Single-Molecule FRET Studies of the Hybridization Mechanism during Noncovalent Adsorption and Desorption of DNA on Graphene Oxide

DNA Nanoparticle Based 2D Biointerface to Study the Effect of Dynamic RGD Presentation on Stem Cell Adhesion and Migration

The native extracellular matrix (ECM) undergoes constant remodeling, where adhesive ligand presentation changes over time and in space to control stem cell function. As such, it is of interest to develop 2D biointerfaces able to study these complex ligand stem-cell interactions. In this study, a novel dynamic bio interface based on DNA hybridization is developed, which can be employed to control ligand display kinetics and used to study dynamic cell-ligand interaction. In this approach, mesoporous silica nanoparticles (MSN) are functionalized with single-strand DNA (MSN-ssDNA) and spin-coated on a glass substrate to create the 2D bio interface. Cell adhesive tripeptide RGD is conjugated to complementary DNA strands (csDNA) of 9, 11, or 20 nucleotides in length, to form csDNA-RGD. The resulting 3 csDNA-RGD conjugates can hybridize with the ssDNA on the MSN surface, presenting RGD with increased ligand dissociation rates as DNA length is shortened. Slow RGD dissociation rates led to enhanced stem cell adhesion and spreading, resulting in elongated cell morphology. Cells on surfaces with slow RGD dissociation rates also exhibited higher motility, migrating in multiple directions compared to cells on surfaces with fast RGD dissociation rates. This study contributes to the existing body of knowledge on dynamic ligand-stem cell interactions.

Plasmonic Probing of Deoxyribonucleic Acid Hybridization at the Single Base Pair Resolution

Partial DNA duplex formation greatly impacts the quality of DNA hybridization and has been extensively studied due to its significance in many biological processes. However, traditional DNA sensing methods suffer from time-consuming amplification steps and hinder the acquisition of information about single-molecule behavior. In this work, we developed a plasmonic method to probe the hybridization process at a single base pair resolution and study the relationship between the complementarity of DNA analytes and DNA hybridization behaviors. We measured single-molecule hybridization events with Au NP-modified ssDNA probes in real time and found two hybridization adsorption events: stable and transient adsorption. The ratio of these two hybridization adsorption events was correlated with the length of the complementary sequences, distinguishing DNA analytes from different complementary sequences. By using dual incident angle excitation, we recognized different single-base complementary sequences. These results demonstrated that the plasmonic method can be applied to study partial DNA hybridization behavior and has the potential to be incorporated into the identification of similar DNA sequences, providing a sensitive and quantitative tool for DNA analysis.

Salmonella typhimurium detection and ablation using OmpD specific aptamer with non-magnetic and magnetic graphene oxide

Foodborne diseases have increased in the last few years due to the increased consumption of packaged and contaminated food. Major foodborne bacteria cause diseases such as diarrhea, vomiting, and sometimes death. So, there is a need for early detection of foodborne bacteria as pre-existing detection techniques are time-taking and tedious. Aptamer has gained interest due to its high stability, specificity, and sensitivity. Here, aptamer has been developed against Salmonella Typhimurium through the Cell-Selex method, and to further find the reason for specificity and sensitivity, OmpD protein was isolated, and binding studies were done. Single molecular FRET experiment using aptamer and graphene oxide studies has also been done to understand the mechanism of FRET and subsequently used for target bacterial detection. Using this assay, Salmonella Typhimurium can be detected up to 10 CFU/mL. Further, Magnetic Graphene oxide was used to develop an assay to separate and ablate bacteria using 808 nm NIR where temperature increase was more than 60 °C within 30 s and has been shown by plating as well as a confocal live dead assay. Thus, using various techniques, bacteria can be detected and ablated using specific aptamer and Graphene oxide.

Carbon Nanomaterials-Based Electrochemical Sensors for Heavy Metal Detection

Heavy metals are commonly found in a wide range of environmental settings metals, but the potential toxicity associated with heavy metal exposure represents a major threat to global public health. It is thus vital that approaches to efficiently, reliably, and effectively detecting heavy metals in a range of sample types be established. Carbon nanomaterials offer many advantageous properties that make them well-suited to the design of sensitive, selective, easy-to-operate electrochemical biosensors ideal for detecting heavy metal ions. The present review offers an overview of recent progress in the development of carbon nanomaterial-based electrochemical sensors used to detect heavy metals. In addition to providing a detailed discussion of certain carbon nanomaterials such as carbon nanotubes, graphene, carbon fibers, carbon quantum dots, carbon nanospheres, mesoporous carbon, and Graphdiyne, we survey the challenges and future directions for this field. Overall, the studies discussed herein suggest that the further development of carbon nanomaterial-modified electrochemical sensors will support the integration of increasingly advanced sensor platforms to aid in detecting heavy metals in foods, environmental samples, and other settings, thereby benefitting human health and society as a whole.

