Simultaneous Non-invasive Analysis of DNA Condensation and Stability by Two-step QD-FRET

Nanomaterials for Fluorescence and Multimodal Bioimaging

Bioconjugated nanomaterials replace molecular probes in bioanalysis and bioimaging in vitro and in vivo. Nanoparticles of silica, metals, semiconductors, polymers, and supramolecular systems, conjugated with contrast agents and drugs for image-guided (MRI, fluorescence, PET, Raman, SPECT, photodynamic, photothermal, and photoacoustic) therapy infiltrate into preclinical and clinical settings. Small bioactive molecules like peptides, proteins, or DNA conjugated to the surfaces of drugs or probes help us to interface them with cells and tissues. Nevertheless, the toxicity and pharmacokinetics of nanodrugs, nanoprobes, and their components become the clinical barriers, underscoring the significance of developing biocompatible next-generation drugs and contrast agents. This account provides state-of-the-art advancements in the preparation and biological applications of bioconjugated nanomaterials and their molecular, cell, and in vivo applications. It focuses on the preparation, bioimaging, and bioanalytical applications of monomodal and multimodal nanoprobes composed of quantum dots, quantum clusters, iron oxide nanoparticles, and a few rare earth metal ion complexes.

DNA-enabled fluorescent-based nanosensors monitoring tumor-related RNA toward advanced cancer diagnosis: A review

As a burgeoning non-invasive indicator for reproducible cancer diagnosis, tumor-related biomarkers have a wide range of applications in early cancer screening, efficacy monitoring, and prognosis predicting. Accurate and efficient biomarker determination, therefore, is of great importance to prevent cancer progression at an early stage, thus reducing the disease burden on the entire population, and facilitating advanced therapies for cancer. During the last few years, various DNA structure-based fluorescent probes have established a versatile platform for biological measurements, due to their inherent biocompatibility, excellent capacity to recognize nucleic and non-nucleic acid targets, obvious accessibility to synthesis as well as chemical modification, and the ease of interfacing with signal amplification protocols. After decades of research, DNA fluorescent probe technology for detecting tumor-related mRNAs has gradually grown to maturity, especially the advent of fluorescent nanoprobes has taken the process to a new level. Here, a systematic introduction to recent trends and advances focusing on various nanomaterials-related DNA fluorescent probes and the physicochemical properties of various involved nanomaterials (such as AuNP, GO, MnO2, SiO2, AuNR, etc.) are also presented in detail. Further, the strengths and weaknesses of existing probes were described and their progress in the detection of tumor-related mRNAs was illustrated. Also, the salient challenges were discussed later, with a few potential solutions.

Single-molecule displacement assay reveals strong binding of polyvalent dendrimer ligands to telomeric G-quadruplex

Binding between a ligand and a receptor is a fundamental step in many natural or synthetic processes. In biosensing, a tight binding with a small dissociation constant (Kd) between the probe and analyte can lead to superior specificity and sensitivity. Owing to their capability of evaluating competitors, displacement assays have been used to estimate Kd at the ensemble average level. At the more sensitive single-molecule level, displacement assays are yet to be established. Here, we developed a single-molecule displacement assay (smDA) in an optical tweezers instrument and used this innovation to evaluate the binding of the L2H2-6OTD ligands to human telomeric DNA G-quadruplexes. After measuring Kd of linear and dendrimer L2H2-6OTD ligands, we found that dendrimer ligands have enhanced binding affinity to the G-quadruplexes due to their polyvalent geometry. This increased binding affinity enhanced inhibition of telomerase elongation on a telomere template in a Telomerase Repeated Amplification Protocol (TRAP). Our experiments demonstrate that the smDA approach can efficiently evaluate binding processes in chemical and biological processes.

Charge Segregation in the Intrinsically Disordered Region Governs VRN1 and DNA Liquid-like Phase Separation Robustness

VERNALIZATION1 (VRN1) is a transcriptional repressor involved in plant vernalization that undergoes liquid-liquid phase separation (LLPS) with DNA. The naturally occurring VRN1-like proteins contain two B3 DNA binding domains connected by an intrinsically disordered region (IDR). The IDR length in VRN1-like proteins has a broad distribution, while the charge segregation pattern is largely conserved. We studied the effect of IDR length and charge segregation on DNA-induced VRN1 phase separation. When only neutral residues (Pro-Ser repeats) were used, the phase separation behavior is sensitive to IDR length, changing from gel-like aggregates (L = 40) to liquid-like droplets (L = 100-120) and clear solution (L = 160). When a pair of continuous patches of positive and negative residues were added to the IDRs, all the VRN1 variants formed robust and durable droplets with DNA independent of the IDR length. To test how robust the system is, we introduced folded green fluorescent protein or the enzyme GPX4 into VRN1 variants with charge segregation in IDR, the resulting proteins form LLPS with DNA as well. Our study implies that VRN1-like proteins use conserved charge segregation pattern to retain functional LLPS during evolution, and demonstrates the possibility of using this system to design novel biosensors or bio-factories by introducing various functional modules.

