Peeling single-stranded DNA from graphite surface to determine oligonucleotide binding energy by force spectroscopy

Quantitative measurement of cation-mediated adhesion of DNA to anionic surfaces

Anionic polyelectrolytes, such as DNA, are attracted to anionic surfaces in the presence of multivalent cations. A major barrier toward molecular-level understanding of these attractive interactions is the paucity of measurements of the binding strength. Here, atomic force microscopy-based single molecule force spectroscopy was used to quantify the binding free energy of double-stranded DNA to an anionic surface, with complementary density functional theory calculations of the binding energies of metal ion-ligand complexes. The results support both electrostatic attraction and ion-specific binding. Our study suggests that the correlated interactions between counterions are responsible for attraction between DNA and an anionic surface, but the strength of this attraction is modulated by the identity of the metal ion. We propose a mechanism in which the strength of metal-ligand binding, as well as the preference for particular binding sites, influence both the concentration dependence and the strength of the DNA-surface interactions.

Sequence-Dependent Surface Coverage of ssDNA Coatings on Single-Wall Carbon Nanotubes

A combination of experimental measurements and molecular dynamics (MD) simulations was used to investigate how the surfaces of single-wall carbon nanotubes (SWCNTs) are covered by adsorbed ssDNA oligos with different base compositions and lengths. By analyzing the UV absorption spectra of ssDNA-coated SWCNTs before and after coating displacement by a transparent surfactant, the mass ratios of adsorbed ssDNA to SWCNTs were determined for poly-T, poly-C, GT-containing, and AT-containing ssDNA oligos. Based on the measured mass ratios, it is estimated that an average of 20, 22, 26, or 32 carbon atoms are covered by one adsorbed thymine, cytosine, adenine, or guanine nucleotide, respectively. In addition, the UV spectra revealed electronic interactions of varying strengths between the nucleobase aromatic rings and the nanotube π-systems. Short poly-T DNA oligos show stronger π-π stacking interactions with SWCNT surfaces than do short poly-C DNA oligos, whereas both long poly-C and poly-T DNA oligos show strong interactions. These experiments were complemented by MD computations on simulated systems that were constrained to match the measured ssDNA/SWCNT mass ratios. The surface coverages computed from the MD results varied with oligo composition in a pattern that correlates higher measured yields of nanotube fluorescence with greater surface coverage.

Atomic force microscopy investigation of DNA denaturation on a highly oriented pyrolytic graphite surface

Understanding of DNA interaction with carbonaceous surfaces (including graphite, graphene and carbon nanotubes) is important for the development of DNA-based biosensors and other biotechnological devices. Though many issues related to DNA adsorption on graphitic surfaces have been studied, some important aspects of DNA interaction with graphite remain unclear. In this work, we use atomic force microscopy (AFM) equipped with super-sharp cantilevers to analyze the morphology and conformation of relatively long DNA molecule adsorbed on a highly oriented pyrolytic graphite (HOPG) surface. We have revealed the effect of DNA embedding into an organic monolayer of N,N'-(decane-1,10-diyl)-bis(tetraglycinamide) (GM), which may "freeze" DNA conformation on a HOPG surface during drying. The dependence of the mean squared point-to-point distance on the contour length suggests that DNA adsorbs on a bare HOPG by a "kinetic trapping" mechanism. For the first time, we have estimated the unfolded fraction of DNA upon contact with a HOPG surface (24 ± 5 %). The obtained results represent a novel experimental model for investigation of the conformation and morphology of DNA adsorbed on graphitic surfaces and provide with a new insight into DNA interaction with graphite.

Interplay of graphene-DNA interactions: Unveiling sensing potential of graphene materials

Graphene-based materials and DNA probes/nanostructures have emerged as building blocks for constructing powerful biosensors. Graphene-based materials possess exceptional properties, including two-dimensional atomically flat basal planes for biomolecule binding. DNA probes serve as excellent selective probes, exhibiting specific recognition capabilities toward diverse target analytes. Meanwhile, DNA nanostructures function as placement scaffolds, enabling the precise organization of molecular species at nanoscale and the positioning of complex biomolecular assays. The interplay of DNA probes/nanostructures and graphene-based materials has fostered the creation of intricate hybrid materials with user-defined architectures. This advancement has resulted in significant progress in developing novel biosensors for detecting DNA, RNA, small molecules, and proteins, as well as for DNA sequencing. Consequently, a profound understanding of the interactions between DNA and graphene-based materials is key to developing these biological devices. In this review, we systematically discussed the current comprehension of the interaction between DNA probes and graphene-based materials, and elucidated the latest advancements in DNA probe-graphene-based biosensors. Additionally, we concisely summarized recent research endeavors involving the deposition of DNA nanostructures on graphene-based materials and explored imminent biosensing applications by seamlessly integrating DNA nanostructures with graphene-based materials. Finally, we delineated the primary challenges and provided prospective insights into this rapidly developing field. We envision that this review will aid researchers in understanding the interactions between DNA and graphene-based materials, gaining deeper insight into the biosensing mechanisms of DNA-graphene-based biosensors, and designing novel biosensors for desired applications.

Ultra-Fast Single-Nucleotide-Variation Detection Enabled by Argonaute-Mediated Transistor Platform

"Test-and-go" single-nucleotide variation (SNV) detection within several minutes remains challenging, especially in low-abundance samples, since existing methods face a trade-off between sensitivity and testing speed. Sensitive detection usually relies on complex and time-consuming nucleic acid amplification or sequencing. Here, a graphene field-effect transistor (GFET) platform mediated by Argonaute protein that enables rapid, sensitive, and specific SNV detection is developed. The Argonaute protein provides a nanoscale binding channel to preorganize the DNA probe, accelerating target binding and rapidly recognizing SNVs with single-nucleotide resolution in unamplified tumor-associated microRNA, circulating tumor DNA, virus RNA, and reverse transcribed cDNA when a mismatch occurs in the seed region. An integrated microchip simultaneously detects multiple SNVs in agreement with sequencing results within 5 min, achieving the fastest SNV detection in a "test-and-go" manner without the requirement of nucleic acid extraction, reverse transcription, and amplification.