Vectorial folding of telomere overhang promotes higher accessibility

Human telomere overhang composed of tandem repeats of TTAGGG folds into G-quadruplex (G4). Unlike in an experimental setting in the test tube in which the entire length is allowed to fold at once, inside the cell, the overhang is expected to fold as it is synthesized directionally (5' to 3') and released segmentally by a specialized enzyme, the telomerase. To mimic such vectorial G4 folding process, we employed a superhelicase, Rep-X which can unwind DNA to release the TTAGGG repeats in 5' to 3' direction. We demonstrate that the folded conformation achieved by the refolding of full sequence is significantly different from that of the vectorial folding for two to eight TTAGGG repeats. Strikingly, the vectorially folded state leads to a remarkably higher accessibility to complementary C-rich strand and the telomere binding protein POT1, reflecting a less stably folded state resulting from the vectorial folding. Importantly, our study points to an inherent difference between the co-polymerizing and post-polymerized folding of telomere overhang that can impact telomere architecture and downstream processes.

Protocol for generation and regeneration of PEG-passivated slides for single-molecule measurements

Single-molecule fluorescence detection by total internal reflection microscope requires surface passivation by polyethylene glycol (PEG) coating, which is labor intensive and is only good for one or two experiments. Here, we present an efficient and reliable protocol for generating and regenerating the PEG surface for multiple rounds of experiments (∼5–10 times) in the same channel. This protocol is very simple, robust, rapid, and versatile; i.e., multiple strategies can be implemented to regenerate different layers of surface. The regeneration strategy saves time, improves the cost effectiveness, and enhances the efficiency of single-molecule experiments.

For complete details on the use and execution of this profile, please refer to Paul et al. (2021a).

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Regeneration of PEG-passivated slide is simple, quick, and cost effective

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Multiple experiments can be performed in a single channel

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Different strategies are implemented for different level of regeneration

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Regeneration leads to highly reproducible results

Detection of Chymotrypsin Using Peptide Sensor Based on Graphene Oxide Modified with Sulfhydryl Group and Gold Nanoparticles

In this study, GO modified with sulfhydryl group was prepared by thiolation on the surface of GO, which makes a meaningful material. GO with sulfhydryl group combined with gold nanoparticles,...

Advanced graphene oxide-based paper sensor for colorimetric detection of miRNA

MicroRNAs (miRNAs), found in blood and body fluids, have emerged as potential non-invasive biomarkers for disease and injury. miRNAs are quantitatively evaluated using typical RNA analysis methods such as the quantitative reverse transcription polymerase chain reaction, microarrays, and Northern blot, all of which require complex procedures and expensive reagents. To utilize miRNAs as practical biomarkers, it will be helpful to develop simple and user-friendly sensors. In this study, a paper-based miRNA sensor was developed by combining two methods: (1) target-recycled DNAzyme (Dz) amplification and (2) graphene oxide-assisted Dz blotting on paper. The Dz spots on paper caused a miRNA-dependent color change in presence of colorimetric reagents and facilitated the quantification of absolute amount of the target miRNA, irrespective of the volume, with high reproducibility. This approach is technologically straightforward and enables quantification of as low as 7.75 fmol miRNA using a portable smartphone.

TRF2 promotes dynamic and stepwise looping of POT1 bound telomeric overhang

Human telomeres are protected by shelterin proteins, but how telomeres maintain a dynamic structure remains elusive. Here, we report an unexpected activity of POT1 in imparting conformational dynamics of the telomere overhang, even at a monomer level. Strikingly, such POT1-induced overhang dynamics is greatly enhanced when TRF2 engages with the telomere duplex. Interestingly, TRF2, but not TRF2ΔB, recruits POT1-bound overhangs to the telomere ds/ss junction and induces a discrete stepwise movement up and down the axis of telomere duplex. The same steps are observed regardless of the length of the POT1-bound overhang, suggesting a tightly regulated conformational dynamic coordinated by TRF2 and POT1. TPP1 and TIN2 which physically connect POT1 and TRF2 act to generate a smooth movement along the axis of the telomere duplex. Our results suggest a plausible mechanism wherein telomeres maintain a dynamic structure orchestrated by shelterin.

Graphene oxide-controlled neutral versus cationic form of a red emitting dye: enhancement of fluorescence by graphene oxide

Fluorescence enhancement of fluorophores in neat solvent media in the presence of graphene oxide (GO) is less known. It is necessary to re-examine the role of GO from the fundamental scientific viewpoint. Herein, we have reported GO controlled conversion from the neutral to cationic form of a red emitting molecule. Besides this, the switching of the role of GO as an enhancer to a quencher of fluorescence depending on the concentration of GO in the presence of proton accepting solvent media was established. Intermolecular proton transfer from the GO surface to fluorophores is responsible for this phenomenon.

