Dynamics of an anti-VEGF DNA aptamer: a single-molecule study

Enhancing the sensitivity and stability of electrochemical aptamer-based sensors by AuNPs@MXene nanocomposite for continuous monitoring of biomarkers

Electrochemical aptamer-based (E-AB) sensors offer exciting potential for real-time tracking of various biomarkers, such as proteins and small molecules, due to their exceptional selectivity and adaptability. However, most E-AB sensors rely on planar gold structures, which inherently limit their sensitivity and operational stability for continuous monitoring of biomarkers. Although gold nanostructures have recently enhanced E-AB sensor performance, no studies have explored the combination of gold nanostructure with other types of nanomaterials for continuous molecular monitoring. To fill this gap, we employed gold nanoparticles and MXene Ti3C2 (AuNPs@MXene), a versatile nanocomposite, in designing an E-AB sensor targeted at vascular endothelial growth factor (VEGF), a crucial human signaling protein. Remarkably, the AuNPs@MXene nanocomposite achieved over thirty-fold and half-fold increases in active surface area compared to bare and AuNPs-modified gold electrodes, respectively, significantly elevating the analytical capabilities of E-AB sensors during continuous operation. After a systematic optimization and characterization process, the newly developed E-AB sensor, powered by AuNPs@MXene nanocomposite, demonstrated both enhanced stability and heightened sensitivity. Overall, our findings open new avenues for the incorporation of nanocomposites in E-AB sensor design, enabling the creation of more sensitive and durable real-time monitoring systems.

Probing Changes in Ca2+-Induced Interaction Forces between Calmodulin and Melittin by Atomic Force Microscopy

Mechanobiology studies the means by which physical forces and mechanical properties change intra- or inter- biological macromolecules. Calmodulin (CaM) is involved in physiological activities and various metabolic processes in eukaryotic cells. Although the configuration changes in the interaction between calmodulin and melittin have been studied, the biomechanical relationship of their interaction has rarely been explored. Here, we measured the adhesion forces between calmodulin and melittin in solutions of gradient concentration of calcium ions using atomic force microscopy (AFM). We found that the specific (Fi) and nonspecific (F0) adhesion forces between single melittin and calmodulin in a PBS solution were 69.4 ± 5.0 and 29.3 ± 8.9 pN, respectively. In the presence of 10-7 to 10-3 M Ca2+ PBS solution, the Fi increased significantly to 93.8 ± 5.0, 139.9 ± 9.0, 140.4 ± 9.7, 171.5 ± 9.0, and 213.3 ± 17.8 pN, indicating that the unbinding force between melittin and calmodulin increased in the presence of Ca2+ in a concentration-dependent manner. These findings demonstrated that biomechanical studies based on AFM could help us better understand the melittin/calmodulin-binding processes in the presence of calcium and help us design and screen peptide drugs based on calmodulin.

Development of Aptamer-Based TID Assays Using Thermophoresis and Microarrays

Aptamers are single-stranded oligonucleotides which can be used as alternative recognition elements for protein detection, because aptamers bind their targets with a high affinity similar to antibodies. Due to the targetinduced conformational changes of aptamers, these oligonucleotides can be applied in various biosensing platforms. In this work, aptamers directed against the vascular endothelial growth factor (VEGF) were used as a model system. VEGF plays a key role in physiological angiogenesis and vasculogenesis. Furthermore, VEGF is involved in the development and growth of cancer and other diseases like agerelated macular degeneration, rheumatoid arthritis, diabetes mellitus, and neurodegenerative disorders. Detecting the protein biomarker VEGF is therefore of great importance for medical research and diagnostics. In this research, VEGFbinding aptamers were investigated for the systematic development of a targetinduced dissociation (TID) assay utilizing thermophoresis and microarrays. The established aptamer-microarray allowed for the detection of 0.1 nM of VEGF. Furthermore, the systematic development of the TID method using the VEGF model protein could help to develop further TID assays for the detection of various protein biomarkers.

The structure-energy landscape of NMDA receptor gating

N-Methyl-D-aspartate (NMDA) receptors are the main calcium-permeable excitatory receptors in the mammalian central nervous system. The NMDA receptor gating is complex, exhibiting multiple closed, open, and desensitized states; however, central questions regarding the conformations and energetics of the transmembrane domains as they relate to the gating states are still unanswered. Here, using single-molecule Förster resonance energy transfer (smFRET), we map the energy landscape of the first transmembrane segment of the Rattus norvegicus NMDA receptor under resting and various liganded conditions. These results show kinetically and structurally distinct changes associated with apo, agonist-bound, and inhibited receptors linked by a linear mechanism of gating at this site. Furthermore, the smFRET data suggest that allosteric inhibition by zinc occurs by an uncoupling of the agonist-induced changes at the extracellular domains from the gating motions leading to an apo-like state, while dizocilpine, a pore blocker, stabilizes multiple closely packed transmembrane states.