Unveiling DNA Translocation in Pristine Graphene Nanopores: Understanding Pore Clogging via Polarizable Simulations

Graphene has garnered remarkable attention in recent years as an attractive nanopore membrane for rapid and accurate sequencing of DNA. The inherent characteristics of graphene offer exquisite experimental control over pore dimensions, encompassing both the width (pore diameter) and height. Despite these promising prospects, the practical deployment of pristine graphene nanopores for DNA sequencing has encountered a formidable challenge in the form of pore clogging, which is primarily attributed to hydrophobic interactions. However, a comprehensive understanding of the atomistic origins underpinning this clogging phenomenon and the nuanced impact of individual nucleobase identities on clogging dynamics remain an underexplored domain. Elucidating the atomistic intricacies governing pore clogging is pivotal to devising strategies for its mitigation and advancing our understanding of graphene nanopore behavior. We harness Drude polarizable simulations to systematically dissect the nucleobase-dependent mechanisms that play a pivotal role in nanopore clogging. We unveil nucleobase-specific interactions that illuminate the multifaceted roles played by both hydrophobic and electrostatic forces in driving nanopore clogging events. Notably, the Drude simulations also unveil the bias-dependent translocation dynamics and its pivotal role in alleviating pore clogging─a facet that remains significantly underestimated in conventional additive (nonpolarizable) simulations. Our findings underscore the indispensability of incorporating polarizability to faithfully capture the intricate dynamics governing graphene nanopore translocation phenomena, thus deepening our insights into this crucial field.

Water-Dispersible Carbon Nano-Test Tubes as a Container for Concentrated DNA Molecules

Water-dispersible carbon nano-test tubes (CNTTs) with an inner and outer diameter of about 25 and 35 nm, respectively, were prepared by the template technique and then their inner carbon surface was selectively oxidized to introduce carboxy groups. The adsorption behavior of DNA molecules on the oxidized CNTTs (Ox-CNTTs) was examined in the presence of Ca2+ cations. Many DNA molecules are attracted to the inner space of Ox-CNTTs based on the Ca2+ -mediated electrostatic interaction between DNA phosphate groups and carboxylate anions on the inner carbon surface. Moreover, the total net charge of the DNA adsorbed was found to be equal to the total charge of the carboxylate anions. This selective adsorption into the interior of Ox-CNTTs can be explained from the fact that the electrostatic interaction onto the inner concave surface is much stronger than that on the outer convex surface. On the other hand, the desorption of DNA easily occurs whenever Ca2+ cations are removed by washing with deionized water. Thus, each of Ox-CNTTs works well as a nano-container for a large amount of DNA molecules, thereby resulting in the occurrence of DNA enrichment in the nanospace.

Single DNA Translocation and Electrical Characterization Based on Atomic Force Microscopy and Nanoelectrodes

Precision DNA translocation control is critical for achieving high accuracy in single molecule-based DNA sequencing. In this report, we describe an atomic force microscopy (AFM) based method to linearize a double-stranded DNA strand during the translocation process and characterize the electrical properties of the moving DNA using a platinum (Pt) nanoelectrode gap. In this method, λDNAs were first deposited on a charged mica substrate surface and topographically scanned. A single DNA suitable for translocation was then identified and electrostatically attached to an AFM probe by pressing the probe tip down onto one end of the DNA strand without chemical functionalizations. Next, the DNA strand was lifted off the mica surface by the probe tip. The pulling force required to completely lift off the DNA agreed well with the theoretical DNA adhesion force to a charged mica surface. After liftoff, the captured DNA was translocated at varied speeds across the substrate and ultimately across the Pt nanoelectrode gap for electrical characterizations. Finally, finite element analysis of the effect of the translocating DNA on the conductivity of the nanoelectrode gap was conducted, validating the range of the gap current measured experimentally during the DNA translocation process.

Probing and Manipulating Noncovalent Interactions in Functional Polymeric Systems

Noncovalent interactions, which usually feature tunable strength, reversibility, and environmental adaptability, have been recognized as driving forces in a variety of biological and chemical processes, contributing to the recognition between molecules, the formation of molecule clusters, and the establishment of complex structures of macromolecules. The marriage of noncovalent interactions and conventional covalent polymers offers the systems novel mechanical, physicochemical, and biological properties, which are highly dependent on the binding mechanisms of the noncovalent interactions that can be illuminated via quantification. This review systematically discusses the nanomechanical characterization of typical noncovalent interactions in polymeric systems, mainly through direct force measurements at microscopic, nanoscopic, and molecular levels, which provide quantitative information (e.g., ranges, strengths, and dynamics) on the binding behaviors. The fundamental understandings of intermolecular and interfacial interactions are then correlated to the macroscopic performances of a series of noncovalently bonded polymers, whose functions (e.g., stimuli-responsiveness, self-healing capacity, universal adhesiveness) can be customized through the manipulation of the noncovalent interactions, providing insights into the rational design of advanced materials with applications in biomedical, energy, environmental, and other engineering fields.

Critical peeling of tethered nanoribbons

The peeling of an immobile adsorbed membrane is a well-known problem in engineering and macroscopic tribology. In the classic setup, picking up at one extreme and pulling off result in a peeling force that is a decreasing function of the pickup angle. As one end is lifted, the detachment front retracts to meet the immobile tail. At the nanoscale, interesting situations arise with the peeling of graphene nanoribbons (GNRs) on gold, as realized, e.g., by atomic force microscopy. The nanosized system shows a constant-force steady peeling regime, where the tip lifting h produces no retraction of the ribbon detachment point, and just an advancement h of the free tail end. This is opposite to the classic case, where the detachment point retracts and the tail end stands still. Here we characterise, by analytical modeling and numerical simulations, a third, experimentally relevant setup where the nanoribbon, albeit structurally lubric, does not have a freely moving tail end, which is instead elastically tethered. Surprisingly, novel nontrivial scaling exponents appear that regulate the peeling evolution. As the detachment front retracts and the tethered tail is stretched, power laws of h characterize the shrinking of the adhered length, the growth of peeling force and the peeling angle. These exponents precede the final total detachment as a critical point, where the entire ribbon eventually hangs suspended between the tip and the tethering spring. These analytical predictions are confirmed by realistic MD simulations, retaining the full atomistic description, also confirming their survival at finite experimental temperatures.