Recent Advances in Self-Exciting Photodynamic Therapy

Photodynamic therapy (PDT) is already (Food and Drug Administration) FDA approved and used in the clinic for oncological treatment of pancreatic, lung, esophagus, bile duct, and of course several cancers of skin. It is an important tool in the oncological array of treatments, but for it exist several shortcomings, the most prominent of which is the shallow depth penetration of light within tissues. One-way researchers have attempted to circumvent this is through the creation of self-exciting "auto-PDT" nanoplatforms, which do not require the presence of an external light source to drive the PDT process. Instead, these platforms are driven either through oxidative chemical excitation in the form of chemiluminescence or radiological excitation from beta-emitting isotopes in the form of Cherenkov luminescence. In both, electronic excitations are generated and then transferred to the photosensitizer (PS) via Resonance Energy Transfer (RET) or Cherenkov Radiation Energy Transfer (CRET). Self-driven PDT has many components, so in this review, using contemporary examples from literature, we will breakdown the important concepts, strategies, and rationale behind the design of these self-propagating PDT nanoplatforms and critically review the aspects which make them successful and different from conventional PDT. Particular focus is given to the mechanisms of excitation and the different methods of transfer of excited electronic energy to the photosensitizer as well as the resulting therapeutic effect. The papers reviewed herein will be critiqued for their apparent therapeutic efficiency, and a basic rationale will be developed for what qualities are necessary to constitute an "effective" auto-PDT platform. This review will take a biomaterial engineering approach to the review of the auto-PDT platforms and the intended audience includes researchers in the field looking for a new perspective on PDT nanoplatforms as well as other material scientists and engineers looking to understand the mechanisms and relations between different parts of the complex "auto-PDT" system.

Enhancing FRET biosensing beyond 10 nm with photon avalanche nanoparticles

Förster Resonance Energy Transfer (FRET) between donor (D) and acceptor (A) molecules is a phenomenon commonly exploited to study or visualize biological interactions at the molecular level. However, commonly used organic D and A molecules often suffer from photobleaching and spectral bleed-through, and their spectral properties hinder quantitative analysis. Lanthanide-doped upconverting nanoparticles (UCNPs) as alternative D species offer significant improvements in terms of photostability, spectral purity and background-free luminescence detection, but they bring new challenges related to multiple donor ions existing in a single large size UCNP and the need for nanoparticle biofunctionalization. Considering the relatively short Förster distance (typically below 5-7 nm), it becomes a non-trivial task to assure sufficiently strong D-A interaction, which translates directly to the sensitivity of such bio-sensors. In this work we propose a solution to these issues, which employs the photon avalanche (PA) phenomenon in lanthanide-doped materials. Using theoretical modelling, we predict that these PA systems would be highly susceptible to the presence of A and that the estimated sensitivity range extends to distances 2 to 4 times longer (i.e. 10-25 nm) than those typically found in conventional FRET systems. This promises high sensitivity, low background and spectral or temporal biosensing, and provides the basis for a radically novel approach to combine luminescence imaging and self-normalized bio-molecular interaction sensing.

Fluorescence-Based Quantification of Messenger RNA and Plasmid DNA Decay Kinetics in Extracellular Biological Fluids and Cell Extracts

Extracellular and intracellular degradation of nucleic acids remains an issue in non-viral gene therapy. Understanding biodegradation is critical for the rational design of gene therapeutics in order to maintain stability and functionality at the target site. However, there are only limited methods available that allow determining the stability of genetic materials in biological environments. In this context, the decay kinetics of fluorescently labeled plasmid DNA (pDNA) and messenger RNA (mRNA) in undiluted biological samples (i.e., human serum, human ascites, bovine vitreous) and cell extracts is studied using fluorescence correlation spectroscopy (FCS) and single particle tracking (SPT). It is demonstrated that FCS is suitable to follow mRNA degradation, while SPT is better suited to investigate pDNA integrity. The half-life of mRNA and pDNA is ≈1-2 min and 1-4 h in biological samples, respectively. The resistance against biodegradation drastically improves by complexation with lipid-based carriers. Taken together, FCS and SPT are able to quantify the integrity of mRNA and pDNA, respectively, as a function of time, both in the extracellular biological fluids and cell extracts. This in turn allows to focus on the important but less understood issue of nucleic acids degradation in more detail and to rationally optimize gene delivery system as therapeutics.