Direct Imaging of Protein Stability and Folding Kinetics in Hydrogels

We apply fast relaxation imaging (FReI) as a novel technique for investigating the folding stability and dynamics of proteins within polyacrylamide hydrogels, which have diverse and widespread uses in biotechnology. FReI detects protein unfolding in situ by imaging changes in fluorescence resonance energy transfer (FRET) after temperature jump perturbations. Unlike bulk measurements, diffraction-limited epifluorescence imaging combined with fast temperature perturbations reveals the impact of local environment effects on protein-biomaterial compatibility. Our experiments investigated a crowding sensor protein (CrH2) and phosphoglycerate kinase (PGK), which undergoes cooperative unfolding. The crowding sensor quantifies the confinement effect of the cross-linked hydrogel: the 4% polyacrylamide hydrogel is similar to aqueous solution (no confinement), while the 10% hydrogel is strongly confining. FRAP measurements and protein concentration gradients in the 4% and 10% hydrogels further support this observation. PGK reveals that noncovalent interactions of the protein with the polymer surface are more important than confinement for determining protein properties in the gel: the mere presence of hydrogel increases protein stability, speeds up folding relaxation, and promotes irreversible binding to the polymer even at the solution-gel interface, whereas the difference between the 4% and the 10% hydrogels is negligible despite their large difference in confinement. The imaging capabilities of FReI, demonstrated to be diffraction limited, further revealed spatially homogeneous protein unfolding across the hydrogels at 500 nm length scales and revealed differences in protein properties at the gel-solution boundary.

Characterizing aptamer small molecule interactions with backscattering interferometry

Aptamers are segments of single-strand DNA or RNA used in a wide array of applications, including sensors, therapeutics, and cellular process regulators. Aptamers can bind many target species, including proteins, peptides, and small molecules (SM) with high affinity and specificity. They are advantageous because they can be identified in vitro by SELEX, produced rapidly and relatively economically using oligonucleotide synthesis. The use of aptamers as SM probes has experienced a recent rebirth, and because of their unique properties they represent an attractive alternative to antibodies. Current assay methodology for characterizing small molecule-aptamer binding is limited by either mass sensitivity, as in biolayer interferometry (BLI) and surface plasmon resonance (SPR), or the need for using a fluorophore, as in thermophoresis. Here we report that backscattering interferometry (BSI), a label-free and free-solution sensing technique, can be used to effectively characterize SM-aptamer interactions, providing Kd values on microliter sample quantities and at low nanomolar sensitivity. To demonstrate this capability we measured the aptamer affinity for three previously reported small molecules; bisphenol A, tenofovir, and epirubicin showing BSI provided values consistent with those published previously. We then quantified the Kd values for aptamers to ampicillin, tetracycline and norepinephrine. All measurements produced R(2) values >0.95 and an excellent signal to noise ratio at target concentrations that enable true Kd values to be obtained. No immobilization or labeling chemistry was needed, expediting the assay which is also insensitive to the large relative mass difference between the interacting molecules.

Ensemble and single-molecule biophysical characterization of D17.4 DNA aptamer-IgE interactions

BACKGROUND

The IgE-binding DNA aptamer 17.4 is known to inhibit the interaction of IgE with the high-affinity IgE Fc receptor FcεRI. While this and other aptamers have been widely used and studied, there has been relatively little investigation of the kinetics and energetics of their interactions with their targets, by either single-molecule or ensemble methods.

METHODS

The dissociation kinetics of the D17.4/IgE complex and the effects of temperature and ionic strength were studied using fluorescence anisotropy and single-molecule spectroscopy, and activation parameters calculated.

RESULTS

The dissociation of D17.4/IgE complex showed a strong dependence on temperature and salt concentration. The koff of D17.4/IgE complex was calculated to be (2.92±0.18)×10(-3) s(-1) at 50 mM NaCl, and (1.44±0.02)×10(-2) s(-1) at 300 mM NaCl, both in 1 mM MgCl2 and 25°C. The dissociation activation energy for the D17.4/IgE complex, Ea, was 16.0±1.9 kcal mol(-1) at 50 mM NaCl and 1 mM MgCl2. Interestingly, we found that the C19A mutant of D17.4 with stabilized stem structure showed slower dissociation kinetics compared to D17.4. Single-molecule observations of surface-immobilized D17.4/IgE showed much faster dissociation kinetics, and heterogeneity not observable by ensemble techniques.

CONCLUSIONS

The increasing koff value with increasing salt concentration is attributed to the electrostatic interactions between D17.4/IgE. We found that both the changes in activation enthalpy and activation entropy are insignificant with increasing NaCl concentration. The slower dissociation of the mutant C19A/IgE complex is likely due to the enhanced stability of the aptamer.

