An official website of the United States government
Trinucleotide repeat (TNR) sequences introduce sequence-directed flexibility in the genomic makeup of all living species leading to unique non-canonical structure formation. In humans, the expansions of TNR sequences are responsible for almost 24 neurodegenerative and neuromuscular diseases because their unique structures disrupt cell functions. The biophysical studies of these sequences affect their electrophoretic mobility and spectroscopic signatures. Here, we demonstrate a novel strategy to characterize and discriminate the TNR sequences by monitoring their capillary flow in the absence of an external driving force using wax-on-plastic microchannels. The wax-on-plastic microfluidic system translates the sequence-directed flexibility of TNR into differential flow dynamics. Several variables were used to characterize sequences including concentration, single- vs. double-stranded samples, type of repeat sequence, length of the repeat sequence, presence of mismatches in duplex, and presence of metal ion. All these variables were found to influence the flow velocities of TNR sequences as these factors directly affect the structural flexibility of TNR at the molecular level. An overall trend was observed as the higher flexibility in the TNR structure leads to lower capillary flow. After testing samples derived from relevant cells harboring expanded TNR sequences, it is concluded that this approach may transform into a reagent-free and pump-free biosensing platform to detect microsatellite expansion diseases.
more »
« less
Unique sequence-dependent properties of trinucleotide repeat monolayers: electrochemical, electrical, and topographic characterization
Trinucleotide repeat (TNR) sequences widely exist in nature and their overgrowth is associated with two dozen neurodegenerative diseases in humans. These sequences have a unique helical flexibility, which affects their biophysical properties. A number of biophysical properties of these sequences have been studied in the past except their surface-tethered monolayers. To address the effect of sequence context and the associated helical flexibility on TNR monolayers, disease-relevant TNRs from three flexibility groups were surface-assembled on gold surfaces. The properties of the TNR films were studied, including charge transfer resistance ( R ct ) by electrochemical impedance spectroscopy (EIS), surface density by chronocoulometry (CC), surface topography by atomic force microscopy (AFM), and electrical conductivity by conducting atomic force microscopy (C-AFM). We found that the TNR film properties are characteristically sequence dependent rather than being dependent on their flexibility rank reported in the literature. The characteristic properties of TNR films studied here may be used for engineering label-free biosensors to detect neurological disorders and build DNA bioelectronics.
more »
« less
- Award ID(s):
- 1940716
- PAR ID:
- 10157474
- Date Published:
- Journal Name:
- Journal of Materials Chemistry B
- ISSN:
- 2050-750X
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
A series of different high κ dielectrics such as HfO2, ZrO2, and Al2O3 thin films were studied as an alternative material for the possible replacement of traditional SiO2. These large areas, as well as conformal dielectrics thin films, were grown by the atomic layer deposition technique on a p-type silicon substrate at two different deposition temperatures (150 and 250 °C). Atomic force microscopic study reveals that the surface of the films is very smooth with a measured rms surface roughness value of less than 0.4 nm in some films. After the deposition of the high κ layer, a top metal electrode was deposited onto it to fabricate metal oxide semiconductor capacitor (MOSCAP) structures. The I–V curve reveals that the sample growth at high temperatures exhibits a high resistance value and lower leakage current densities. Frequency-dependent (100 kHz to 1 MHz) C–V characteristics of the MOSCAPs were studied steadily. Furthermore, we have prepared a metal oxide semiconductor field-effect transistor device with Al-doped ZnO as a channel material, and the electrical characteristic of the device was studied. The effect of growth temperature on the structure, surface morphology, crystallinity, capacitance, and dielectric properties of the high κ dielectrics was thoroughly analyzed through several measurement techniques, such as XRD, atomic force microscopy, semiconductor parameter analysis, and ultraviolet-visible spectroscopy.more » « less
-
null (Ed.)Crosslinked porous protein crystals are a new biomaterial that can be engineered to encapsulate, stabilize, and organize guest molecules, nanoparticles, and biological moieties. In this study, for the first time, the combined interactions of DNA strands with porous protein crystals are quantitatively measured by high-resolution atomic force microscopy (AFM) and chemical force microscopy. The surface structure of protein crystals with unusually large pores was observed in liquid via high-resolution AFM. Force–distance ( F – D ) curves were also obtained using AFM tips modified to present or capture DNA. The modification of AFM tips allowed the tips to covalently bind DNA that was pre-loaded in the protein crystal nanopores. The modified tips enabled the interactions of DNA molecules with protein crystals to be quantitatively studied while revealing the morphology of the buffer-immersed protein crystal surface in detail, thereby preserving the structure and properties of protein crystals that could be disrupted or destroyed by drying. The hexagonal space group was manifest at the crystal surface, as were the strong interactions between DNA and the porous protein crystals in question. In sum, this study furthered our understanding of how a new protein-based biomaterial can be used to bind guest DNA assemblies.more » « less
-
Machine learning approaches for improving atomic force microscopy instrumentation and data analyticsAtomic force microscopy (AFM) is a part of the scanning probe microscopy family. It provides a platform for high-resolution topographical imaging, surface analysis as well as nanomechanical property mapping for stiff and soft samples (live cells, proteins, and other biomolecules). AFM is also crucial for measuring single-molecule interaction forces and important parameters of binding dynamics for receptor-ligand interactions or protein-protein interactions on live cells. However, performing AFM measurements and the associated data analytics are tedious, laborious experimental procedures requiring specific skill sets and continuous user supervision. Significant progress has been made recently in artificial intelligence (AI) and deep learning (DL), extending into microscopy. In this review, we summarize how researchers have implemented machine learning approaches so far to improve the performance of atomic force microscopy (AFM), make AFM data analytics faster, and make data measurement procedures high-throughput. We also shed some light on the different application areas of AFM that have significantly benefited from applications of machine learning frameworks and discuss the scope and future possibilities of these crucial approaches.more » « less
-
This communication measures the inter-helical angle of the 10-23 DNAzyme-substrate complex by atomic force microscopy (AFM). specificity. Herein, we have devised a strategy to assemble the DNAzyme-substrate complex into a periodic DNA 2D array, which allows reliable study of the conformation of the 10-23 DNAzyme by AFM imaging and fast Fourier transform (FFT). Specifically, the angle between the two flanking helical domains of the catalytic core has been determined via the repeating distance of 2D array. We expect that the same strategy can generally be applicable for studying other nucleic acid structures.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1039/d0tb00507j
