties measured. Nanoparticles of GdPO4·H2O were synthesized in a water/oil microemulsion using IGEPAL CO-520 as surfactant, resulting in 50 to 100 nm particles that are highly dispersible and stable in water. Using surface modification chemistry previously established for zirconium phosphonate surfaces, the particles are directly modified with 5'-phosphate terminated oligonucleotides, and the specific interaction of the divalent phosphate with Gd(3+) sites at the surface is demonstrated. The ability of the modified nanoparticles to act as MRI contrast agents was determined by performing MR relaxivity measurements at 14.1 T. Solutions of nanopure water, Feridex, and Omniscan (FDA approved contrast agents) in 0.25% agarose were used for comparison and control purposes. MRI data confirm that GdPO4·H2O nanoparticles have relaxivities (r1, r2) comparable to those of commercially available contrast agents. In addition, the data suggest that biofunctionalization of the surface of the nanoparticles does not prevent their function as MRI contrast agents.

Instantaneous and quantitative functionalization of gold nanoparticles with thiolated DNA using a pH-assisted and surfactant-free route

The attachment of thiolated DNA to gold nanoparticles (AuNPs) has enabled many landmark works in nanobiotechnology. This conjugate chemistry is typically performed using a salt-aging protocol where, in the presence of an excess amount of DNA, NaCl is gradually added to increase DNA loading over 1-2 days. To functionalize large AuNPs, surfactants need to be used, which may generate difficulties for downstream biological applications. We report herein a novel method using a pH 3.0 citrate buffer to complete the attachment process in a few minutes. More importantly, it allows for quantitative DNA adsorption, eliminating the need to quantify the number of adsorbed DNA and allowing the adsorption of multiple DNAs with different sequences at predetermined ratios. The method has been tested for various DNAs over a wide range of AuNP sizes. Our work suggests a synergistic effect between pH and salt in DNA attachment and reveals the fundamental kinetics of AuNP aggregation versus DNA adsorption, providing a novel means to modulate the interactions between DNA and AuNPs.

Luminescent nanoparticles and their use for in vitro and in vivo diagnostics

Fluorescence spectroscopy has been shown to be a useful tool for a broad variety of biological and medical applications. Many of the analytical methods, as used for tumor marker and gene mutation detection, recognition of pathogens or monitoring of cell-related processes, are based on the labeling of the investigating object with luminescent nanoparticles. Owing to their size, which is comparable to that of biomolecules, and to their extraordinary optical properties, luminescent nanoparticles could well improve the sensitivity and flexibility of current detection techniques. This article provides a general overview of the synthesis, properties and application of luminescent semiconductor, metal and inorganic nanoparticles for in vitro and in vivo diagnostics, also reflecting the aspect of biocompatibility.

Aptamer-functionalized hydrogel microparticles for fast visual detection of mercury(II) and adenosine

With a low optical background, high loading capacity, and good biocompatibility, hydrogels are ideal materials for immobilization of biopolymers to develop optical biosensors. We recently immobilized mercury and lead binding DNAs within a monolithic gel and demonstrated ultrasensitive visual detection of these heavy metals. The high sensitivity was attributed to the enrichment of the analytes into the gels. The signaling kinetics was slow, however, taking about 1 h to obtain a stable optical signal because of a long diffusion distance. In this work, we aim to understand the analyte enrichment process and improve the signaling kinetics by preparing hydrogel microparticles. DNA-functionalized gel beads were synthesized using an emulsion polymerization technique and most of the beads were between 10 and 50 μm. Acrydite-modified DNA was incorporated by copolymerization. Visual detection of 10 nM Hg(2+) was still achieved and a stable signal was obtained in just 2 min. The gel beads could be spotted to form a microarray and dried for storage. A new visual sensor for adenosine was designed and immobilized within the gel beads. The adenosine aptamer binds its target about 1000-fold less tightly compared to the mercury binding DNA, allowing a comparison to be made on analyte enrichment by aptamer-functionalized hydrogels.

Biomimetic sensing based on chemically induced assembly of a signaling DNA aptamer on a fluid bilayer membrane

The adenosine aptamer was split into two halves and linked to a fluid liposome surface; addition of adenosine resulted in aptamer assembly, which did not occur if the split aptamer was attached to silica nanoparticles, demonstrating the feasibility of using aptamer probes to study diffusion within lipid membranes.

Surface science of DNA adsorption onto citrate-capped gold nanoparticles

Single-stranded DNA can be adsorbed by citrate capped gold nanoparticles (AuNPs), resulting in increased AuNP stability, which forms the basis of a number of biochemical and analytical applications, but the fundamental interaction of this adsorption reaction remains unclear. In this study, we measured DNA adsorption kinetics, capacity, and isotherms, demonstrating that the adsorption process is governed by electrostatic forces. The charge repulsion among DNA strands and between DNA and AuNPs can be reduced by adding salt, reducing pH or by using noncharged peptide nucleic acid (PNA). Langmuir adsorption isotherms are obtained, indicating the presence of both adsorption and desorption of DNA from AuNPs. While increasing salt concentration facilitates DNA adsorption, the desorption rate is also enhanced in higher salt due to DNA compaction. DNA adsorption capacity is determined by DNA oligomer length, DNA concentration, and salt. Previous studies indicated faster adsorption of short DNA oligomers by AuNPs, we find that once adsorbed, longer DNAs are much more effective in protecting AuNPs from aggregation. DNA adsorption is also facilitated by using low pH buffers and high alcohol concentrations. A model based on electrostatic repulsion on AuNPs is proposed to rationalize the DNA adsorption/desorption behavior.