GENERAL SIGNIFICANCE

The activation parameters obtained by applying transition state analysis to kinetic data can provide details on mechanisms of molecular recognition and have applications in drug design. Single-molecule dissociation kinetics showed greater kinetic complexity than was observed in the ensemble in-solution systems, potentially reflecting conformational heterogeneity of the aptamer. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions.

Error-based extraction of states and energy landscapes from experimental single-molecule time-series

Characterization of states, the essential components of the underlying energy landscapes, is one of the most intriguing subjects in single-molecule (SM) experiments due to the existence of noise inherent to the measurements. Here we present a method to extract the underlying state sequences from experimental SM time-series. Taking into account empirical error and the finite sampling of the time-series, the method extracts a steady-state network which provides an approximation of the underlying effective free energy landscape. The core of the method is the application of rate-distortion theory from information theory, allowing the individual data points to be assigned to multiple states simultaneously. We demonstrate the method's proficiency in its application to simulated trajectories as well as to experimental SM fluorescence resonance energy transfer (FRET) trajectories obtained from isolated agonist binding domains of the AMPA receptor, an ionotropic glutamate receptor that is prevalent in the central nervous system.

Structural dynamics of the glycine-binding domain of the N-methyl-D-aspartate receptor

N-Methyl-D-aspartate receptors mediate the slow component of excitatory neurotransmission in the central nervous system. These receptors are obligate heteromers containing glycine- and glutamate-binding subunits. The ligands bind to a bilobed agonist-binding domain of the receptor. Previous x-ray structures of the glycine-binding domain of NMDA receptors showed no significant changes between the partial and full agonist-bound structures. Here we have used single molecule fluorescence resonance energy transfer (smFRET) to investigate the cleft closure conformational states that the glycine-binding domain of the receptor adopts in the presence of the antagonist 5,7-dichlorokynurenic acid (DCKA), the partial agonists 1-amino-1-cyclobutanecarboxylic acid (ACBC) and L-alanine, and full agonists glycine and D-serine. For these studies, we have incorporated the unnatural amino acid p-acetyl-L-phenylalanine for specific labeling of the protein with hydrazide derivatives of fluorophores. The single molecule fluorescence resonance energy transfer data show that the agonist-binding domain can adopt a wide range of cleft closure states with significant overlap in the states occupied by ligands of varying efficacy. The difference lies in the fraction of the protein in a more closed-cleft form, with full agonists having a larger fraction in the closed-cleft form, suggesting that the ability of ligands to select for these states could dictate the extent of activation.

Spatial recognition and mapping of proteins using DNA aptamers

Atomic force microscopy-based adhesion force measurements have emerged as a powerful tool for the biophysical analyses of biological systems. Such measurements can now be extended to detection and mapping of biomolecules on surfaces via integrated imaging and force spectroscopy techniques. Critical to these experiments is the choice of the biomolecular recognition probe. In this study, we demonstrate how oligonucleotide aptamers can be used as versatile probes to simultaneously image and spatially locate targets on surfaces. We focus on two structurally distinct proteins relevant to the clotting cascade - human α-thrombin and vascular endothelial growth factor. Via AFM-recognition mapping using specific DNA aptamers on a commercially available instrument, we show a clear consistency between height and force measurements obtained simultaneously. Importantly, we are able to observe changes in binding due to changes in the external microenvironment, which demonstrate the ability to study fluctuating biological systems in real time. The aptamer specificity and the ability to distinguish their targets are shown through positive and negative controls. It is therefore possible to generate high resolution maps to spatially and temporally identify proteins at the molecular level on complex surfaces.

Single-molecule FRET studies of HIV TAR-DNA hairpin unfolding dynamics

We directly measure the dynamics of the HIV trans-activation response (TAR)-DNA hairpin with multiple loops using single-molecule Förster resonance energy transfer (smFRET) methods. Multiple FRET states are identified that correspond to intermediate melting states of the hairpin. The stability of each intermediate state is calculated from the smFRET data. The results indicate that hairpin unfolding obeys a "fraying and peeling" mechanism, and evidence for the collapse of the ends of the hairpin during folding is observed. These results suggest a possible biological function for hairpin loops serving as additional fraying centers to increase unfolding rates in otherwise stable systems. The experimental and analytical approaches developed in this article provide useful tools for studying the mechanism of multistate DNA hairpin dynamics and of other general systems with multiple parallel pathways of chemical reactions.