A Smart DNA Tweezer for Detection of Human Telomerase Activity

Reliable and accurate detection of telomerase activity is crucial to better understand its role in cancer cells and to further explore its function in cancer diagnosis and treatment. Here, we construct a smart DNA tweezer (DT) for detection of telomerase activity. The DT is assembled by three specially designed single-stranded oligonucleotides: a central strand dually labeled with donor/acceptor fluorophores and two arm strands containing overhangs complementary to telomerase reaction products (TRPs). It can get closed through hybridization with TRPs and get reopen through strand displacement reaction by TRPs' complementary sequences. First, under the action of telomerase, telomerase binding substrates (TS) are elongated to generate TRPs ended with telomeric repeats (TTAGGG) _n. TRPs hybridize with the two arm overhangs cooperatively and strain DT to closed state, inducing an increased fluorescence resonance energy transfer (FRET) efficiency, which is utilized for telomerase activity detection. Second, upon introduction of a removal strand (RS) complementary to TRPs, the closed DT is relaxed to open state via the toehold-mediated strand displacement, inducing a decreased FRET efficiency, which is utilized for determination of TRP length distribution. The detection limit of telomerase activity is equivalent to 141 cells/μL for HeLa cells, and telomerase-active cellular extracts can be differentiated from telomerase-inactive cellular extracts. Furthermore, TRPs owning 1, 2, 3, 4, and ≥5 telomeric repeats are identified to account for 25.6%, 20.5%, 15.7%, 12.5%, and 25.7%, respectively. The proposed strategy will offer a new approach for reliable, accurate detection of telomerase activity and product length distribution for deeper studying its role and function in cancer.

Specific Systems for Imaging

Microscopy allows for the characterization of small objects invisible to the naked eye, a technique that, since its conception, has played a key role in the development across nearly every field of science and technology. Given the nanometer size of the materials explored in the field of nanotechnology, the contributions of modern microscopes that can visualize these materials are indispensable, and the ever-improving technology is paramount to the future success of the field. This chapter will focus on four fundamental areas of microscopy used in the field of nanotechnology including fluorescence microscopy (Sect. 3.1), particle tracking and photoactivated localization microscopy (Sect. 3.2), quantum dots and fluorescence resonance energy transfer (Sect. 3.3), and cellular MRI and PET labeling (Sect. 3.4). The functionality, as well as the current and recommended usage of each given imaging system, will be discussed.

Cadmium-containing quantum dots: properties, applications, and toxicity

The marriage of biology with nanomaterials has significantly accelerated advancement of biological techniques, profoundly facilitating practical applications in biomedical fields. With unique optical properties (e.g., tunable broad excitation, narrow emission spectra, robust photostability, and high quantum yield), fluorescent quantum dots (QDs) have been reasonably functionalized with controllable interfaces and extensively used as a new class of optical probe in biological researches. In this review, we summarize the recent progress in synthesis and properties of QDs. Moreover, we provide an overview of the outstanding potential of QDs for biomedical research and innovative methods of drug delivery. Specifically, the applications of QDs as novel fluorescent nanomaterials for biomedical sensing and imaging have been detailedly highlighted and discussed. In addition, recent concerns on potential toxicity of QDs are also introduced, ranging from cell researches to animal models.

A dual-colored ratiometric-fluorescent oligonucleotide probe for the detection of human telomerase RNA in cell extracts

A dual-colored ratiometric-fluorescent oligonucleotide probe is designed for the detection of human telomerase RNA (hTR) in cell extracts.

Polyplexes assembled from self-peptides and regulatory nucleic acids blunt toll-like receptor signaling to combat autoimmunity

Autoimmune diseases occur when the immune system incorrectly recognizes self-molecules as foreign; in the case of multiple sclerosis (MS), myelin is attacked. Intriguingly, new studies reveal toll-like receptors (TLRs), pathways usually involved in generating immune responses against pathogens, play a significant role in driving autoimmune disease in both humans and animal models. We reasoned polyplexes formed from myelin self-antigen and regulatory TLR antagonists might limit TLR signaling during differentiation of myelin-specific T cells, inducing tolerance by biasing T cells away from inflammatory phenotypes. Complexes were formed by modifying myelin peptide with cationic amino acids to create peptides able to condense the anionic nucleic-acid based TLR antagonist. These immunological polyplexes eliminate synthetic polymers commonly used to condense polyplexes and do not rely on gene expression; however, the complexes mimic key features of traditional polyplexes such as tunable loading and co-delivery. Using these materials and classic polyplex analysis techniques, we demonstrate condensation of both immune signals, protection from enzymatic degradation, and tunable physicochemical properties. We show polyplexes reduce TLR signaling, and in primary dendritic cell and T cell co-culture, reduce myelin-driven inflammation. During mouse models of MS, these tolerogenic polyplexes improve the progression, severity, and incidence of disease.