Regeneration of PEG slide for multiple rounds of single-molecule measurements

Single-molecule fluorescence detection of protein and other biomolecules requires a polyethylene glycol (PEG)-passivated surface. Individual channels on a PEG-passivated slide are typically used only a few times, limiting the number of experiments per slide. Here, we report several strategies for regenerating PEG surfaces for multiple rounds of experiments. First, we show regeneration of DNA- or RNA-tethered surfaces by washing out the bound protein by 0.1% sodium dodecyl sulfate, which is significantly more effective than 6 M urea, 6 M GdmCl, or 100 μM proteinase K. Strikingly, 10 consecutive experiments in five different systems produced indistinguishable results both in molecule count and protein activity. Second, duplexed DNA unwound by helicase or denatured by 50 mM NaOH was reannealed with a complementary strand to regenerate the duplexed substrate with an exceptionally high recovery rate. Third, the biotin-PEG layer was regenerated by using 7 M NaOH to strip off NeutrAvidin, which can be reapplied for additional experiments. We demonstrate five cycles of regenerating antibody immobilized surface by which three different protein activity was measured. Altogether, our methods represent reliable and reproducible yet simple and rapid strategies that will enhance the efficiency of single-molecule experiments.

Vital insights into prokaryotic genome compaction by nucleoid-associated protein (NAP) and illustration of DNA flexure angles at single-molecule resolution

Integration Host Factor (IHF) is a heterodimeric site-specific nucleoid-associated protein (NAP), well known for its DNA bending ability. Although the IHF induced bending states of DNA have been captured by both X-ray Crystallography and Atomic Force Microscopy (AFM), the range of flexibility and degree of heterogeneity in terms of quantitative analysis of the nucleoprotein complex has largely remained unexplored. Binding of IHF leads to introduction of two kinks in the dsDNA that allowed us to come up with a quadrilateral model. The findings have further been extended by calculating the angles of flexibility, that gives the idea of the degree of dynamicity of the nucleoprotein complex. We have monitored and compared the trajectories of the conformational dynamics of a dsDNA upon binding of wild-type (wt) and single-chain (sc) IHF at millisecond resolution through single-molecule FRET (smFRET). Our findings reveal that the nucleoprotein complex exists in a 'Slacked-Dynamic' state throughout the observation window where many of them have switched between multiple 'Wobbling States' in the course of attainment of packaged form. This study opens up an opportunity to improve the understanding of the functions of other nucleoid-associated proteins (NAPs) by complementing the previous detailed atomic-level structural analysis, which eventually will allow accessibility towards a better hypothesis.

Förster resonance energy transfer (FRET) and applications thereof

FRET is a nonradiative process of energy transfer that is based on the dipole-dipole interactions between molecules that are fluorescent. Transfer of energy takes place rapidly from a donor molecule to an acceptor molecule in juxtaposition such as 0 to 10 nm without photonic radiation. FRET has occupied a center stage in biotechnology and biological studies. It is used to gain information on conformation changes in single molecules. The pharmaceutical industry has also developed large fluorescence detection systems with very small sample sizes, at the level of single molecules, using fluorescence correlation spectroscopy.

E. coli Rep helicase and RecA recombinase unwind G4 DNA and are important for resistance to G4-stabilizing ligands

G-quadruplex (G4) DNA structures can form physical barriers within the genome that must be unwound to ensure cellular genomic integrity. Here, we report unanticipated roles for the Escherichia coli Rep helicase and RecA recombinase in tolerating toxicity induced by G4-stabilizing ligands in vivo. We demonstrate that Rep and Rep-X (an enhanced version of Rep) display G4 unwinding activities in vitro that are significantly higher than the closely related UvrD helicase. G4 unwinding mediated by Rep involves repetitive cycles of G4 unfolding and refolding fueled by ATP hydrolysis. Rep-X and Rep also dislodge G4-stabilizing ligands, in agreement with our in vivo G4-ligand sensitivity result. We further demonstrate that RecA filaments disrupt G4 structures and remove G4 ligands in vitro, consistent with its role in countering cellular toxicity of G4-stabilizing ligands. Together, our study reveals novel genome caretaking functions for Rep and RecA in resolving deleterious G4 structures.