An adaptable pentaloop defines a robust neomycin-B RNA aptamer with conditional ligand-bound structures

Aptamers can be highly specific for their targets, which implies precise molecular recognition between aptamer and target. However, as small polymers, their structures are more subject to environmental conditions than the more constrained longer RNAs such as those that constitute the ribosome. To understand the balance between structural and environmental factors in establishing ligand specificity of aptamers, we examined the RNA aptamer (NEO1A) previously reported as specific for neomycin-B. We show that NEO1A can recognize other aminoglycosides with similar affinities as for neomycin-B and its aminoglycoside specificity is strongly influenced by ionic strength and buffer composition. NMR and 2-aminopurine (2AP) fluorescence studies of the aptamer identified a flexible pentaloop and a stable binding pocket. Consistent with a well-structured binding pocket, docking analysis results correlated with experimental measures of the binding energy for most ligands. Steady state fluorescence studies of 2AP-substituted aptamers confirmed that A16 moves to a more solvent accessible position upon ligand binding while A14 moves to a less solvent accessible position, which is most likely a base stack. Analysis of binding affinities of NEO1A sequence variants showed that the base in position 16 interacts differently with each ligand and the interaction is a function of the buffer constituents. Our results show that the pentaloop provides NEO1A with the ability to adapt to external influences on its structure, with the critical base at position 16 adjusting to incorporate each ligand into a stable pocket by hydrophobic interactions and/or hydrogen bonds depending on the ligand and the ionic environment.

Conformational dynamics of an ATP-binding DNA aptamer: a single-molecule study

Nucleic acid aptamers are single-stranded RNA or DNA molecules that bind to their targets with high specificity and affinity. Although their biomedical applications have been booming, it is still debatable whether an aptamer recognizes its target through "induced fit" or "conformational selection", a central question in molecular recognition. To address this question, an ATP-binding DNA aptamer was selected as a model system and the conformational properties of this aptamer with and without the presence of ATP were investigated by single-pair Förster resonance energy transfer (spFRET) spectroscopy. The single-molecule results indicate that the aptamer can fold into a double-stranded-like structure, similar to the ligand-bound conformation, even without the presence of ATP. The folded structure is thermally stable at high salt concentrations and becomes rather dynamic at low salt concentrations. Although in the latter condition, the aptamer prefers unfolded structures, it can occasionally migrate to the folded conformation for a short time before being unfolded again. The binding of ATP to the aptamer stabilizes the folded structure, which populates the ligand-bound state of the aptamer, thus shifting the conformational equilibrium. Collectively, our data support that the ATP-binding DNA aptamer recognizes ATP ligand through "conformational selection".

Tracking the emergence of high affinity aptamers for rhVEGF165 during capillary electrophoresis-systematic evolution of ligands by exponential enrichment using high throughput sequencing

Capillary electrophoresis-systematic evolution of ligands by exponential enrichment (CE-SELEX) is a powerful technique for isolating aptamers for various targets, from large proteins to small peptides with molecular weights of several kilodaltons. One of the unique characteristics of CE-SELEX is the relatively high heterogeneity of the ssDNA pools that remains even after multiple rounds of selection. Enriched sequences or highly abundant oligonucleotide motifs are rarely reported in CE-SELEX studies. In this work, we employed 454 pyrosequencing to profile the evolution of an oligonucleotide pool through multiple rounds of CE-SELEX selection against the target recombinant human vascular endothelial growth factor 165 (rhVEGF165). High throughput sequencing allowed up to 3 × 10(4) sequences to be obtained from each selected pool and compared to the unselected library. Remarkably, the highest abundance contiguous sequence (contig) was only present in 0.8% of sequences even after four rounds of selection. Closer analyses of the most abundant contigs, the top 1000 oligonucleotide fragments, and even the eight original FASTA files showed no evidence of prevailing motifs in the selected pools. The sequencing results also provided insight into why many CE-SELEX selections obtain pools with reduced affinities after many rounds of selection (typically >4). Preferential amplification of a particular short polymerase chain reaction (PCR) product allowed this nonbinding sequence to overtake the pool in later rounds of selection suggesting that further refinement of primer design or amplification optimization is necessary. High affinity aptamers with 10(-8) M dissociation constants for rhVEGF165 were identified. The affinities of the higher abundance contigs were compared with aptamers randomly chosen from the final selection pool using affinity capillary electrophoresis (ACE) and fluorescence polarization (FP). No statistical difference in affinity between the higher abundance contigs and the randomly chosen aptamers was observed, supporting the premise that CE-SELEX selects a uniquely heterogeneous pool of high affinity aptamers.