Rapid and High-Throughput SARS-CoV-2 RNA Detection without RNA Extraction and Amplification by Using a Microfluidic Biochip

The ongoing outbreak of the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) has spread globally and poses a threat to public health and National economic development. Rapid and high-throughput SARS-CoV-2 RNA detection without the need of RNA extraction and amplification remain a key challenge. In this study, a new SARS-CoV-2 RNA detection strategy using a microfluidic biochip for the rapid and ultrasensitive detection of SARS-CoV-2 without RNA extraction and amplification was developed. This new strategy takes advantage of the specific SARS-CoV-2 RNA and probe DNA reaction in the microfluidic channel, fluorescence signal regulation by nanomaterials, and accurate sample control by the microfluidic chip. It presents an ultralow limit of detection of 600 copies mL-1 in a large linear detection regime from 1 aM to 100 fM. Fifteen samples were simultaneously detected in 40 min without the need for RNA purification and amplification. The detection accuracy of the strategy was validated through quantitative reverse transcription polymerase chain reaction (qRT-PCR), with a recovery of 99-113 %. Therefore, the SARS-CoV-2 RNA detection strategy proposed in this study can potentially be used for the quantitative diagnosis of viral infectious diseases.

Exploring graphene oxide intrinsic electroactivity to elucidate the non-covalent interactions with DNA oligonucleotides

We show here how the electrochemical reduction signal of graphene oxide nanocolloids is inhibited upon the formation of non-covalent interactions with single stranded DNA oligonucleotides. The drop in the reduction current intensity is strongly influenced by the nucleobase sequence, and can therefore be directly correlated to the specific DNA homo-oligonucleotide.

Large-Area Interfaces for Single-Molecule Label-free Bioelectronic Detection

Bioelectronic transducing surfaces that are nanometric in size have been the main route to detect single molecules. Though enabling the study of rarer events, such methodologies are not suited to assay at concentrations below the nanomolar level. Bioelectronic field-effect-transistors with a wide (μm²-mm²) transducing interface are also assumed to be not suited, because the molecule to be detected is orders of magnitude smaller than the transducing surface. Indeed, it is like seeing changes on the surface of a one-kilometer-wide pond when a droplet of water falls on it. However, it is a fact that a number of large-area transistors have been shown to detect at a limit of detection lower than femtomolar; they are also fast and hence innately suitable for point-of-care applications. This review critically discusses key elements, such as sensing materials, FET-structures, and target molecules that can be selectively assayed. The amplification effects enabling extremely sensitive large-area bioelectronic sensing are also addressed.

Binding between an amine cationic surfactant and DNA and surface properties of the resultant aggregates

Binding between cetyltrimethylammonium bromide, a cationic surfactant, and a variety of lengths of single stranded DNA was measured using fluorescence polarization and a simple cooperative model was used to obtain dissociation constants on the order of 1 × 10^-5 for the aggregates that formed. Aggregation depended on strand length where strands much shorter than 40 nucleotides (for example strands of 24-nucleotides) were too short to form the same size aggregates. Other factors such as salt concentration and temperature also affected aggregate formation: increasing either the salt concentration or performing binding at the highest temperature studied (60 °C) made it more difficult for aggregates to form. Both heating and dilution of aggregates caused the anisotropy signal to decrease, which suggested that the complexes fell apart under these conditions. Force spectroscopy of aggregate surfaces showed that both electrostatic and hydrophobic adhesive forces were present between aggregates and derivatized AFM tips. These findings can be used to better understand the stability of cationic surfactant-DNA aggregates and may provide guidance for lipid nanoparticle design used in vaccine development and therapeutics.

Sequence-Independent DNA Adsorption on Few-Layered Oxygen-Functionalized Graphene Electrodes: An Electrochemical Study for Biosensing Application

DNA is strongly adsorbed on oxidized graphene surfaces in the presence of divalent cations. Here, we studied the effect of DNA adsorption on electrochemical charge transfer at few-layered, oxygen-functionalized graphene (GO_x) electrodes. DNA adsorption on the inkjet-printed GO_x electrodes caused amplified current response from ferro/ferricyanide redox probe at concentration range 1 aM–10 nM in differential pulse voltammetry. We studied a number of variables that may affect the current response of the interface: sequence type, conformation, concentration, length, and ionic strength. Later, we showed a proof-of-concept DNA biosensing application, which is free from chemical immobilization of the probe and sensitive at attomolar concentration regime. We propose that GO_x electrodes promise a low-cost solution to fabricate a highly sensitive platform for label-free and chemisorption-free DNA biosensing.

Sugar-Pucker Force-Induced Transition in Single-Stranded DNA

The accurate knowledge of the elastic properties of single-stranded DNA (ssDNA) is key to characterize the thermodynamics of molecular reactions that are studied by force spectroscopy methods where DNA is mechanically unfolded. Examples range from DNA hybridization, DNA ligand binding, DNA unwinding by helicases, etc. To date, ssDNA elasticity has been studied with different methods in molecules of varying sequence and contour length. A dispersion of results has been reported and the value of the persistence length has been found to be larger for shorter ssDNA molecules. We carried out pulling experiments with optical tweezers to characterize the elastic response of ssDNA over three orders of magnitude in length (60-14 k bases). By fitting the force-extension curves (FECs) to the Worm-Like Chain model we confirmed the above trend:the persistence length nearly doubles for the shortest molecule (60 b) with respect to the longest one (14 kb). We demonstrate that the observed trend is due to the different force regimes fitted for long and short molecules, which translates into two distinct elastic regimes at low and high forces. We interpret this behavior in terms of a force-induced sugar pucker conformational transition (C3'-endo to C2'-endo) upon pulling ssDNA.