Imaging of transfection and intracellular release of intact, non-labeled DNA using fluorescent nanodiamonds

Efficient delivery of stabilized nucleic acids (NAs) into cells and release of the NA payload are crucial points in the transfection process. Here we report on the fabrication of a nanoscopic cellular delivery carrier that is additionally combined with a label-free intracellular sensor device, based on biocompatible fluorescent nanodiamond particles. The sensing function is engineered into nanodiamonds by using nitrogen-vacancy color centers, providing stable non-blinking luminescence. The device is used for monitoring NA transfection and the payload release in cells. The unpacking of NAs from a poly(ethyleneimine)-terminated nanodiamond surface is monitored using the color shift of nitrogen-vacancy centers in the diamond, which serve as a nanoscopic electric charge sensor. The proposed device innovates the strategies for NA imaging and delivery, by providing detection of the intracellular release of non-labeled NAs without affecting cellular processing of the NAs. Our system highlights the potential of nanodiamonds to act not merely as labels but also as non-toxic and non-photobleachable fluorescent biosensors reporting complex molecular events.

Quantification of cellular and nuclear uptake rates of polymeric gene delivery nanoparticles and DNA plasmids via flow cytometry

Non-viral, biomaterial-mediated gene delivery has the potential to treat many diseases, but is limited by low efficacy. Elucidating the bottlenecks of plasmid mass transfer can enable an improved understanding of biomaterial structure-function relationships, leading to next-generation rationally designed non-viral gene delivery vectors. As proof of principle, we transfected human primary glioblastoma cells using a poly(beta-amino ester) complexed with eGFP plasmid DNA. The polyplexes transfected 70.6±0.6% of the cells with 101±3% viability. The amount of DNA within the cytoplasm, nuclear envelope, and nuclei was assessed at multiple time points using fluorescent dye conjugated plasmid up to 24h post-transfection using a quantitative multi-well plate-based flow cytometry assay. Conversion to plasmid counts and degradation kinetics were accounted for via quantitative PCR (plasmid degradation rate constants were determined to be 0.62h(-1) and 0.084h(-1) for fast and slow phases respectively). Quantitative cellular uptake, nuclear association, and nuclear uptake rate constants were determined by using a four-compartment first order mass-action model. The rate limiting step for these poly(beta-amino ester)/DNA polyplex nanoparticles was determined to be cellular uptake (7.5×10(-4)h(-1)) and only 0.1% of the added dose was taken up by the human brain cancer cells, whereas 12% of internalized DNA successfully entered the nucleus (the rate of nuclear internalization of nuclear associated plasmid was 1.1h(-1)). We describe an efficient new method for assessing cellular and nuclear uptake rates of non-viral gene delivery nanoparticles using flow cytometry to improve understanding and design of polymeric gene delivery nanoparticles.

STATEMENT OF SIGNIFICANCE

In this work, a quantitative high throughput flow cytometry-based assay and computational modeling approach was developed for assessing cellular and nuclear uptake rates of non-viral gene delivery nanoparticles. This method is significant as it can be used to elucidate structure-function relationships of gene delivery nanoparticles and improve their efficiency. This method was applied to a particular type of biodegradable polymer, a poly(beta-amino ester), that transfected human brain cancer cells with high efficacy and without cytotoxicity. A four-compartment first order mass-action kinetics model was found to model the experimental transport data well without requiring external fitting parameters. Quantitative rate constants were identified for the intracellular transport, including DNA degradation rate from polyplexes, cellular uptake rate, and nuclear uptake rate, with cellular uptake identified as the rate-limiting step.

A review on fluorescent inorganic nanoparticles for optical sensing applications

Fluorescent inorganic nanoparticles are immerging novel materials that can be adopted for a large number of optical bioassays and chemical sensing probes.

Two-step energy transfer enables use of phenylalanine in action-EET for distance constraint determination in gaseous biomolecules

Two-step energy transfer is observed between phenylalanine, tyrosine, and modified cysteine. This gas-phase system enables use of phenylalanine in energy transfer experiments, provides specific distance information for structure determination, and is easily examined with mass spectrometry.

Quantum dots: bright and versatile in vitro and in vivo fluorescence imaging biosensors

Colourful cells and tissues: semiconductor quantum dots and their versatile applications in multiplexed bioimaging research.

Mn-doped CdS/ZnS/CdS QD-based fluorescent nanosensor for rapid, selective, and ultrasensitive detection of copper(ii) ion

Energy levels of Mn-doped QD-based nanosensor and the quenching mechanism of the nanosensor by Cu²⁺.

Dual core quantum dots for highly quantitative ratiometric detection of trypsin activity in cystic fibrosis patients

We present herein two colour encoded silica nanospheres (2nanoSi) for the fluorescence quantitative ratiometric determination of trypsin in humans. Current detection methods for cystic fibrosis diagnosis are slow, costly and suffer from false positives. The 2nanoSi proved to be a highly sensitive, fast (minutes), and single-step approach nanosensor for the screening and diagnosis of cystic fibrosis, allowing the quantification of trypsin concentrations in a wide range relevant for clinical applications (25-350 μg L(-1)). Furthermore, as trypsin is directly related to the development of cystic fibrosis (CF), different human genotypes, i.e. CF homozygotic, CF heterozygotic, and unaffected, respectively, can be determined using our 2nanoSi nanospheres. We anticipate the 2nanoSi system to be a starting point for non-invasive, easy-to-use and cost effective ratiometric fluorescent biomarkers for recessive genetic diseases like human cystic fibrosis. In a screening program in which the goal is to detect disease and also the carrier status, early diagnosis could be of great help.