Super-resolution mbPAINT for optical localization of single-stranded DNA

We demonstrate the application of superlocalization microscopy to identify sequence-specific portions of single-stranded DNA (ssDNA) with sequence resolution of 50 nucleotides, corresponding to a spatial resolution of 30 nm. Super-resolution imaging was achieved using a variation of a single-molecule localization method, termed as "motion blur" point accumulation for imaging in nanoscale topography (mbPAINT). The target ssDNA molecules were immobilized on the substrate. Short, dye-labeled, and complementary ssDNA molecules stochastically bound to the target ssDNA, with repeated binding events allowing super-resolution. Sequence specificity was demonstrated via the use of a control, noncomplementary probe. The results support the possibility of employing relatively inexpensive short ssDNAs to identify gene sequence specificity with improved resolution in comparison to the existing methods.

Extending single molecule fluorescence observation time by amplitude-modulated excitation

We present a hardware-based method that can improve single molecule fluorophore observation time by up to 1500% and super-localization by 47% for the experimental conditions used. The excitation was modulated using an acousto-optic modulator (AOM) synchronized to the data acquisition and inherent data conversion time of the detector. The observation time and precision in super-localization of four commonly used fluorophores were compared under modulated and traditional continuous excitation, including direct total internal reflectance excitation of Alexa 555 and Cy3, non-radiative Förster resonance energy transfer (FRET) excited Cy5, and direct epi-fluorescence wide field excitation of Rhodamine 6G. The proposed amplitude-modulated excitation does not perturb the chemical makeup of the system or sacrifice signal and is compatible with multiple types of fluorophores. Amplitude-modulated excitation has practical applications for any fluorescent study utilizing an instrumental setup with time-delayed detectors.

Photobleaching lifetimes of cyanine fluorophores used for single-molecule Förster resonance energy transfer in the presence of various photoprotection systems

Lengthening smFRET lifetimes: We investigated various photoprotection system combinations to find the combination that optimally extended the photobleach lifetime of a Cy3/Cy5 smFRET pair attached to a DNA hairpin in a single-molecule environment. We found that the glucose/glucose oxygen-scavenging solution in combination with redox-based photostabilization solutions yielded the longest average photobleaching lifetimes.

Modified capillary electrophoresis based measurement of the binding between DNA aptamers and an unknown concentration target

The recognition of targets such as biomacromolecules, viruses and cells by their aptamers is crucial in aptamer-based biosensor platforms and research into protein function. However, it is difficult to evaluate the binding constant of aptamers and their targets that are hard to purify and quantify, especially when the targets are undefined. Therefore, we aimed to develop a modified capillary electrophoresis based method to determine the dissociation constant of aptamers whose targets are hard to quantify. A protein target, human thrombin, and one of its aptamers were used to validate our modified method. We demonstrated that the result calculated by our method, only depending on the aptamer's concentrations, was consistent with the classical method, which depended on the concentrations of both the aptamers and the targets. Furthermore, a series of DNA aptamers binding with avian influenza virus H9N2 were confirmed by a four-round selection of capillary electrophoresis-systematic evolution of ligands by exponential enrichment, and we identified the binding constant of these aptamers by directly using the whole virus as the target with the modified method. In conclusion, our modified method was validated to study the interaction between the aptamer and its target, and it may also advance the evaluation of other receptor-ligand interactions.

Biophysical characterization of VEGF-aHt DNA aptamer interactions

The binding of the well-studied DNA aptamer aHt (5'-ATACCAGTCTATTCAATTGGGCCCGTCCGTAT GGTGGGTGTGCTGGCCAG-3'), which has been demonstrated to recognize human vascular endothelial growth factor (VEGF₁₆₅) to recombinant VEGF was characterized using fluorescence anisotropy, isothermal titration calorimetry and analytical ultracentrifugation. The negatively-charged DNA aptamer is selective for VEGF and does not recognize positively-charged hen egg lysozyme, or bovine serum albumin. In contrast to the VEGF association of the previously-described aV DNA aptamer, where the binding is enthalpically driven and sequence-specific, the binding of the aHt aptamer to VEGF is entropically-driven and not abolished by scrambling of the sequence.

Affinity improvement of a VEGF aptamer by in silico maturation for a sensitive VEGF-detection system

Systematic evolution of ligands by exponential enrichment (SELEX) is an efficient method to identify aptamers; however, it sometimes fails to identify aptamers that bind to their target with high affinity. Thus, post-SELEX optimization of aptamers is required to improve aptamer binding affinity. We developed in silico maturation based on a genetic algorithm (1) as an efficient mutagenesis method to improve aptamer binding affinity. In silico maturation was performed to improve a VEGF-binding DNA aptamer (VEap121). The VEap121 aptamer is considered to fold into a G-quadruplex structure and this structure may be important for VEGF recognition. Using in silico maturation, VEap121 was mutated with the exception of the guanine tracts that are considered to form the G-quartet. As a result, four aptamers were obtained that showed higher affinity compared with VEap121. The dissociation constant (K(d)) of the most improved aptamer (3R02) was 300 pM. The affinity of 3R02 was 16-fold higher than that of VEap121. Moreover, a bivalent aptamer was constructed by connecting two identical 3R02s through a 10-mer thymine linker for further improvement of affinity. The bivalent aptamer (3R02 Bivalent) bound to VEGF with a K(d) value of 30 pM. Finally, by constructing a VEGF-detection system using a VEGF antibody as the capture molecule and monovalent 3R02 as the detection molecule, a more sensitive assay was developed compared with the system using VEap121. These results indicate that in silico maturation could be an efficient method to improve aptamer affinity for construction of sensitive detection systems.