Attomolar-Level Ultrasensitive and Multiplex microRNA Detection Enabled by a Nanomaterial Locally Assembled Microfluidic Biochip for Cancer Diagnosis

Non-invasive early diagnosis is of great significance in disease pathologic development and subsequent medical treatments, and microRNA (miRNA) detection has attracted critical attention in early cancer screening and diagnosis. High-throughput, sensitive, economic, and fast miRNA sensing platforms are necessary to realize the low-concentration miRNA detection in clinical diagnosis and biological studies. Here, we developed an attomolar-level ultrasensitive, rapid, and multiple-miRNA simultaneous detection platform enabled by nanomaterial locally assembled microfluidic biochips. This platform presents a large linear detection regime of 1 aM-10 nM, an ultralow detection limit of 0.146 aM with no amplification, a short detection time of 35 min with multiplex miRNA sensing capability, and a small sample volume consumption of 2 μL. The detection results of five miRNAs in real samples from breast cancer patients and healthy humans indicate its excellent capacity for practical applications in early cancer diagnosis. The proposed ultrasensitive, rapid, and multiple-miRNA detection microfluidic biochip platform is a universal miRNA detection approach and an important and valuable tool in early cancer screening and diagnosis as well as biological studies.

Graphene-Based FRET Aptasensors

Graphene-based FRET aptasensors can be realized only by unique combinations of aptamer that can be freely functionalized by chemical modification, and graphene/graphene oxide that works as an excellent fluorescence acceptor at the same time as aptamer adsorbates. This review describes the principles of the sensor, several applications to microchannel devices, improvement of the sensing performance by molecular design of the aptamer and remarks on future prospects based on an introduction of recent works and achievements, including the author's paper. The sensor employs DNA modified with graphene/graphene oxide at the terminal as the molecular probe. This system is supported by the excellent property of DNA that does not lose the molecular recognition ability even due to a chemical modification at the terminal. I hope that this review will be useful for developing research on higher performance of graphene aptasensors in the future.

Spectral-Phase Interferometry Detection of Ochratoxin A via Aptamer-Functionalized Graphene Coated Glass

In this work, we report a novel method of label-free detection of small molecules based on direct observation of interferometric signal change in graphene-modified glasses. The interferometric sensor chips are fabricated via a conventional wet transfer method of CVD-grown graphene onto the glass coverslips, lowering the device cost and allowing for upscaling the sensor fabrication. For the first time, we report the use of graphene functionalized by the aptamer as the bioreceptor, in conjunction with Spectral-Phase Interferometry (SPI) for detection of ochratoxin A (OTA). In a direct assay with an OTA-specific aptamer, we demonstrated a quick and significant change of the optical signal in response to the maximum tolerable level of OTA concentration. The sensor regeneration is possible in urea solution. The developed platform enables a direct method of kinetic analysis of small molecules using a low-cost optical chip with a graphene-aptamer sensing layer.

Mechanistic insight into biopolymer induced iron oxide mineralization through quantification of molecular bonding

Microbial production of iron (oxyhydr)oxides on polysaccharide rich biopolymers occurs on such a vast scale that it impacts the global iron cycle and has been responsible for major biogeochemical events. Yet the physiochemical controls these biopolymers exert on iron (oxyhydr)oxide formation are poorly understood. Here we used dynamic force spectroscopy to directly probe binding between complex, model and natural microbial polysaccharides and common iron (oxyhydr)oxides. Applying nucleation theory to our results demonstrates that if there is a strong attractive interaction between biopolymers and iron (oxyhydr)oxides, the biopolymers decrease the nucleation barriers, thus promoting mineral nucleation. These results are also supported by nucleation studies and density functional theory. Spectroscopic and thermogravimetric data provide insight into the subsequent growth dynamics and show that the degree and strength of water association with the polymers can explain the influence on iron (oxyhydr)oxide transformation rates. Combined, our results provide a mechanistic basis for understanding how polymer-mineral-water interactions alter iron (oxyhydr)oxides nucleation and growth dynamics and pave the way for an improved understanding of the consequences of polymer induced mineralization in natural systems.

Unexpected sequence adsorption features of polynucleotide ssDNA on graphene oxide

The sequence features of single-stranded DNA (ssDNA) adsorbed on a graphene oxide (GO) surface are important for applications of the DNA/GO functional structure in biosensors, biomedicine, and materials science. In this study, molecular dynamics (MD) simulations were used to examine the adsorption of polynucleotide ssDNAs (A₁₂, C₁₂, G₁₂, and T₁₂) and single nucleotides (A, C, G, and T) on the GO surface. For the latter case, the nucleotide-GO interaction energy followed the trend G > A > C > T, even though it was influenced by specific adsorption sites. In the case of polynucleotides, unexpectedly polythymidine (T₁₂) had the strongest interaction with the GO surface. The angle distributions of the adsorbed nucleobases indicated that T₁₂ was more likely to form a quasi-parallel structure with GO compared to A₁₂, C₁₂, or G₁₂. This was attributed to the weakest π-stacking interactions of thymine. Weaker intra-molecular base-stacking interactions made it easier to break the structures of pyrimidine bases relative to those of purine bases. Weaker inter-molecular base-stacking interactions between T₁₂ and the GO surface enabled T₁₂ to adjust its structure easily to a more stable one by slipping on the surface. This result provides a new understanding of polynucleotide ssDNA adsorption on GO surfaces, which will help in the design of functional DNA/GO structure-based platforms.