Quantum dots in diagnostics and detection: principles and paradigms

Quantum dots are semiconductor nanocrystals that exhibit exceptional optical and electrical behaviors not found in their bulk counterparts. Following seminal work in the development of water-soluble quantum dots in the late 1990's, researchers have sought to develop interesting and novel ways of exploiting the extraordinary properties of quantum dots for biomedical applications. Since that time, over 10,000 articles have been published related to the use of quantum dots in biomedicine, many of which regard their use in detection and diagnostic bioassays. This review presents a didactic overview of fundamental physical phenomena associated with quantum dots and paradigm examples of how these phenomena can and have been readily exploited for manifold uses in nanobiotechnology with a specific focus on their implementation in in vitro diagnostic assays and biodetection.

Challenges associated with Penetration of Nanoparticles across Cell and Tissue Barriers: A Review of Current Status and Future Prospects

Nanoparticles (NPs) have emerged as an effective modality for the treatment of various diseases including cancer, cardiovascular and inflammatory diseases. Various forms of NPs including liposomes, polymer particles, micelles, dendrimers, quantum dots, gold NPs and carbon nanotubes have been synthesized and tested for therapeutic applications. One of the greatest challenges that limit the success of NPs is their ability to reach the therapeutic site at necessary doses while minimizing accumulation at undesired sites. The biodistribution of NPs is determined by body's biological barriers that manifest in several distinct ways. For intravascular delivery of NPs, the barrier manifests in the form of: (i) immune clearance in the liver and spleen, (ii) permeation across the endothelium into target tissues, (iii) penetration through the tissue interstitium, (iv) endocytosis in target cells, (v) diffusion through cytoplasm and (vi) eventually entry into the nucleus, if required. Certain applications of NPs also rely on delivery through alternate routes including skin and mucosal membranes of the nose, lungs, intestine and vagina. In these cases, the diffusive resistance of these tissues poses a significant barrier to delivery. This review focuses on the current understanding of penetration of NPs through biological barriers. Emphasis is placed on transport barriers and not immunological barriers. The review also discusses design strategies for overcoming the barrier properties.

Amphiphilic biodegradable PEG-PCL-PEI triblock copolymers for FRET-capable in vitro and in vivo delivery of siRNA and quantum dots

Amphiphilic triblock copolymers represent a versatile delivery platform capable of co-delivery of nucleic acids, drugs, and/or dyes. Multifunctional cationic triblock copolymers based on poly(ethylene glycol), poly-ε-caprolactone, and polyethylene imine, designed for the delivery of siRNA, were evaluated in vitro and in vivo. Moreover, a nucleic acid-unpacking-sensitive imaging technique based on quantum dot-mediated fluorescence resonance energy transfer (QD-FRET) was established. Cell uptake in vitro was measured by flow cytometry, whereas transfection efficiencies of nanocarriers with different hydrophilic block lengths were determined in vitro and in vivo by quantitative real-time PCR. Furthermore, after the proof of concept was demonstrated by fluorescence spectroscopy/microscopy, a prototype FRET pair was established by co-loading QDs and fluorescently labeled siRNA. The hydrophobic copolymer mediated a 5-fold higher cellular uptake and good knockdown efficiency (61 ± 5% in vitro, 55 ± 18% in vivo) compared to its hydrophilic counterpart (13 ± 6% in vitro, 30 ± 17% in vivo), which exhibited poor performance. FRET was demonstrated by UV-induced emission of the acceptor dye. Upon complex dissociation, which was simulated by the addition of heparin, a dose-dependent decrease in FRET efficiency was observed. We believe that in vitro/in vivo correlation of the structure and function of polymeric nanocarriers as well as sensitive imaging functionality for mechanistic investigations are prerequisites for a more rational design of amphiphilic gene carriers.

Nanostructure-induced DNA condensation

The control of the DNA condensation process is essential for compaction of DNA in chromatin, as well as for biological applications such as nonviral gene therapy. This review endeavours to reflect the progress of investigations on DNA condensation effects of nanostructure-based condensing agents (such as nanoparticles, nanotubes, cationic polymer and peptide agents) observed by using atomic force microscopy (AFM) and other techniques. The environmental effects on structural characteristics of nanostructure-induced DNA condensates are also discussed.

