High-Throughput Strategy for Enhancing Aptamer Performance across Different Environmental Conditions.

Aptamers selected under specific environmental conditions (e.g., pH, ion concentration, and temperature) often exhibit greatly reduced affinity when used in other contexts. This can be especially problematic for biomedical applications in which aptamers are exposed to sample matrices with distinctive chemical properties, such as blood, sweat, or urine. We present a high-throughput screening procedure for adapting existing aptamers for use in samples whose chemical composition differs considerably from the original selection conditions. Building on prior work from our group, we have utilized a modified DNA sequencer capable of screening up to 107 unique aptamer mutants for target binding under the desired assay conditions. As an exemplar, we screened all 11,628 single- and double-substitution mutants for a previously reported glucose aptamer that was originally selected in high-ionic strength buffer and exhibited relatively low affinity in physiological conditions. After a single round of screening, we identified aptamer mutants with ∼four-fold increased affinity in physiological conditions. Interestingly, we found that the impact of single-base substitutions was relatively modest but observed considerably greater binding improvements among the double mutants, highlighting the importance of cooperative effects between mutations. This approach should be generalizable to other aptamers and environmental conditions for a range of applications.

A massively parallel screening platform for converting aptamers into molecular switches.

Aptamer-based molecular switches that undergo a binding-induced conformational change have proven valuable for a wide range of applications, such as imaging metabolites in cells, targeted drug delivery, and real-time detection of biomolecules. Since conventional aptamer selection methods do not typically produce aptamers with inherent structure-switching functionality, the aptamers must be converted to molecular switches in a post-selection process. Efforts to engineer such aptamer switches often use rational design approaches based on in silico secondary structure predictions. Unfortunately, existing software cannot accurately model three-dimensional oligonucleotide structures or non-canonical base-pairing, limiting the ability to identify appropriate sequence elements for targeted modification. Here, we describe a massively parallel screening-based strategy that enables the conversion of virtually any aptamer into a molecular switch without requiring any prior knowledge of aptamer structure. Using this approach, we generate multiple switches from a previously published ATP aptamer as well as a newly-selected boronic acid base-modified aptamer for glucose, which respectively undergo signal-on and signal-off switching upon binding their molecular targets with second-scale kinetics. Notably, our glucose-responsive switch achieves ~30-fold greater sensitivity than a previously-reported natural DNA-based switch. We believe our approach could offer a generalizable strategy for producing target-specific switches from a wide range of aptamers.

Flow-Cell-Based Technology for Massively Parallel Characterization of Base-Modified DNA Aptamers.

Aptamers incorporating chemically modified bases can achieve superior affinity and specificity compared to natural aptamers, but their characterization remains a labor-intensive, low-throughput task. Here, we describe the "non-natural aptamer array" (N2A2) system, in which a minimally modified Illumina MiSeq instrument is used for the high-throughput generation and characterization of large libraries of base-modified DNA aptamer candidates based on both target binding and specificity. We first demonstrate the capability to screen multiple different base modifications to identify the optimal chemistry for high-affinity target binding. We next use N2A2 to generate aptamers that can maintain excellent specificity even in complex samples, with equally strong target affinity in both buffer and diluted human serum. For both aptamers, affinity was formally calculated with gold-standard binding assays. Given that N2A2 requires only minor mechanical modifications to the MiSeq, we believe that N2A2 offers a broadly accessible tool for generating high-quality affinity reagents for diverse applications.

A system for multiplexed selection of aptamers with exquisite specificity without counterselection.

Aptamers have proven to be valuable tools for the detection of small molecules due to their remarkable ability to specifically discriminate between structurally similar molecules. Most aptamer selection efforts have relied on counterselection to eliminate aptamers that exhibit unwanted cross-reactivity to interferents or structurally similar relatives to the target of interest. However, because the affinity and specificity characteristics of an aptamer library are fundamentally unknowable a priori, it is not possible to determine the optimal counterselection parameters. As a result, counterselection experiments require trial-and-error approaches that are inherently inefficient and may not result in aptamers with the best combination of affinity and specificity. In this work, we describe a high-throughput screening process for generating high-specificity aptamers to multiple targets in parallel while also eliminating the need for counterselection. We employ a platform based on a modified benchtop sequencer to conduct a massively parallel aptamer screening process that enables the selection of highly specific aptamers against multiple structurally similar molecules in a single experiment, without any counterselection. As a demonstration, we have selected aptamers with high affinity and exquisite specificity for three structurally similar kynurenine metabolites that differ by a single hydroxyl group in a single selection experiment. This process can easily be adapted to other small-molecule analytes and should greatly accelerate the development of aptamer reagents that achieve exquisite specificity for their target analytes.

Discovery of indole-modified aptamers for highly specific recognition of protein glycoforms.

Glycosylation is one of the most abundant forms of post-translational modification, and can have a profound impact on a wide range of biological processes and diseases. Unfortunately, efforts to characterize the biological function of such modifications have been greatly hampered by the lack of affinity reagents that can differentiate protein glycoforms with robust affinity and specificity. In this work, we use a fluorescence-activated cell sorting (FACS)-based approach to generate and screen aptamers with indole-modified bases, which are capable of recognizing and differentiating between specific protein glycoforms. Using this approach, we were able to select base-modified aptamers that exhibit strong selectivity for specific glycoforms of two different proteins. These aptamers can discriminate between molecules that differ only in their glycan modifications, and can also be used to label glycoproteins on the surface of cultured cells. We believe our strategy should offer a generally-applicable approach for developing useful reagents for glycobiology research.

