Positioning Isolation and Biochemical Analysis of Single DNA Molecules Based on Nanomanipulation and Single-Molecule PCR

Single-Molecule Nanomechanical Genotyping with DNA Origami-Based Shape IDs

Atomic force microscopy (AFM)-based nanomechanical imaging provides a sub-10-nm-resolution approach for imaging biomolecules under ambient conditions. Here we describe how to generate a set of DNA origami-based shape IDs (triangular and cross shape, with and without streptavidin) to site-specifically label target genomic DNA sequences containing two single-nucleotide polymorphisms (SNPs). Adjacent labeling sites separated by only 30 nucleobases (~10 nm) can be differentiated under AFM imaging. We can directly genotype single molecules of human genomic DNA.

Enhancement of the polymerase chain reaction by tungsten disulfide

In this paper, we demonstrated that the polymerase chain reaction (PCR) could be dramatically enhanced by tungsten disulfide (WS₂). The results showed that the PCR efficiency could be increased with the addition of WS₂ and at a lower annealing temperature, which simplified the design and operation of PCR. Moreover, PCR with WS₂ showed better specificity and efficiency as compared with graphene oxide (GO) for a human genome DNA sample. The mechanism of enhancement of PCR by WS₂ was discussed according to the typical structure and the characteristics of selective adsorption of single-stranded DNA by WS₂. The results suggested that WS₂ as a PCR enhancer can promote the PCR performance and extend the PCR application in biomedical research, clinical diagnostic, and bioanalysis.

WS₂ as a PCR enhancer can promote the PCR performance and extend PCR bioapplication.

Nanomanipulation of Individual DNA Molecules Covered by Single-Layered Reduced Graphene Oxide Sheets on a Solid Substrate

Nanomanipulation of single DNA molecules has great potential in fundamental genetic research and clinical analysis, and is a good model system for studying the interfacial effects on physiochemical processes, which occur when manipulating the linear DNA molecules with an atomic force microscope (AFM) tip. Here, we demonstrate that AFM nanomanipulation can be carried out on DNA molecules covered by a single-layered reduced graphene oxide sheet. Nanomanipulation, which includes cutting, pushing, and sweeping operations, specific to the covered DNA molecules can be achieved in a well-controlled manner using AFM in the PeakForce Quantitative Nano-Mechanics mode. It was found that the normal force required to cut covered DNA strands is over five times greater than that required for naked strands. This technique provides a distinctive method for the construction of graphene architecture by tailoring the underlying artificial DNA nanostructures.

DNA origami-based shape IDs for single-molecule nanomechanical genotyping

Variations on DNA sequences profoundly affect how we develop diseases and respond to pathogens and drugs. Atomic force microscopy (AFM) provides a nanomechanical imaging approach for genetic analysis with nanometre resolution. However, unlike fluorescence imaging that has wavelength-specific fluorophores, the lack of shape-specific labels largely hampers widespread applications of AFM imaging. Here we report the development of a set of differentially shaped, highly hybridizable self-assembled DNA origami nanostructures serving as shape IDs for magnified nanomechanical imaging of single-nucleotide polymorphisms. Using these origami shape IDs, we directly genotype single molecules of human genomic DNA with an ultrahigh resolution of ∼10 nm and the multiplexing ability. Further, we determine three types of disease-associated, long-range haplotypes in samples from the Han Chinese population. Single-molecule analysis allows robust haplotyping even for samples with low labelling efficiency. We expect this generic shape ID-based nanomechanical approach to hold great potential in genetic analysis at the single-molecule level.

Silicone oil promotes amyloid-like aggregation of αB-crystallin

Silicone oil induced changes of secondary structures of αB-crystallin (CRYAB) and promoted its aggregation into amyloid-like nanostructures.

Gold nanoparticle-assisted polymerase chain reaction: effects of surface ligands, nanoparticle shape and material

The concentration, shape, material, and surface functionalization effects of gold nanoparticles on PCR outcome have been studied with two PCR gene diagnostic models.

The regulation of PCR by thiolated single-stranded DNA for enhanced specificity

5′-end 6-mercapto-1-hexane-labeled single-stranded DNA (HS-ssDNA) can dramatically enhance the specificity of DNA duplication during the polymerase chain reaction (PCR).

Genetic analysis with nanoPCR

Polymerase chain reaction (PCR) has become a standard and important molecular biological technique with numerous applications in genetic analysis, forensics and in vitro diagnostics. Since its invention in the 1980s, there has been dramatic performance improvement arising from long-lasting efforts to optimize amplification conditions in both academic studies and commercial applications. More recently, a range of nanometer-sized materials including metal nanoparticles, semiconductor quantum dots, carbon nanomaterials and polymer nanoparticles, have shown unique effects in tuning amplification processes of PCR. It is proposed that these artificial nanomaterials mimic protein components in the natural DNA replication machinery in vivo. These so-called nanomaterials-assisted PCR (nanoPCR) strategies shed new light on powerful PCR with unprecedented sensitivity, selectivity and extension rate. In this review, we aim to summarize recent progress in this direction and discuss possible mechanisms for such performance improvement and potential applications in genetic analysis (particularly gene typing and haplotyping) and diagnostics.

Special Feature — Nanobiotechnology/Nanomedicine

Applications of Nanomedicine.

A Comprehensive Overview of the Development and Prospects of Nanobiotechnology in China.

Nanobiotechnology in the Republic of Korea.

Nanomedicine: Prospective Diagnostic and Therapeutic Potentials.

Nanotechnology: What it is and how it can be Applied in Healthcare.