Functionalized quantum dots for biosensing and bioimaging and concerns on toxicity

Considerable efforts have been devoted to the development of novel functionalized nanomaterials for bio-oriented applications. With unique optical properties and molar scale production, colloidal photoluminescent quantum dots (QDs) have been properly functionalized with controlled interfaces as new class of optical probes with extensive use in biomedical research. In this review, we present a brief summary on the current research interests of using fine engineered QDs as a nanoplatform for biomedical sensing and imaging applications. In addition, recent concerns on the potential toxic effects of QDs are described as a general guidance for the development on QD formulations in future studies.

Recent advances in nanoparticle-based Förster resonance energy transfer for biosensing, molecular imaging and drug release profiling

Förster resonance energy transfer (FRET) may be regarded as a "smart" technology in the design of fluorescence probes for biological sensing and imaging. Recently, a variety of nanoparticles that include quantum dots, gold nanoparticles, polymer, mesoporous silica nanoparticles and upconversion nanoparticles have been employed to modulate FRET. Researchers have developed a number of "visible" and "activatable" FRET probes sensitive to specific changes in the biological environment that are especially attractive from the biomedical point of view. This article reviews recent progress in bringing these nanoparticle-modulated energy transfer schemes to fruition for applications in biosensing, molecular imaging and drug delivery.

Understanding nonviral nucleic acid delivery with quantum dot-FRET nanosensors

Nonviral delivery of nucleic acids is a potentially safe and viable therapeutic modality for inherited and acquired diseases. However, current systems have proven too inefficient for widespread clinical translation. The rational design of improved carriers depends on a quantitative, mechanistic understanding of the rate-limiting barriers to efficient intracellular delivery. Separation of the nucleic acid from the carrier is one of the barriers, which may be analyzed by Förster resonance energy transfer (FRET), a mechanism used to detect interactions between fluorescently labeled molecules. When applied to the molecular components of polymer or lipid-based nanocomplexes, FRET provides information on their complexation status, uptake, release and degradation. Recently, the design of FRET systems incorporating quantum dots as energy donors has led to improved signal stability, allowing prolonged measurements, as well as increased sensitivity, enabling direct detection and the potential for multiplexing. The union of quantum dots and FRET is providing new insights into the mechanisms of nonviral nucleic acid delivery through convergent characterization of delivery barriers, and has the potential to accelerate the design of improved carriers to realize the potential of nucleic acid therapeutics and gene medicine.

Quantum dot enabled molecular sensing and diagnostics

Since its emergence, semiconductor nanoparticles known as quantum dots (QDs) have drawn considerable attention and have quickly extended their applicability to numerous fields within the life sciences. This is largely due to their unique optical properties such as high brightness and narrow emission band as well as other advantages over traditional organic fluorophores. New molecular sensing strategies based on QDs have been developed in pursuit of high sensitivity, high throughput, and multiplexing capabilities. For traditional biological applications, QDs have already begun to replace traditional organic fluorophores to serve as simple fluorescent reporters in immunoassays, microarrays, fluorescent imaging applications, and other assay platforms. In addition, smarter, more advanced QD probes such as quantum dot fluorescence resonance energy transfer (QD-FRET) sensors, quenching sensors, and barcoding systems are paving the way for highly-sensitive genetic and epigenetic detection of diseases, multiplexed identification of infectious pathogens, and tracking of intracellular drug and gene delivery. When combined with microfluidics and confocal fluorescence spectroscopy, the detection limit is further enhanced to single molecule level. Recently, investigations have revealed that QDs participate in series of new phenomena and exhibit interesting non-photoluminescent properties. Some of these new findings are now being incorporated into novel assays for gene copy number variation (CNV) studies and DNA methylation analysis with improved quantification resolution. Herein, we provide a comprehensive review on the latest developments of QD based molecular diagnostic platforms in which QD plays a versatile and essential role.

FRET from quantum dots to photodecompose undesired acceptors and report the condensation and decondensation of plasmid DNA

Protection of genes against enzymatic degradation and overcoming of cellular barriers are critical for efficient gene delivery. The effectiveness of gene delivery by nonviral vectors depends mostly on the extent of DNA packaging or condensation. We show that Förster resonance energy transfer (FRET)-mediated photodecomposition of undesired acceptors in doubly labeled plasmid DNA (pDNA) and FRET recovery after acceptor photodecomposition (FRET-RAP) are effective methods for the detection of DNA condensation and decondensation. Our hypothesis is that undesired acceptors within the Förster distance of highly-photostable donors in precondensed DNA can be selectively photodecomposed by FRET. We investigate this hypothesis by the random labeling of pcDNA3.1-GL3 and pUC18DNA with quantum dots (QDs) as the energy donor and AlexaFluor594 or Cy5 as the acceptor. At first, the random labeling generates efficient FRET, also called intrinsic FRET, in precondensed DNA, which prevents us from decoding any changes in the FRET efficiency during DNA condensation. Next, we suppressed the intrinsic FRET by the FRET-mediated photodecomposition of acceptors within the Förster distance of QDs. Conversely, many acceptors kept intact beyond the Förster distance provide us with high FRET efficiency during the condensation of pDNA using protamine. Further, the FRET efficiency is significantly decreased during the decondensation of DNA using heparan sulfate and glutathione. The random labeling of DNA using excess acceptors around photostable donors followed by the FRET-mediated photodecomposition of undesired acceptors can be a promising method for not only the sensitive detection of DNA condensation by FRET but also the customization of biomolecular sensors.

