Capture and isolation of flowing cells particulates from body fluids has enormous implications in diagnosis, monitoring, drug testing, yet monovalent adhesion molecules used for this purpose result inefficient cell capture difficulty retrieving the captured cells. Inspired by marine creatures that present long tentacles containing multiple adhesive domains to effectively food particulates, we developed a platform approach isolate using 3D DNA network comprising repeating aptamer extend over...

Replicating bacterial chromosomes continuously demix from each other and segregate within a compact volume inside the cell called nucleoid. Although many proteins involved in this process have been identified, nature of global forces that shape has remained unclear because limited knowledge micromechanical properties chromosome. In work, we demonstrate experimentally fundamentally soft chromosome entropic can it crowded intracellular environment. We developed unique “micropiston” measured...

Dynamical instrument limitations, such as finite detection bandwidth, do not simply add statistical errors to fluctuation measurements, but can create significant systematic biases that affect the measurement of steady-state properties. Such effects must be considered when calibrating ultra-sensitive force probes by analyzing observed Brownian fluctuations. In this article, we present a novel method for extracting true spring constant and diffusion coefficient harmonically confined particle...

We present a miniature centrifuge force microscope (CFM) that repurposes benchtop for high-throughput single-molecule experiments with high-resolution particle tracking, large range, temperature control and simple push-button operation. Incorporating DNA nanoswitches to enable repeated interrogation by of single molecular pairs, we demonstrate increased throughput, reliability the ability characterize population heterogeneity. perform spatiotemporally multiplexed collect 1,863 bond rupture...

A DNA nanotechnology approach enables label-free and unamplified detection of cellular microRNAs using gel electrophoresis.

Nanometer-sized features and molecular recognition properties make DNA a useful material for nanoscale construction, but degradation in biological fluids poses considerable roadblock to biomedical applications of nanotechnology. Here, we report the remarkable biostability multistranded motif called paranemic crossover (PX) DNA. Compared double stranded DNA, PX has dramatically enhanced (sometimes >1000 fold) resistance by four different nucleases, bovine human serum, urine. We trace cause...

DNA serves as nature's information storage molecule, and has been the primary focus of engineered systems for biological computing data storage. Here we combine recent efforts in self-assembly toehold-mediated strand displacement to develop a rewritable multi-bit memory system. The system operates by encoding distinct reversible conformations nanoswitch decoding gel electrophoresis. We demonstrate 5-bit capable writing, erasing, rewriting binary representations alphanumeric symbols, well...

Base stacking interactions between adjacent bases in DNA and RNA are important for many biological processes biotechnology applications. Previous work has estimated energies pairs of bases, but contributions individual remained unknown. Here, we use a Centrifuge Force Microscope high-throughput single molecule experiments to measure bases. We found strongest purines (G|A at -2.3 ± 0.2 kcal/mol) weakest pyrimidines (C|T -0.5 0.1 kcal/mol). Hybrid with phosphorylated, methylated, nucleotides...

Precise manipulation of single molecules has already led to remarkable insights in physics, chemistry, biology, and medicine. However, widespread adoption single-molecule techniques been impeded by equipment cost the laborious nature making measurements one molecule at a time. We have solved these issues developing an approach that enables massively parallel force using centrifugal force. This is realized instrument we call centrifuge microscope which objects orbiting sample are subjected...

The ability to manipulate and observe single biological molecules has led both fundamental scientific discoveries new methods in nanoscale engineering. A common challenge many single-molecule experiments is reliably linking surfaces, identifying their interactions. We have met this by nanoengineering a novel DNA-based linker that behaves as force-activated switch, providing molecular signature can eliminate errant data arising from non-specific multiple By integrating receptor ligand into...

Detection of nucleic acid sequences is important for applications such as medicine and forensics, but many detection strategies involve multiple time-consuming steps or require expensive lab equipment. Here we report a programmable DNA nanoswitch that undergoes predefined conformational change upon binding target sequence, flipping the switch from linear "off" state to looped "on" state. The presence sequence determined without amplification using standard gel electrophoresis separate on off...