Correlation Between Brain Tissue Damage and Inertial Cavitation Dose Quantified Using Passive Cavitation Imaging.

Focused ultrasound (FUS)-induced cavitation-mediated brain therapies have become emerging therapeutic modalities for neurologic diseases. Cavitation monitoring is essential to ensure the safety of all cavitation-mediated therapeutic techniques as inertial cavitation can be associated with tissue damage. The objective of this study was to reveal the correlation between the inertial cavitation dose, quantified by passive cavitation imaging (PCI), and brain tissue histologic-level damage induced by FUS in combination with microbubbles. An ultrasound image-guided FUS system consisting of a single-element FUS transducer (1.5 MHz) and a co-axially aligned 128-element linear ultrasound imaging array was used to perform FUS treatment of mice. Mice were sonicated by FUS with different peak negative pressures (0.5 MPa, 1.1 MPa, 4.0 MPa and 6.5 MPa) in the presence of systemically injected microbubbles. The acoustic emissions from the FUS-activated microbubbles were passively detected by the imaging array. The pre-beamformed channel data were acquired and processed offline using the frequency-domain delay, sum and integration algorithm to generate inertial cavitation maps. All the mice were sacrificed after the FUS treatment, and their brains were harvested and processed for hematoxylin and eosin staining. The obtained inertial cavitation maps revealed the dynamic changes of microbubble behaviors during FUS treatment at different pressure levels. It was found that the inertial cavitation dose quantified based on PCI had a linear correlation with the scale of histologic-level tissue damage. Findings from this study suggested that PCI can be used to predict histologic-level tissue damage associated with the FUS-induced cavitation.

Ultrasound Characterization of Bone Demineralization Using a Support Vector Machine.

We propose an ultrasound-guided remote measurement technique, utilizing an acoustic radiation force beam as our excitation source and a receiving hydrophone, to assess non-invasively a bone's mechanical properties. Features, such as velocity, were extracted from the acoustic pressure received from the bone surface. The typical velocity of an intact bone (3540 m/s) was higher in comparison to that of a demineralized bone (2231 m/s). According to the receiver operating characteristic curve, the optimal velocity cutoff value of ≥3096 m/s yields 80% sensitivity and 82.61% specificity between intact and demineralized bone. Utilizing a support vector machine, the hours of bone demineralization were successfully classified with maximum accuracy >80% using 18% training data. The results indicate the potential application of our proposed technique and support vector machine for monitoring bone mechanical properties.

Acoustic field characterization of a clinical magnetic resonance-guided high-intensity focused ultrasound system inside the magnet bore.

PURPOSE: With the expanding clinical application of magnetic resonance-guided high-intensity focused ultrasound (MR-HIFU), acoustic field characterization of MR-HIFU systems is needed for facilitating regulatory approval and ensuring consistent and safe power output of HIFU transducers. However, the established acoustic field measurement techniques typically use equipment that cannot be used in a magnetic resonance imaging (MRI) suite, thus posing a challenge to the development and execution of HIFU acoustic field characterization techniques. In this study, we developed and characterized a technique for HIFU acoustic field calibration within the MRI magnet bore, and validated the technique with standard hydrophone measurements outside of the MRI suite. METHODS: A clinical Philips MR-HIFU system (Sonalleve V2, Philips, Vantaa, Finland) was used to assess the proposed technique. A fiber-optic hydrophone with a long fiber was inserted through a 24-gauge angiocatheter and fixed inside a water tank that was placed on the HIFU patient table above the acoustic window. The long fiber allowed the hydrophone control unit to be placed outside of the magnet room. The location of the fiber tip was traced on MR images, and the HIFU focal point was positioned at the fiber tip using the MR-HIFU therapy planning software. To perform acoustic field mapping inside the magnet, the HIFU focus was positioned relative to the fiber tip using an MRI-compatible 5-axis robotic transducer positioning system embedded in the HIFU patient table. To perform validation measurements of the acoustic fields, the HIFU table was moved out of the MRI suite, and a standard laboratory hydrophone measurement setup was used to perform acoustic field measurements outside the magnetic field. RESULTS: The pressure field scans along and across the acoustic beam path obtained inside the MRI bore were in good agreement with those obtained outside of the MRI suite. At the HIFU focus with varying nominal acoustic powers of 10-500 W, the peak positive pressure and peak negative pressure measured inside the magnet bore were 3.87-68.67 MPa and 3.56-12.06 MPa, respectively, while outside the MRI suite the corresponding pressures were 3.27-67.32 MPa and 3.06-12.39 MPa, respectively. There was no statistically significant difference (P > 0.05) between measurements inside the magnet bore and outside the MRI suite for the p+ and p- at any acoustic power level. The spatial-peak pulse-average intensities (ISPPA ) for these powers were 312-17816 W/cm2 and 220-15698 W/cm2 for measurements inside and outside the magnet room, respectively. In addition, when the scanning step size of the HIFU focus was increased from 100 µm to 500 µm, the execution time for scanning a 4 × 4 mm2 area decreased from 210 min to 10 min, the peak positive pressure decreased by 14%, the peak negative pressure decreased by 5%, and the lateral full width at half maximum dimension of pressure profiles increased from 1.15 mm to 1.55 mm. CONCLUSIONS: The proposed hydrophone measurement technique offers a convenient and reliable method for characterizing the acoustic fields of clinical MR-HIFU systems inside the magnet bore. The technique was validated for use by measurements outside the MRI suite using a standard hydrophone calibration technique. This technique can be a useful tool in MR-HIFU quality assurance and acoustic field assessment.