Graphene Quantum Dot Oxidation Governs Noncovalent Biopolymer Adsorption

Graphene quantum dots (GQDs) are an allotrope of carbon with a planar surface amenable to functionalization and nanoscale dimensions that confer photoluminescence. Collectively, these properties render GQDs an advantageous platform for nanobiotechnology applications, including optical biosensing and delivery. Towards this end, noncovalent functionalization offers a route to reversibly modify and preserve the pristine GQD substrate, however, a clear paradigm has yet to be realized. Herein, we demonstrate the feasibility of noncovalent polymer adsorption to GQD surfaces, with a specific focus on single-stranded DNA (ssDNA). We study how GQD oxidation level affects the propensity for polymer adsorption by synthesizing and characterizing four types of GQD substrates ranging ~60-fold in oxidation level, then investigating noncovalent polymer association to these substrates. Adsorption of ssDNA quenches intrinsic GQD fluorescence by 31.5% for low-oxidation GQDs and enables aqueous dispersion of otherwise insoluble no-oxidation GQDs. ssDNA-GQD complexation is confirmed by atomic force microscopy, by inducing ssDNA desorption, and with molecular dynamics simulations. ssDNA is determined to adsorb strongly to no-oxidation GQDs, weakly to low-oxidation GQDs, and not at all for heavily oxidized GQDs. Finally, we reveal the generality of the adsorption platform and assess how the GQD system is tunable by modifying polymer sequence and type.

Length feature of ssDNA adsorption onto graphene oxide with both large unoxidized and oxidized regions

DNA/GO functional structures have been widely used in biosensors, biomedicine and materials science. However, most studies about DNA/GO functional structures do not take into account the coexistence of both large unoxidized and oxidized regions on GO sheets. This special local structure provides the boundary region, which is the junction area between unoxidized and oxidized regions, and exhibits a special amphiphilic property of the GO sheets. Here based on molecular dynamics simulations, our results predict that the adsorption efficiency of long strand ssDNA molecules adsorbed on GO is 43%. Further analysis has shown that the ssDNA adsorption behaviors on the GO surface are more likely to start in the boundary region, even for 20 mer ssDNA molecules. Looking into the adsorption dynamic process we can see that the hydrogen bonds between ssDNA and GO are very active and easily broken and formed, especially for the boundary region of the GO surface, resulting in easy capture and adsorption of the ssDNA molecules on this region. The result provides insightful understanding of the adsorption behavior of ssDNA molecules on this amphiphilic GO surface and is helpful in the design of DNA/GO functional structure-based biosensors.

Programmable CRISPR-responsive smart materials

Stimuli-responsive materials activated by biological signals play an increasingly important role in biotechnology applications. We exploit the programmability of CRISPR-associated nucleases to actuate hydrogels containing DNA as a structural element or as an anchor for pendant groups. After activation by guide RNA-defined inputs, Cas12a cleaves DNA in the gels, thereby converting biological information into changes in material properties. We report four applications: (i) branched poly(ethylene glycol) hydrogels releasing DNA-anchored compounds, (ii) degradable polyacrylamide-DNA hydrogels encapsulating nanoparticles and live cells, (iii) conductive carbon-black-DNA hydrogels acting as degradable electrical fuses, and (iv) a polyacrylamide-DNA hydrogel operating as a fluidic valve with an electrical readout for remote signaling. These materials allow for a range of in vitro applications in tissue engineering, bioelectronics, and diagnostics.

Step-defect guided delivery of DNA to a graphene nanopore

Precision placement and transport of biomolecules are critical to many single-molecule manipulation and detection methods. One such method is nanopore sequencing, in which the delivery of biomolecules towards a nanopore controls the method's throughput. Using all-atom molecular dynamics, here we show that the precision transport of biomolecules can be realized by utilizing ubiquitous features of graphene surface-step defects that separate multilayer domains. Subject to an external force, we found that adsorbed DNA moved much faster down a step defect than up, and even faster along the defect edge, regardless of whether the motion was produced by a mechanical force or a solvent flow. We utilized this direction dependency to demonstrate a mechanical analogue of an electric diode and a system for delivering DNA molecules to a nanopore. The defect-guided delivery principle can be used for the separation, concentration and storage of scarce biomolecular species, on-demand chemical reactions and nanopore sensing.

Sensitive detection of lung cancer biomarkers using an aptameric graphene-based nanosensor with enhanced stability

We present an electrolyte-gated graphene field effect transistor (GFET) nanosensor using aptamer for rapid, highly sensitive and specific detection of a lung cancer biomarker interleukin-6 (IL-6) with enhanced stability. The negatively charged aptamer folds into a compact secondary conformation upon binding with IL-6, thus altering the carrier concentration of graphene and yielding a detectable change in the drain-source current I_ds. Aptamer has smaller size than other receptors (e.g. antibodies), making it possible to bring the charged IL-6 more closely to the graphene surface upon affinity binding, thereby enhancing the sensitivity of the detection. Thanks to the higher stability of aptamer over antibodies, which degrade easily with increasing storage time, consistent sensing performance was obtained by our nanosensor over extended-time (>24 h) storage at 25 °C. Additionally, due to the GFET-enabled rapid transduction of the affinity recognition to IL-6, detection of IL-6 can be achieved in several minutes (<10 min). Experimental results indicate that this nanosensor can rapidly and specifically respond to the change in IL-6 levels with high consistency after extended-time storage and a detection limit (DL) down to 139 fM. Therefore, our nanosensor holds great potential for lung cancer diagnosis at its early stage.

Conformations and cryo-force spectroscopy of spray-deposited single-strand DNA on gold

Cryo-electron microscopy can determine the structure of biological matter in vitrified liquids. However, structure alone is insufficient to understand the function of native and engineered biomolecules. So far, their mechanical properties have mainly been probed at room temperature using tens of pico-newton forces with a resolution limited by thermal fluctuations. Here we combine force spectroscopy and computer simulations in cryogenic conditions to quantify adhesion and intra-molecular properties of spray-deposited single-strand DNA oligomers on Au(111). Sub-nanometer resolution images reveal folding conformations confirmed by simulations. Lifting shows a decay of the measured stiffness with sharp dips every 0.2-0.3 nm associated with the sequential peeling and detachment of single nucleotides. A stiffness of 30-35 N m^-1 per stretched repeat unit is deduced in the nano-newton range. This combined study suggests how to better control cryo-force spectroscopy of adsorbed heterogeneous (bio)polymer and to potentially enable single-base recognition in DNA strands only few nanometers long.