In just over a decade since its discovery, research on graphene has exploded due to number of potential applications in electronics, materials, and medicine. water-soluble form oxide, the material shown promise as biosensor preferential absorption single-stranded polynucleotides fluorescence quenching properties. The rational design these biosensors, however, requires an improved understanding binding thermodynamics ultimately predictive model sequence-specific binding. Toward goals, here we...

Detection of viruses is critical for controlling disease spread. Recent emerging viral threats, including Zika virus, Ebola and SARS-CoV-2 responsible coronavirus 2019 (COVID-19) highlight the cost difficulty in responding rapidly. To address these challenges, we develop a platform low-cost rapid detection RNA with DNA nanoswitches that mechanically reconfigure response to specific viruses. Using virus as model system, show nonenzymatic selective multiplexed between related strains. For...

Molecular biomarkers play a key role in the clinic, aiding diagnostics and prognostics, research laboratory, contributing to our basic understanding of diseases. Detecting multiple diverse molecular within single accessible assay would have great utility, providing more comprehensive picture for clinical evaluation research, but is challenge with standard methods. Here, we report programmable DNA nanoswitches multiplexed detection up 6 at once each combination producing unique barcode...

DNA nanotechnology uses the programmable assembly of to create nanoscale objects. Recent work from our laboratory suggested that terminal stacking interactions between adjacent strands could be a design parameter for nanotechnology. Here, we explore idea by creating tetrahedra with sticky ends containing identical base pairing but different interactions. Testing all 16 combinations, found melting temperature varied up 10 °C altering single stack in design. We also show 4 bp end weak does not...

DNA nanostructures are typically assembled by thermal annealing in buffers containing magnesium. We demonstrate the assembly of at constant temperatures ranging from 4° to 50°C solutions different counterions. The choice counterions and temperature influence isothermal several motifs designed three-dimensional crystals. Molecular dynamics simulations show more fluctuations structure select monovalent ions (Na + K ) compared divalent (Mg 2+ Ca ). A key highlight is successful...

We present a simple and secure system for encrypting decrypting information using DNA self-assembly. Binary data is encoded in the geometry of nanostructures with two distinct conformations. Removing or leaving out single component reduces these structures to an encrypted solution ssDNA, whereas adding back this missing "decryption key" causes spontaneous formation message through self-assembly, enabling rapid read via gel electrophoresis. Applications include authentication, messaging, barcoding.

Biostability of different-sized DNA tetrahedra were analyzed against two nucleases and in fetal bovine serum. Results show that nanostructure size can influence nuclease degradation, but suggest a complex relationship is specific.

Hog pancreas kallikrein does not cause a blood pressure drop in the rat, but lowers dog. Since this lack of effect could be due to inability hog act upon rat plasma, vitro release kallidin with plasma different species was studied. Human, dog, swine, guinea pig, and ox plasmas were incubated for periods time kallikrein, bradykininogen (kallidinogen) consumed released measured. It found that any pig plasma; it releases small amounts greater bovine, human plasma. The consumption showed same sequence.

Abstract Custom‐built DNA nanostructures are now used in applications such as biosensing, molecular computation, biomolecular analysis, and drug delivery. While the functionality biocompatibility of makes useful applications, field faces a challenge making biostable nanostructures. Being natural material, is most suited for biological but also easily degraded by nucleases. Several methods have been employed to study nuclease degradation rates enhancement resistance. This protocol describes...

Alzheimer's disease (AD) is the most common neurodegenerative disorder, with significant research efforts devoted to identifying new biomarkers for clinical diagnosis and treatment. MicroRNAs have emerged as likely regulators AD, now implicated having roles in several biological processes related progression of disease. In this work, we use miRacles assay (microRNA activated conditional looping engineered switches) single-step detection AD-related microRNAs. The technology based on...