Oligonucleotide Detection and Optical Measurement with Graphene Oxide in the Presence of Bovine Serum Albumin Enabled by Use of Surfactants and Salts

As graphene oxide-based oligonucleotide biosensors improve, there is a growing need to explore their ability to retain high sensitivity for low target concentrations in the context of biological fluids. Therefore, we innovatively combined assay milieu factors that could influence the key performance parameters of DNA hybridization and graphene oxide (GO) colloid dispersion, verifying their suitability to enhance oligonucleotide–GO interactions and biosensor performance. As a model system, we tested single-strand (ss) DNA detection in a complex solution containing bovine serum albumin (BSA) and salts with surfactants. A fluorescein conjugated 30-mer oligonucleotide ssDNA probe was combined with its complementary cDNA target, together with solute dispersed GO and either non-ionic (Triton X-100 and Tween-20) or anionic sodium dodecyl sulfate (SDS) surfactants. In this context, we compared the effect of divalent Mg2+ or monovalent Na+ salts on GO binding for the quench-based detection of specific target–probe DNA hybridization. GO biosensor strategies for quench-based DNA detection include a “turn on” enhancement of fluorescence upon target–probe interaction versus a “turn off” decreased fluorescence for the GO-bound probe. We found that the sensitive and specific detection of low concentrations of oligonucleotide target was best achieved using a strategy that involved target–probe DNA hybridization in the solution with a subsequent modified “turn-off” GO capture and the quenching of the unhybridized probe. Using carefully formulated assay procedures that prevented GO aggregation, the preferential binding and quenching of the unhybridized probe were both achieved using 0.1% BSA, 0.065% SDS and 6 mM NaCl. This resulted in the sensitive measurement of the specific target–probe complexes remaining in the solution. The fluorescein-conjugated single stranded probe (FAM–ssDNA) exhibited linearity to cDNA hybridization with concentrations in the range of 1–8 nM, with a limit of detection equivalent to 0.1 pmoles of target in 100 µL of assay mix. We highlight a general approach that may be adopted for oligonucleotide target detection within complex solutions.

Graphene Oxide-Based Nanostructured DNA Sensor

Quick detection of DNA sequence is vital for many fields, especially, early-stage diagnosis. Here, we develop a graphene oxide-based fluorescence quenching sensor to quickly and accurately detect small amounts of a single strand of DNA. In this paper, fluorescent magnetic nanoparticles (FMNPs) modified with target DNA sequence (DNA-t) were bound onto the modified graphene oxide acting as the fluorescence quenching element. FMNPs are made of iron oxide (Fe₃O₄) core and fluorescent silica (SiO₂) shell. The average particle size of FMNPs was 74 ± 6 nm and the average thickness of the silica shell, estimated from TEM results, was 30 ± 4 nm. The photoluminescence and magnetic properties of FMNPs have been investigated. Target oligonucleotide (DNA-t) was conjugated onto FMNPs through glutaraldehyde crosslinking. Meanwhile, graphene oxide (GO) nanosheets were produced by a modified Hummers method. A complementary oligonucleotide (DNA-c) was designed to interact with GO. In the presence of GO-modified with DNA-c, the fluorescence intensity of FMNPs modified with DNA-t was quenched through a FRET quenching mechanism. Our study indicates that FMNPs can not only act as a FRET donor, but also enhance the sensor accuracy by magnetically separating the sensing system from free DNA and non-hybridized GO. Results indicate that this sensing system is ideal to detect small amounts of DNA-t with limitation detection at 0.12 µM.

Optical Graphene-Based Biosensor for Nucleic Acid Detection; Influence of Graphene Functionalization and Ionic Strength

A main challenge for optical graphene-based biosensors detecting nucleic acid is the selection of key parameters e.g. graphenic chemical structure, nanomaterial dispersion, ionic strength, and appropriate molecular interaction mechanisms. Herein we study interactions between a fluorescein-labelled DNA (FAM-DNA) probe and target single-stranded complementary DNA (cDNA) on three graphenic species, aiming to determine the most suitable platform for nucleic acid detection. Graphene oxide (GO), carboxyl graphene (GO-COOH) and reduced graphene oxide functionalized with PEGylated amino groups (rGO-PEG-NH₂, PEG (polyethylene glycol)) were dispersed and characterized by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The influence of ionic strength on molecular interaction with DNA was examined by fluorescence resonance energy transfer (FRET) comparing fluorescence intensity and anisotropy. Results indicated an effect of graphene functionalization, dispersion and concentration-dependent quenching, with GO and GO-COOH having the highest quenching abilities for FAM-DNA. Furthermore, GO and GO-COOH quenching was accentuated by the addition of either MgCl₂ or MgSO₄ cations. At 10 mM MgCl₂ or MgSO₄, the cDNA induced a decrease in fluorescence signal that was 2.7-fold for GO, 3.4-fold for GO-COOH and 4.1-fold for rGO-PEG-NH₂. Best results, allowing accurate target detection, were observed when selecting rGO-PEG-NH₂, MgCl₂ and fluorescence anisotropy as an advantageous combination suitable for nucleic acid detection and further rational design biosensor development.

An electricity-fluorescence double-checking biosensor based on graphene for detection of binding kinetics of DNA hybridization

In this paper, an electricity-fluorescence double-checking biosensor based on graphene materials has been presented for detection of DNA hybridization kinetics.