Role of conformational dynamics in α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA) receptor partial agonism

We have investigated the range of cleft closure conformational states that the agonist-binding domains of the α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA) receptors occupy when bound to a series of willardiine derivatives using single-molecule FRET. These studies show that the agonist-binding domain exhibits varying degrees of dynamics when bound to the different willardiines with differing efficacies. The chlorowillardiine- and nitrowillardiine-bound form of the agonist-binding domain probes a narrower range of cleft closure states relative to the iodowillardiine bound form of the protein, with the antagonist (αS)-α-amino-3-[(4-carboxyphenyl)methyl]-3,4-dihydro-2,4-dioxo-1(2H)-pyrimidinepropanoic acid (UBP-282)-bound form exhibiting the widest range of cleft closure states. Additionally, the average cleft closure follows the order UBP-282 > iodowillardiine > chlorowillardiine > nitrowillardiine-bound forms of agonist-binding domain. These single-molecule FRET data, along with our previously reported data for the glutamate-bound forms of wild type and T686S mutant proteins, show that the mean currents under nondesensitizing conditions can be directly correlated to the fraction of the agonist-binding domains in the "closed" cleft conformation. These results indicate that channel opening in the AMPA receptors is controlled by both the ability of the agonist to induce cleft closure and the dynamics of the agonist-binding domain when bound to the agonist.

Single-molecule measurements of the binding between small molecules and DNA aptamers

Aptamers that bind small molecules can serve as basic biosensing platforms. Evaluation of the binding constant between an aptamer and a small molecule helps to determine the effectiveness of the aptamer-based sensors. Binding constants are often measured by a series of experiments with varying ligand or aptamer concentrations. Such experiments are time-consuming, material nonprudent, and prone to low reproducibility. Here, we use laser tweezers to determine the dissociation constant for aptamer-ligand interactions at the single-molecule level from only one ligand concentration. Using an adenosine 5'-triphosphate disodium salt (ATP) binding aptamer as an example, we have observed that the mechanical stabilities of aptamers bound with ATP are higher than those without a ligand. Comparison of the change in free energy of unfolding (ΔG(unfold)) between these two aptamers yields a ΔG of 33 ± 4 kJ/mol for the binding. By applying a Hess-like cycle at room temperature, we obtained a dissociation constant (K(d)) of 2.0 ± 0.2 μM, a value consistent with the K(d) obtained from our equilibrated capillary electrophoresis (CE) (2.4 ± 0.4 μM) and close to that determined by affinity chromatography in the literature (6 ± 3 μM). We anticipate that our laser tweezers and CE methodologies may be used to more conveniently evaluate the binding between receptors and ligands and also serve as analytical tools for force-based biosensing.

A novel aptasensor based on silver nanoparticle enhanced fluorescence

In the present study, we report a novel aptasensor based on silver nanoparticle enhanced fluorescence for the detection of adenosine. First, the distance dependence nature of silver nanoparticle enhanced fluorescence was investigated through fluorescent dyes modified oligonucleotides to control the spacing distance between dyes and AgNP. The results showed that the fluorescence intensity reached the maximum value with the spacing distance of dyes about 8 nm from AgNP surface. The fluorescence intensity decreases when the spacing distance is either above or below this value. Based on this result, a fluorescence switch is constructed. In the "OFF" state, without the target molecules, there is a greater spacing distance between the Cy3 dyes and the AgNP giving comparatively lower fluorescence intensity. While in the "ON" state, in the presence of target molecules, the fluorescence signals increased for the conformation structure change of the aptamer which shorten the spacing distance between the Cy3 dyes and the AgNP to 8 nm. Using adenosine as target, the aptasensor produced a linear range from 200 nM to 200 μM with a correlation coefficient of 0.9949 and the detection limit was 48 nM estimated using 3σ. The aptasensor was also found to be specific in targeting adenosine. The presented method shows a new strategy of combining aptamer recognition and silver nanoparticle for fluorescence signal enhancement and increasing sensitivity.