Intracellular nucleic acid interactions facilitated by quantum dots: conceptualizing theranostics

The concept of theranostics arises from the unification of both diagnostic and therapeutic applications into a single package. The implementation of nanoparticles, such as semiconductor quantum dots (QDs), to achieve theranostic applications, offers great potential for development of methods that are suitable for personalized medicine. Researchers have taken advantage of the physiochemical properties of QDs to elicit novel bioconjugation techniques that enable the attachment of multifunctional moieties on the surface of QDs. In this review, the diagnostic and therapeutic applications of QDs that feature the use of nucleic acids are highlighted with a particular emphasis on the possibility of combinatorial applications. Nucleic acid research is of particular interest for gene therapy, and is relevant to the understanding of gene regulation pathways and gene expression dynamics. Recent toxicity studies featuring multifunctional QDs are also examined. Future perspectives discussing the expected development of this field conclude the article.

Nucleic acid-based nanoengineering: novel structures for biomedical applications

Nanoengineering exploits the interactions of materials at the nanometre scale to create functional nanostructures. It relies on the precise organization of nanomaterials to achieve unique functionality. There are no interactions more elegant than those governing nucleic acids via Watson-Crick base-pairing rules. The infinite combinations of DNA/RNA base pairs and their remarkable molecular recognition capability can give rise to interesting nanostructures that are only limited by our imagination. Over the past years, creative assembly of nucleic acids has fashioned a plethora of two-dimensional and three-dimensional nanostructures with precisely controlled size, shape and spatial functionalization. These nanostructures have been precisely patterned with molecules, proteins and gold nanoparticles for the observation of chemical reactions at the single molecule level, activation of enzymatic cascade and novel modality of photonic detection, respectively. Recently, they have also been engineered to encapsulate and release bioactive agents in a stimulus-responsive manner for therapeutic applications. The future of nucleic acid-based nanoengineering is bright and exciting. In this review, we will discuss the strategies to control the assembly of nucleic acids and highlight the recent efforts to build functional nucleic acid nanodevices for nanomedicine.

Uptake and intracellular fate of multifunctional nanoparticles: a comparison between lipoplexes and polyplexes via quantum dot mediated Förster resonance energy transfer

Lipoplexes and polyplexes represent the two major nanocarrier systems for nucleic acid delivery. Previous studies examining their uptake and intracellular unpacking rely on organic fluorophores fraught with low signal intensity and photobleaching. In this work quantum dot mediated Förster resonance energy transfer (QD-FRET) was first used to study and compare the cellular uptake and the intracellular fate of oligodeoxynucelotide (ODN)-based lipoplexes and polyplexes. QD605-amine and Cy5-labeled ODN (Cy5-GTI2040) were chosen as the FRET pair. By adjusting the lipid/ODN ratio of lipoplexes and the nitrogen/phosphate (N/P) ratio of polyplexes, lipoplexes and polyplexes with comparable physical properties were produced. The biological activities of dual-labeled lipoplexes and polyplexes remained unaltered compared to their unlabeled counterparts as evidenced by their comparable antisense activities against protein R2 in KB cells. Flow cytometry and confocal microscopy revealed similar pattern of uptake for these two types of nanoparticles, although polyplexes had a higher dissociation rate than lipoplexes in KB cells. We demonstrate that QD-FRET is a sensitive tool to study the uptake and intracellular unpacking of lipoplexes and polyplexes, which may help optimize their formulations for various theranostics applications.

Tuning physical properties of nanocomplexes through microfluidics-assisted confinement

The future of genetic medicine hinges on successful intracellular delivery of nucleic acid-based therapeutics. While significant effort has concentrated on developing nanocarriers to improve the delivery aspects, scant attention has been paid to the synthetic process of poorly controlled nanocomplex formation. Proposed here is a reliable system to better control the complexation process, and thus the physical properties of the nanocomplexes, through microfluidics-assisted confinement (MAC) in picoliter droplets. We show that these homogeneous MAC-synthesized nanocomplexes exhibit narrower size distribution, lower cytotoxicity, and higher transfection efficiency compared to their bulk-synthesized counterparts. MAC represents a physical approach to control the energetic self-assembly of polyelectrolytes, thereby complementing the chemical innovations in nanocarrier design to optimize nucleic acid and peptide delivery.