Optimizing single DNA molecules manipulation by AFM

Recent progress in single DNA manipulation with atomic force microscope has proved its potential in analysing genetic information at the molecular level instead of macro ensemble approach. However, current manipulation of DNA is mainly carried out by manual operations, which is labour-intensive and time-consuming, thus limits the further applications in other fields. In this paper, an optimized DNA manipulation method is successfully established. An image correlation technique is introduced to realize automatic thermal drift compensation. Combined with elaborately designed tip movement control for different manipulation purposes, accurate and efficient DNA manipulations such as dissection, folding and picking are realized. The efficiency has been improved for an order of magnitude compare to manual manipulations, whereas the performance is demonstrated to be the same. This newly developed method has shed light on high-efficiency nanomanipulation of small molecules with complex structures, and thus provides the possibility of deeply understanding the intrinsic properties of single biomolecules.

A new DNA combing method for biochemical analysis

A simple molecular combing method for analysis of biochemical reactions, called the moving droplet method, has been developed. In this method, small droplets containing DNA molecules run down a sloped glass substrate, and this creates a moving interface among the air, droplet, and substrate that stretches the DNA molecules. This method requires a much smaller volume of sample solution than other established combing methods, allowing wider application in various fields. Using this method, lambdaDNA molecules were stretched and absorbed to a glass substrate, and single-molecule analysis of DNA synthesis by DNA polymerases was performed.

Nanoparticle superstructures made by polymerase chain reaction: collective interactions of nanoparticles and a new principle for chiral materials

Polymerase chain reaction (PCR) was realized on the surface of gold nanoparticles (NPs) as a tool for self-organization at nanoscale and as a step toward programmable production of sufficient quantities of functional metallic superstructures. The assembly is controlled by varying the density of the primer on the surface of gold NPs and the number of PCR cycles generating a mixture of dimers, trimers, tetramers, etc., with gradually increasing complexity. This process leads to strong chirality of the assemblies arising from the three-dimensional positioning of NPs in space which had never been observed before. A circular dichroism band of the superstructures coincides with the plasmon oscillations of the multi-NP systems of Au colloids. This new collective optical property of NPs embracing the diversity of shapes and diameters in the starting dispersions opens unique opportunities for the development of negative index materials.

Optimization of specimen preparation of thin cell section for AFM observation

High resolution imaging of intracellular structures of ultrathin cell section samples is critical to the performance of precise manipulation by atomic force microscopy (AFM). Here, we test the effect of multiple factors during section sample preparation on the quality of the AFM image. These factors include the embedding materials, the annealing process of the specimen block, section thickness, and section side. We found that neither the embedding materials nor the temperature and speed of the annealing process has any effect on AFM image resolution. However, the section thickness and section side significantly affect the surface topography and AFM image resolution. By systematically testing the image quality of both sides of cell sections over a wide range of thickness (40-1000 nm), we found that the best resolution was obtained with upper-side sections approximately 50-100 nm thick. With these samples, we could observe precise structure details of the cell, including its membrane, nucleoli, and other organelles. Similar results were obtained for other cell types, including Tca8113, C6, and ECV-304. In brief, by optimizing the condition of ultrathin cell section preparation, we were able to obtain high resolution intracellular AFM images, which provide an essential basis for further AFM manipulation.

A combined atomic force/fluorescence microscopy technique to select aptamers in a single cycle from a small pool of random oligonucleotides

We develop a method, which utilizes a combined atomic force microscope (AFM)/fluorescence microscope and small copy number polymerase chain reaction (PCR), to affinity-select individual aptamer species in a single cycle from a small pool of random-sequence oligonucleotides (oligos). In this method, a library of small beads, each of which is functionalized with fluorescent oligos of different sequences, is created. This library of oligo-functionalized beads is flowed over immobilized target molecules on a glass cover slip. High-affinity target-specific aptamers bind tightly to the target for prolonged periods and resist subsequent washes, resulting in a strong fluorescence signal on the substrate surface. This signal is observed from underneath the sample via fluorescence microscopy. The AFM tip, situated above the sample, is then directed to the coordinates of the fluorescence signal and is used to capture a three-dimensional high-resolution image of the surface-bound bead and to extract the bead (plus attached oligo). The extracted oligo is PCR-amplified, sequenced, and may then be subjected to further biochemical analysis. Here, we describe the underlying principles of this method, the required microscopy instrumentation, and the results of proof-of-principle experiments. In these experiments, we selected aptamers in eight trials from a binary pool containing a 1:1 mixture of thrombin aptamer oligo and a nonsense oligo. In each of the eight trials, the positive control aptamer was successfully detected, imaged, extracted, and characterized by PCR amplification and sequencing. In no case was the nonsense oligo selected, indicating good selectivity at this early stage of technology development.

Creation of Cadmium Sulfide Nanostructures Using AFM Dip-Pen Nanolithography

A dip-pen nanolithography (DPN) process capable of depositing nanoscaled structures of semiconducting CdS materials was developed by careful control of the reaction speed between the precursors. The new development expanded the scope of the powerful DPN process and provided more insight in the deposition mechanism. Features ranging from several hundreds of nanometers to sub-50 nanometers were generated and characterized. The effects of the surface property of the substrate, the relative humidity, the translating rate, and the temperature were systematically investigated. X-ray photoelectron spectroscopy (XPS) was used to verify the chemical composition of the patterns. In principle, this simple and convenient method should be applicable to deposit various metal sulfides on suitable substrates.

Radial compression elasticity of single DNA molecules studied by vibrating scanning polarization force microscopy

The radial compression properties of single DNA molecules have been studied using vibrating scanning polarization force microscopy. By imaging DNA molecules at different vibration amplitude set-point values, we obtain the correlations between radially applied force and DNA compression, from which the radial compressive elasticity can be deduced. The estimated elastic modulus is approximately 20-70 MPa under small external forces (<0.4 nN) and increases to approximately 100-200 MPa for large loads.