Direct Evidence for the Polymeric Nature of Polydopamine

Inspired by the adhesive proteins of mussels, polydopamine (pDA) has emerged as one of the most widely employed materials for surface functionalization. Despite numerous attempts at characterization, little consensus has emerged regarding whether pDA is a covalent polymer or a noncovalent aggregate of low molecular weight species. Here, we employed single-molecule force spectroscopy (SMFS) to characterize pDA films. Retraction of a pDA-coated cantilever from an oxide surface shows the characteristic features of a polymer with contour lengths of up to 200 nm. pDA polymers are generally weakly bound to the surface through much of their contour length, with occasional "sticky" points. Our findings represent the first direct evidence for the polymeric nature of pDA and provide a foundation upon which to better understand and tailor its physicochemical properties.

Graphene-based aptasensors: from molecule-interface interactions to sensor design and biomedical diagnostics

Graphene-based nanomaterials have been widely utilized to fabricate various biosensors for environmental monitoring, food safety, and biomedical diagnostics. The combination of aptamers with graphene for creating biofunctional nanocomposites improved the sensitivity and selectivity of fabricated biosensors due to the unique molecular recognition and biocompatibility of aptamers. In this review, we highlight recent advances in the design, fabrication, and biomedical sensing application of graphene-based aptasensors within the last five years (2013-current). The typical studies on the biomedical fluorescence, colorimetric, electrochemical, electrochemiluminescence, photoelectrochemical, electronic, and force-based sensing of DNA, proteins, enzymes, small molecules, ions, and others are demonstrated and discussed in detail. More attention is paid to a few key points such as the conjugation of aptamers with graphene materials, the fabrication strategies of sensor architectures, and the importance of aptamers on improving the sensing performances. It is expected that this work will provide preliminary and useful guidance for readers to understand the fabrication of graphene-based biosensors and the corresponding sensing mechanisms in one way, and in another way will be helpful to develop novel high performance aptasensors for biological analysis and detection.

Insight into the DNA adsorption on nitrogen-doped positive carbon dots

Considerable biosensors have been fabricated on the basis of DNA interaction with carbon nanomaterials, such as graphene oxide (GO) nanosheets. Few studies have focused on the rational design of sensors between carbon dots (CDs) and DNA due to the limited understanding of the real forces behind the adsorption of DNA on CDs. In this work, nitrogen doping-positive CDs (N-CDs), which can quench fluorophore-labeled DNA, were investigated to ascertain the interaction between the CDs and DNA. With reference to DNA adsorption on GO, the adsorption capacity and kinetics of N-CDs for DNA were studied. Desorption of DNA from these surfaces was also measured. Moreover, DNA desorption and anchoring force of N-CDs to DNA were different from those of GO, given that the prepared N-CDs and GO were positively and negatively charged, respectively. Accordingly, DNA was adsorbed on N-CDs mainly via electrostatic adsorption and other forces, such as nucleobase effect, hydrophobic interaction, and van der Waals (vdW) forces. This study enhanced the basic knowledge of DNA adsorption on some CDs for further study in the application of CDs in bioanalysis or biomedicine.

With the reference of DNA adsorption on GO, the adsorption capacity, kinetics of N-CDs to DNA were investigated.

Direct Measurement of π Coupling at the Single-Molecule Level using a Carbon Nanotube Force Sensor

We report a carbon nanotube (CNT) force sensor that combines a suspended CNT transistor with dual-trap optical tweezers to explore the interactions between two individual molecules in the near-equilibrium regime with sub-piconewton resolution. The directly measured equilibrium force (1.2 ± 0.5 pN) is likely related to the binding force between a CNT and a single DNA base, where two aromatic rings spontaneously attract to each other due to the noncovalent forces between them. On the basis of our force measurements, the binding free energy per base is calculated (∼0.34 eV), which is in good agreement with theoretical simulations. Moreover, three-dimensional scanning photocurrent microscopy enables us to simultaneously monitor the morphology changes of the CNT, leading to a comprehensive reconstruction of the CNT-DNA binding dynamics. These experimental results shed light on the fundamental understanding of the mechanical coupling between CNTs and DNA molecules and, more importantly, provide a new platform for direct observation of intermolecular interfaces at the single-molecule level.

Versatile Types of DNA-Based Nanobiosensors for Specific Detection of Cancer Biomarker FEN1 in Living Cells and Cell-Free Systems

Flap structure-specific endonuclease 1 (FEN1) is overexpressed in various types of human cancer cells and has been recognized as a promising biomarker for cancer diagnosis in the recent years. In order to specifically detect the abundance and activity of this cancer-overexpressed enzyme, different types of DNA-based nanodevices were created during our investigations. It is shown in our studies that these newly designed biosensors are highly sensitive and specific for FEN1 in living cells as well as in cell-free systems. It is expected that these nanoprobes could be useful for monitoring FEN1 activity in human cancer cells, and also for cell-based screening of FEN1 inhibitors as new anticancer drugs.

A graphene aptasensor for biomarker detection in human serum

This paper presents an affinity graphene nanosensor for detection of biomarkers in undiluted and non-desalted human serum. The affinity nanosensor is a field-effect transistor in which graphene serves as the conducting channel. The graphene surface is sequentially functionalized with a nanolayer of the polymer polyethylene glycol (PEG) and a biomarker-specific aptamer. The aptamer is able to specifically bind with and capture unlabeled biomarkers in serum. A captured biomarker induces a change in the electric conductivity of the graphene, which is measured in a buffer of optimally chosen ionic strength to determine the biomarker concentration. The PEG layer effectively rejects nonspecific adsorption of background molecules in serum while still allowing the aptamer to be readily accessible to serum-borne biomarkers and increases the effective Debye screening length on the graphene surface. Thus, the aptamer-biomarker binding sensitively changes the graphene conductivity, thereby achieving specific and label-free detection of biomarkers with high sensitivity and without the need to dilute or desalt the serum. Experimental results demonstrate that the graphene nanosensor is capable of specifically capturing human immunoglobulin E (IgE), used as a representative biomarker, in human serum in the concentration range of 50 pM-250 nM, with a resolution of 14.5 pM and a limit of detection of 47 pM.