Structural landscape of isolated agonist-binding domains from single AMPA receptors

α-amino-3-hydroxy-5-methyl-4-isoxazole propionate (AMPA) receptors mediate fast excitatory neurotransmission by converting chemical signals into electrical signals. Thus, it is important to understand the relationship between their chemical biology and their function. Single molecule fluorescence resonance energy transfer (smFRET) was used to examine the conformations explored by the agonist binding domain of the AMPA receptor for wild type and T686 mutant proteins. Each form of the agonist binding domain exhibited a dynamic, multi-state sequential equilibrium, which could only be identified using wavelet shrinkage, a signal processing technique that removes experimental shot-noise. These results illustrate that the extent of activation is dependent not on a rigid closed cleft, but instead on the probability that a given subunit will occupy a closed cleft conformation, which in turn is not only determined by the lowest energy state but by the range of states that the protein explores.

Improved resolution of complex single-molecule FRET systems via wavelet shrinkage

The resolution of complex interactions found in single-molecule fluorescence resonance energy transfer (smFRET) experiments is hindered by noise. Wavelet shrinkage is proven to reduce noise, but traditional methods introduce artifacts when acting on discontinuous signals, such as those acquired in smFRET experiments. Modifications to the basic method that are specific to smFRET are developed and tested on simulated systems. Use of the Haar wavelet basis produces the most optimally denoised estimates. We also assess various thresholding methods, develop a time-localized noise estimator, and implement a translation-invariant wavelet transformation to reduce artifacts associated with discontinuities and inadequate distinction of noise. The time-local estimator enhances noise reduction by 5-20%, and translation-invariant transformation nearly eliminates the aforementioned artifacts. Kinetic parameters extracted from denoised estimates are accurate to within 5% of the simulated values. Overall, the improved resolution results in the complete and accurate characterization of both simple and complex smFRET systems.

Biophysical characterization of DNA and RNA aptamer interactions with hen egg lysozyme

This work characterized the binding of an RNA aptamer recognizing hen egg white lysozyme, as well as a literature-reported single-stranded DNA analog of sequence identical to the original RNA aptamer, using fluorescence anisotropy, isothermal titration calorimetry (ITC) and analytical ultracentrifugation. The polyanionic DNA aptamer analog is selective for lysozyme even over cationic cytochrome c and has been reported to be successfully used in biosensing applications. The association however, is predominantly of electrostatic character, strongly salt-sensitive and entropically-driven, in contrast to previously described enthalpically-driven antibody-lysozyme and DNA aptamer-VEGF interactions. With a moderate selectivity for their target, high salt-sensitivity along with fast association and dissociation behavior, these molecules might serve as pseudo-affinity ligands for biomolecular separations.

A folding-based electrochemical aptasensor for detection of vascular endothelial growth factor in human whole blood

We herein report a folding-based electrochemical DNA aptasensor for the detection of vascular endothelial growth factor (VEGF) directly in complex biological samples, including blood serum and whole blood. The electrochemical signal generation is coupled to a large, target-induced conformational change in a methylene blue-modified and surface immobilized anti-VEGF aptamer. The sensor is sensitive, selective and essentially reagentless: we can readily detect VEGF down to 5 pM (190 pg/mL) directly in 50% blood serum. Similar to other aptasensors of this class, the VEGF sensor is also regenerable and reusable. In addition, the sensor performs comparably well even when fabricated on a gold-plated screen-printed carbon electrode and can potentially be implemented as a cost-effective, single-use biosensor for diseases diagnosis and therapy monitoring. The exceptional sensitivity, selectivity, and reusability of this electrochemical aptasensor platform suggest it may be a promising strategy for a wide variety of sensing applications.

Molecular interaction studies of vascular endothelial growth factor with RNA aptamers

With widespread applications in biosensors, diagnostics and therapeutics, unraveling the mechanism of the interactions between aptamers and their targets has become extremely important. In this study, the interaction forces between an aptamer and its protein target were successfully measured via AFM-based force spectroscopy at the molecular level. The angiogenic protein, vascular endothelial growth factor (VEGF(165)) covalently tethered to a mixed self-assembled monolayer surface and an anti-VEGF(165) aptamer attached to an AFM cantilever was used to probe this interaction. By comparing the binding probability and the force distribution of this system in a series of experiments, the interaction between the aptamer and the protein was confirmed and the effect of loading rate on the rupture force was studied. The specificity of the aptamer was investigated by measuring interactions with VEGF(121), an isoform of VEGF missing a critical binding domain, and VEGF(165) isoform blocked with heparin. The lower frequency of binding events compared with that of VEGF(165) reflected that despite a high affinity to its preferential target, the selectivity of this aptamer is impaired to some extent due to the flexible structure of aptamers. By changing the concentration of Mg(2+) ion in the binding buffer, we could verify the effect of metal ions as stabilizers of aptamer conformation. The results provide evidence at the molecular level that the structural stability of aptamer is closely related to higher binding force and that rigid aptamer tertiary structures require higher forces to unbind the aptamer/protein complex.