Sensing polymer/DNA polyplex dissociation using quantum dot fluorophores

We characterized the dissociation of polymer/DNA polyplexes designed for gene delivery using water-soluble quantum dots (QDs). A pH-responsive pentablock copolymer was designed to form stable complexes with plasmid DNA via tertiary amine segments. Dissociation of the polyplex was induced using chloroquine where the efficiency of this process was sensed through changes in QD fluorescence. We found that increasing concentrations of pentablock copolymer and DNA led to quenching of QD fluorescence, while chloroquine alone had no measurable effect. The mechanism of quenching was elucidated by modeling the process as the combination of static and dynamic quenching from the pentablock copolymer and DNA, as well as self-quenching due the bridging of QDs. Tertiary amine homopolymers were also used to study the effect of chain length on quenching. Overall, these QDs were found to be highly effective at monitoring the dissociation of pentablock copolymer/DNA polyplexes in vitro and may have potential for studying the release of DNA within cells.

A dual-emission Förster resonance energy transfer nanoprobe for sensing/imaging pH changes in the biological environment

A dual-emission nanoprobe that can sense changes in the environmental pH is designed based on the concept of pH-responsive Förster resonance energy transfer induced by the conformational transition of an associating polyelectrolyte, N-palmitoyl chitosan, bearing a donor (Cy3) or an acceptor (Cy5) moiety. We demonstrate that the developed pH-responsive nanoprobe can be used to ratiometrically image and thus discriminate the pH changes in the biological environment at different length scales.

Intracellular trafficking and decondensation kinetics of chitosan-pDNA polyplexes. Mol Ther. 2010;18:1787-1795. [PMID: 20628361 DOI: 10.1038/mt.2010.143]

The transfection efficiency (TE) of chitosan-plasmid DNA (pDNA) polyplexes can be critically modulated by the polymer degree of deacetylation (DDA) and molecular weight (MW). This study was performed to test the hypothesis that the TE dependence on chitosan MW and DDA is related to the polyplex stability, hence their intracellular decondensation/unpacking kinetics. Major barriers to nonviral gene transfer were studied by image-based quantification. Although uptake increased with increased DDA, it did not appear to be a structure-dependent process affecting TE, nor was nuclear entry. Colocalization analysis showed that all chitosans trafficked through lysosomes with similar kinetics. Fluorescent resonant energy transfer (FRET) analysis revealed a distinct relationship between TE and polyplex dissociation rate. The most efficient chitosans showed an intermediate stability and a kinetics of dissociation, which occurred in synchrony with lysosomal escape. In contrast, a rapid dissociation before lysosomal escape was found for the inefficient low DDA chitosan whereas the highly stable and inefficient complex formed by a high MW and high DDA chitosan did not dissociate even after 24 hours. This study identified that the kinetics of decondensation in relation to lysosomal escape was a most critical structure-dependent process affecting the TE of chitosan polyplexes.

Quantum dot-based theranostics

Luminescent semiconductor nanocrystals, also known as quantum dots (QDs), have advanced the fields of molecular diagnostics and nanotherapeutics. Much of the initial progress for QDs in biology and medicine has focused on developing new biosensing formats to push the limit of detection sensitivity. Nevertheless, QDs can be more than passive bio-probes or labels for biological imaging and cellular studies. The high surface-to-volume ratio of QDs enables the construction of a "smart" multifunctional nanoplatform, where the QDs serve not only as an imaging agent but also a nanoscaffold catering for therapeutic and diagnostic (theranostic) modalities. This mini review highlights the emerging applications of functionalized QDs as fluorescence contrast agents for imaging or as nanoscale vehicles for delivery of therapeutics, with special attention paid to the promise and challenges towards QD-based theranostics.

Balancing protection and release of DNA: tools to address a bottleneck of non-viral gene delivery

Engineering polymeric gene-delivery vectors to release an intact DNA payload at the optimal time and subcellular compartment remains a formidable challenge. An ideal vector would provide total protection of complexed DNA from degradation prior to releasing it efficiently near or within the nucleus of a target cell. While optimization of polymer properties, such as molecular weight and charge density, has proved largely inadequate in addressing this challenge, applying polymeric carriers that respond to temperature, light, pH and redox environment to trigger a switch from a tight, protective complex to a more relaxed interaction favouring release at the appropriate time and place has shown promise. Currently, a paucity of gene carriers able to satisfy the contrary requirements of adequate DNA protection and efficient release contributes to the slow progression of non-viral gene therapy towards clinical translation. This review highlights the promising carrier designs that may achieve an optimal balance of DNA protection and release. It also discusses the imaging techniques and three-dimensional in vitro models that can help study these two barriers in the non-viral gene transfer process. Ultimately, efficacious non-viral gene therapy will depend on the combination of intelligent material design, innovative imaging techniques and sophisticated in vitro model systems to facilitate the rational design of polymeric gene-delivery vectors.