Platinated graphene oxide: A nanoplatform for efficient gene-chemo combination cancer therapy

Cisplatin (CisPt) is one of the most effective antitumor drugs against a wide range of solid cancers, and recent studies have indicated that combination of CisPt and RNA interference (RNAi) agents would effectively enhance therapeutic index, while the development of simple yet robust dual-delivery systems still remains a challenge. Here, we demonstrated that platinated graphene oxide is an excellent platform to achieve such goal. Nano-Graphene oxide (NGO) was easily platinated by CisPt, and the resulting CisPt/NGO was characterized by several aspects. As a proof-of-concept, an antisense microRNA-21 (Anti-miR-21) was employed as a potential RNAi agent. While most previous work functionalized NGO with cationic polymers for gene delivery, we demonstrated that platinated NGO is a potent carrier to load Anti-miR-21 with improved capacity and adsorption stability. With Anti-miR-21 loading, the system displayed significantly enhanced cytotoxicity to cancer cells, suggesting a synergistic effect. Finally, the underlying mechanism of the improved efficacy was explored, which can be ascribed to the cell apoptosis induced by Anti-miR-21 for gene silencing. This work demonstrated platinated graphene oxide as an effective nanocarrier to co-deliver CisPt and gene therapy for the treatment of cancer.

Angle-Dependent Atomic Force Microscopy Single-Chain Pulling of Adsorbed Macromolecules from Planar Surfaces Unveils the Signature of an Adsorption-Desorption Transition

The adsorption-desorption behavior of polymer chains is at the heart of macromolecular surface science and technology. With the current developments in atomic force microscopy (AFM), it has now become possible to address the desorption problem from the perspective of a single macromolecule. Here, we report on desorption of single polymer chains on planar surfaces by AFM-based single molecule force spectroscopy (SMFS) as a function of the pulling angle with respect to the surface-normal direction. SMFS experiments were performed in water with various substrates using different polymers covalently attached to the AFM probe tip. End-grafting at the AFM tip was achieved by surface-initiated polymerization using initiator functionalized tips. We found that the desorption force increases with a decreasing pulling angle, i.e., an enhanced adhesion of the polymer chain was observed. The magnitude of the desorption force shows a weak angular dependence at pulling angles close to the surface normal. A significant increase of the force is observed at shallower pulling from a certain pulling angle. This behavior carries the signature of an adsorption-desorption transition. The angular dependence of the normalized desorption force exhibits a universal behavior. We compared and interpreted our results using theoretical predictions for single-chain adsorption-desorption transitions.

Size-Dependent Affinity of Glycine and Its Short Oligomers to Pyrite Surface: A Model for Prebiotic Accumulation of Amino Acid Oligomers on a Mineral Surface

The interaction strength of progressively longer oligomers of glycine, (Gly), di-Gly, tri-Gly, and penta-Gly, with a natural pyrite surface was directly measured using the force mode of an atomic force microscope (AFM). In recent years, selective activation of abiotically formed amino acids on mineral surfaces, especially that of pyrite, has been proposed as an important step in many origins of life scenarios. To investigate such notions, we used AFM-based force measurements to probe possible non-covalent interactions between pyrite and amino acids, starting from the simplest amino acid, Gly. Although Gly itself interacted with the pyrite surface only weakly, progressively larger unbinding forces and binding frequencies were obtained using oligomers from di-Gly to penta-Gly. In addition to an expected increase of the configurational entropy and size-dependent van der Waals force, the increasing number of polar peptide bonds, among others, may be responsible for this observation. The effect of chain length was also investigated by performing similar experiments using l-lysine vs. poly-l-lysine (PLL), and l-glutamic acid vs. poly-l-glutamic acid. The results suggest that longer oligomers/polymers of amino acids can be preferentially adsorbed on pyrite surfaces.

TDDFT Study of the Optical Excitation of Nucleic Acid Bases-C60 Complexes

The potential of C₆₀ as a nucleic acid base (NAB) optical sensor is theoretically explored. We investigate the adsorption of four NABs, namely, adenine, cytosine, guanine, and thymine, on C₆₀ in the gas phase. For the optimal NAB@C₆₀ adsorption configurations, obtained using a dispersion-corrected density functional, we calculate the vis-near-ultraviolet optical response using time-dependent density functional theory. While the isolated C₆₀ and NAB molecules do not exhibit visible optical excitation, we find that C₆₀/NAB conjugation gives rise to distinct spectral features in the visible range. These results suggest that C₆₀ conjugation can be applied for photodetection of individual NABs.

Structural Disruption of an Adenosine-Binding DNA Aptamer on Graphene: Implications for Aptasensor Design

We report on the predicted structural disruption of an adenosine-binding DNA aptamer adsorbed via noncovalent interactions on aqueous graphene. The use of surface-adsorbed biorecognition elements on device substrates is needed for integration in nanofluidic sensing platforms. Upon analyte binding, the conformational change in the adsorbed aptamer may perturb the surface properties, which is essential for the signal generation mechanism in the sensor. However, at present, these graphene-adsorbed aptamer structure(s) are unknown, and are challenging to experimentally elucidate. Here we use molecular dynamics simulations to investigate the structure and analyte-binding properties of this aptamer, in the presence and absence of adenosine, both free in solution and adsorbed at the aqueous graphene interface. We predict this aptamer to support a variety of stable binding modes, with direct base-graphene contact arising from regions located in the terminal bases, the centrally located binding pockets, and the distal loop region. Considerable retention of the in-solution aptamer structure in the adsorbed state indicates that strong intra-aptamer interactions compete with the graphene-aptamer interactions. However, in some adsorbed configurations the analyte adenosines detach from the binding pockets, facilitated by strong adenosine-graphene interactions.