Denoising single-molecule FRET trajectories with wavelets and Bayesian inference

A method to denoise single-molecule fluorescence resonance energy (smFRET) trajectories using wavelet detail thresholding and Bayesian inference is presented. Bayesian methods are developed to identify fluorophore photoblinks in the time trajectories. Simulated data are used to quantify the improvement in static and dynamic data analysis. Application of the method to experimental smFRET data shows that it distinguishes photoblinks from large shifts in smFRET efficiency while maintaining the important advantage of an unbiased approach. Known sources of experimental noise are examined and quantified as a means to remove their contributions via soft thresholding of wavelet coefficients. A wavelet decomposition algorithm is described, and thresholds are produced through the knowledge of noise parameters in the discrete-time photon signals. Reconstruction of the signals from thresholded coefficients produces signals that contain noise arising only from unquantifiable parameters. The method is applied to simulated and observed smFRET data, and it is found that the denoised data retain their underlying dynamic properties, but with increased resolution.

Aptamer-based multicolor fluorescent gold nanoprobes for multiplex detection in homogeneous solution

The design of a novel multicolor fluorescent gold nanoprobe for homogeneous detection of small-molecule targets is reported, which combines the specific binding abilities of aptamers with the ultrahigh quenching ability of gold nanoparticles (AuNPs). Dye-tagged aptamers and their complementary sequence with thiol labels are co-assembled at the surface of AuNPs. As a proof of concept, it is demonstrated that such a multicolor fluorescent gold nanoprobe can simultaneously detect adenosine, potassium ion, and cocaine with high selectivity. This potentially generic strategy is shown to be promising for rapid screening of small molecular targets.

Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure

MOTIVATION

There are many important proteins which bind single-stranded nucleic acids, such as the nucleocapsid protein in HIV and the RecA DNA repair protein in bacteria. The presence of such proteins can strongly alter the secondary structure of the nucleic acid molecules. Therefore, accurate modeling of the interaction between single-stranded nucleic acids and such proteins is essential to fully understand many biological processes.

RESULTS

We develop a model for predicting nucleic acid secondary structure in the presence of single-stranded binding proteins, and implement it as an extension of the Vienna RNA Package. All parameters needed to model nucleic acid secondary structures in the absence of proteins have been previously determined. This leaves the footprint and sequence-dependent binding affinity of the protein as adjustable parameters of our model. Using this model we are able to predict the probability of the protein binding at any position in the nucleic acid sequence, the impact of the protein on nucleic acid base pairing, the end-to-end distance distribution for the nucleic acid and FRET distributions for fluorophores attached to the nucleic acid.

AVAILABILITY

Source code for our modified version of the Vienna RNA package is freely available at http://bioserv.mps.ohio-state.edu/Vienna+P, implemented in C and running on Linux.

Biophysical characterization of DNA aptamer interactions with vascular endothelial growth factor

The binding of a DNA aptamer (5'-CCGTCTTCCAGACAAGAGTGCAGGG-3') to recombinant human vascular endothelial growth factor (VEGF(165)) was characterized using surface plasmon resonance (SPR), fluorescence anisotropy and isothermal titration calorimetry (ITC). Results from both fluorescence anisotropy and ITC indicated that a single aptamer molecule binds to each VEGF homodimer, unlike other VEGF inhibitors that exhibit 2(ligand):1(VEGF homodimer) stoichiometry. In addition, ITC revealed that the association of the aptamer to VEGF at 20 degrees C is enthalpically driven, with an unfavorable entropy contribution. SPR kinetic studies, with careful control of possible mass transfer effects, demonstrated that the aptamer binds to VEGF with an association rate constant k(on) = 4.79 +/- 0.03 x 10(4) M(-1) s(-1) and a dissociation rate constant k(off) = 5.21 +/- 0.02 x 10(-4) s(-1) at 25 degrees C. Key recognition hot-spots were determined by a combination of aptamer sequence substitutions, truncations, and extensions. Most single-nucleotide substitutions, particularly within an mfold-predicted stem, suppress binding, whereas those within a predicted loop have a minimal effect. The 5'-end of the aptamer plays a key role in VEGF recognition, as a single-nucleotide truncation abolished VEGF binding. Conversely, an 11-fold increase in the association rate (and affinity) is observed with a single cytosine nucleotide extension, due to pairing of the 3'-GGG with 5'-CCC in the extended aptamer. Our approach effectively maps the secondary structural elements in the free aptamer, which present the unpaired interface for high affinity VEGF recognition. These data demonstrate that a directed binding analysis can be used in concert with library screening to characterize and improve aptamer/ligand recognition.