Probing Single-Molecule Adhesion of a Stimuli Responsive Oligo(ethylene glycol) Methacrylate Copolymer on a Molecularly Smooth Hydrophobic MoS2 Basal Plane Surface

Molybdenum disulfide (MoS₂) has been receiving increasing attention in scientific research due to its unique properties. Up to now, several techniques have been developed to prepare exfoliated nanosize MoS₂ dispersions to facilitate its applications. To improve its desired performance, as-prepared MoS₂ dispersion needs further appropriate modification by polymers. Thus, understanding polymer-MoS₂ interaction is of great scientific importance and practical interest. Here, we report our results on molecular interactions of a biocompatible stimuli-responsive copolymer with the basal plane surface of MoS₂ determined using single molecule force spectroscopy (SMFS). Under isothermal conditions, the single-molecule adhesion force of oligo(ethylene glycol) methacrylate copolymer was found to increase from 50 to 75 pN with increasing NaCl concentration from 1 mM to 2 M, as a result of increasing hydrophobicity of the polymers. The theoretical analysis demonstrated that single-molecule adhesion force is determined by two contributions: the adhesion energy per monomer and the entropic free energy of the stretched polymer chain. Further data analysis revealed a significant increase in the adhesion energy per monomer with a negligible change in the other contribution with increasing salt concentration. The hydrophobic attraction (HA) was found to be the main contribution for the higher adhesion energy in electrolyte solutions of higher NaCl concentrations where the zero-frequency of van der Waals interaction were effectively screened. The results illustrate that oligo(ethylene glycol) methacrylate copolymer is a promising polymer for functionalizing MoS₂ and that one can simply change the salt concentration to modulate the single-molecule interactions for desired applications.

Adsorption of DNA Fragments at Aqueous Graphite and Au(111) via Integration of Experiment and Simulation

We combine single molecule force spectroscopy measurements with all-atom metadynamics simulations to investigate the cross-materials binding strength trends of DNA fragments adsorbed at the aqueous graphite C(0001) and Au(111) interfaces. Our simulations predict this adsorption at the level of the nucleobase, nucleoside, and nucleotide. We find that despite challenges in making clear, careful connections between the experimental and simulation data, reasonable consistency between the binding trends between the two approaches and two substrates was evident. On C(0001), our simulations predict a binding trend of dG > dA ≈ dT > dC, which broadly aligns with the experimental trend. On Au(111), the simulation-based binding strength trends reveal stronger adsorption for the purines relative to the pyrimadines, with dG ≈ dA > dT ≈ dC. Moreover, our simulations provide structural insights into the origins of the similarities and differences in adsorption of the nucleic acid fragments at the two interfaces. In particular, our simulation data offer an explanation for the differences observed in the relative binding trend between adenosine and guanine on the two substrates.

Real-Time Monitoring of Insulin Using a Graphene Field-Effect Transistor Aptameric Nanosensor

This paper presents an approach to the real-time, label-free, specific, and sensitive monitoring of insulin using a graphene aptameric nanosensor. The nanosensor is configured as a field-effect transistor, whose graphene-based conducting channel is functionalized with a guanine-rich IGA3 aptamer. The negatively charged aptamer folds into a compact and stable antiparallel or parallel G-quadruplex conformation upon binding with insulin, resulting in a change in the carrier density, and hence the electrical conductance, of the graphene. The change in the electrical conductance is then measured to enable the real-time monitoring of insulin levels. Testing has shown that the nanosensor offers an estimated limit of detection down to 35 pM and is functional in Krebs-Ringer bicarbonate buffer, a standard pancreatic islet perfusion medium. These results demonstrate the potential utility of this approach in label-free monitoring of insulin and in timely prediction of accurate insulin dosage in clinical diagnostics.

Visualization and Inhibition of Mitochondria-Nuclear Translocation of Apoptosis Inducing Factor by a Graphene Oxide-DNA Nanosensor

High concentrations of oxidized low density lipoprotein (oxLDL) induce aberrant apoptosis of vascular smooth muscle cells (VSMCs) in atherosclerotic plaques. This apoptosis cannot be blocked completely by the inhibition of caspase, and it eventually potentiates plaque disruption and risk for cardiovascular disease. Given the important role of apoptosis inducing factor (AIF) in caspase-independent apoptosis, here we develop an AIF-targeting nanosensor by the assembly of graphene oxide (GO) nanosheets and dye-labeled DNA hybrid structures. This nanosensor selectively localizes in the cytosol of VSMCs, where it exhibits a "turn-off" fluorescence signal. Under oxLDL stimuli, the release of AIF from mitochondria into cytosol liberates the DNA hybrid structures from the surface of GO and results in a "turn-on" fluorescence signal. This nanosensor is shown to possess rapid response, high sensitivity, and selectivity for AIF that enables real-time imaging of AIF translocation in VSMCs. Using this novel nanosensor, a better assessment of the apoptotic level of VSMCs and a more accurate evaluation of the extent of atherosclerotic lesions can be obtained. More importantly, the abundant binding between DNA hybrid structures and AIF inhibits the translocation of AIF into the nucleus and subsequent apoptosis in VSMCs. This inhibition may help stabilize plaque and reduce the risk of heart attack and stroke.

Pulling angle-dependent force microscopy

In this paper, we describe a method allowing one to perform three-dimensional displacement control in force spectroscopy by atomic force microscopy (AFM). Traditionally, AFM force curves are measured in the normal direction of the contacted surface. The method described can be employed to address not only the magnitude of the measured force but also its direction. We demonstrate the technique using a case study of angle-dependent desorption of a single poly(2-hydroxyethyl methacrylate) (PHEMA) chain from a planar silica surface in an aqueous solution. The chains were end-grafted from the AFM tip in high dilution, enabling single macromolecule pull experiments. Our experiments give evidence of angular dependence of the desorption force of single polymer chains and illustrate the added value of introducing force direction control in AFM.

Single-molecule force spectroscopy of fast reversible bonds

Cantilever stiffness dominates AFM force spectroscopy of fast reversible bonds. Fast rebinding and fluctuations of compliant linkers are averaged by the slow dynamics of the cantilever.