Towards single-molecule DNA sequencing: assays with low nonspecific adsorption

Fabrication strategies for chiral self-assembly surface

Chiral self-assembly is the spontaneous organization of individual building blocks from chiral (bio)molecules to macroscopic objects into ordered superstructures. Chiral self-assembly is ubiquitous in nature, such as DNA and proteins, which formed the foundation of biological structures. In addition to chiral (bio) molecules, chiral ordered superstructures constructed by self-assembly have also attracted much attention. Chiral self-assembly usually refers to the process of forming chiral aggregates in an ordered arrangement under various non-covalent bonding such as H-bond, π-π interactions, van der Waals forces (dipole-dipole, electrostatic effects, etc.), and hydrophobic interactions. Chiral assembly involves the spontaneous process, which followed the minimum energy rule. It is essentially an intermolecular interaction force. Self-assembled chiral materials based on chiral recognition in electrochemistry, chiral catalysis, optical sensing, chiral separation, etc. have a broad application potential with the research development of chiral materials in recent years.

DNA skybridge: 3D structure producing a light sheet for high-throughput single-molecule imaging

Real-time visualization of single-proteins or -complexes on nucleic acid substrates is an essential tool for characterizing nucleic acid binding proteins. Here, we present a novel surface-condition independent and high-throughput single-molecule optical imaging platform called ‘DNA skybridge’. The DNA skybridge is constructed in a 3D structure with 4 μm-high thin quartz barriers in a quartz slide. Each DNA end is attached to the top of the adjacent barrier, resulting in the extension and immobilization of DNA. In this 3D structure, the bottom surface is out-of-focus when the target molecules on the DNA are imaged. Moreover, the DNA skybridge itself creates a thin Gaussian light sheet beam parallel to the immobilized DNA. This dual property allows for imaging a single probe-tagged molecule moving on DNA while effectively suppressing interference with the surface and background signals from the surface.

Exonucleolytic degradation of high-density labeled DNA studied by fluorescence correlation spectroscopy

The exonucleolytic degradation of high-density labeled DNA by exonuclease III was monitored using two-color fluorescence correlation spectroscopy (FCS). One strand of the double stranded template DNA was labeled on either one or two base types and additionally at one end via a 5' Cy5 tagged primer. Exonucleolytic degradation was followed via the diffusion time, the brightness of the remaining DNA as well as the concentration of released labeled bases. We found a hydrolyzation rate of about 11 to 17 nucleotides per minute per enzyme (nt/min/enzyme) for high-density labeled DNA, which is by a factor of about 4 slower than for unlabeled DNA. The exonucleolytic degradation of a 488 base pair long double stranded DNA resulted in a short double stranded DNA segment of 112 ± 40 base pairs (bp) length with two single-stranded tails.

Enhancing single molecule imaging in optofluidics and microfluidics

Microfluidics and optofluidics have revolutionized high-throughput analysis and chemical synthesis over the past decade. Single molecule imaging has witnessed similar growth, due to its capacity to reveal heterogeneities at high spatial and temporal resolutions. However, both resolution types are dependent on the signal to noise ratio (SNR) of the image. In this paper, we review how the SNR can be enhanced in optofluidics and microfluidics. Starting with optofluidics, we outline integrated photonic structures that increase the signal emitted by single chromophores and minimize the excitation volume. Turning then to microfluidics, we review the compatible functionalization strategies that reduce noise stemming from non-specific interactions and architectures that minimize bleaching and blinking.

New nucleotide analogues with enhanced signal properties

We describe synthesis and testing of a novel type of dye-modified nucleotides which we call macromolecular nucleotides (m-Nucs). Macromolecular nucleotides comprise a nucleotide moiety, a macromolecular linear linker, and a large macromolecular ligand carrying multiple fluorescent dyes. With incorporation of the nucleotide moiety into the growing nucleic acid strand during enzymatic synthesis, the macromolecular ligand together with the coupled dyes is bound to the nucleic acid. By the use of this new class of modified nucleotides, signals from multiple dye molecules can be obtained after a single enzymatic incorporation event. The modified nucleotides are considered especially useful in the fields of nanobiotechnology, where signal stability and intensity is a limiting factor.

Evaluation of non-specific binding suppression schemes for neutravidin and alkaline phosphatase at the surface of reticulated vitreous carbon electrodes

Non-specific binding (NSB) of high-molecular-weight proteins onto electrode surfaces can complicate the application of electroanalytical techniques to clinical and environmental research, particularly in biosensor applications. We present herein various strategies to modify the surface of reticulated vitreous carbon (RVC) electrodes to suppress non-specific binding of biomolecules onto its surface. Non-specific binding and specific binding (SB) of two enzyme conjugates, neutravidin-alkaline phosphatase (NA-ALP) and biotinylated alkaline phosphatase (B-ALP), and also neutravidin itself, were studied using hydroquinone diphosphate (HQDP) as an enzyme substrate for ALP inside the pores of RVC electrodes that had been subjected to various modification schemes. The extent of NSB and SB of these biomolecules inside RVC pores was assessed by measuring the initial rate of generation of an electroactive product, hydroquinone (HQ), of the enzyme-catalyzed reaction, using linear scan voltammetry (LSV) for HQ detection. Electrodes functionalized with phenylacetic acid and poly(ethylene glycol) (PEG) showed low NSB and high SB (when biotin capture ligands were included in the modification scheme) in comparison with unmodified electrodes and RVC electrodes modified in other ways. A simple sandwich bioassay for neutravidin was performed on the RVC electrode with the lowest NSB. A concentration detection limit of 52+/-2 ng mL(-1) and an absolute detection limit of 5.2+/-0.2 ng were achieved for neutravidin when this assay was performed using a 100 microL sample size.

Comparison of the nonspecific binding of DNA-conjugated gold nanoparticles between polymeric and monomeric self-assembled monolayers

The nonspecific binding of DNA-conjugated gold nanoparticles (AuNPs) to solid surfaces is more difficult to control than that of DNA molecules due to the more attractive interactions from the large number of DNA molecules per AuNP. This paper reports that the polymeric self-assembled monolayers (SAMs) formed on indium-tin oxide (ITO) electrodes significantly inhibit the nonspecific binding of DNA-conjugated AuNPs. The random copolymers used to prepare the polymeric SAMs consist of three functional parts: an ITO-reactive silane group, a DNA-blocking poly(ethylene glycol) (PEG) group, and an amine-reactive N-acryloxysuccinimide group. In order to compare the polymeric SAMs with various monomeric SAMs, the relative nonspecific binding of the DNA-conjugated AuNPs to the ITO electrodes modified with (3-aminopropyl)triethoxysilane (APTES), 3-aminopropylphosphonic acid, 3-phosphonopropionic acid, or 11-phosphonoundecanoic acid is examined by measuring the electrocatalytic anodic current of hydrazine caused by the nonspecifically absorbed AuNPs and by counting the AuNPs adsorbed onto modified ITO electrodes. Carboxylic-acid-terminated and amine-terminated monomeric SAMs cause high levels of nonspecific binding of DNA-conjugated AuNPs. The monomeric SAM modified with the carboxylic-acid-terminated poly(amidoamine) dendrimer shows low levels of nonspecific binding (2.0% nonspecific binding relative to APTES) due to the high surface density of the negative charge. The simply prepared polymeric SAM produces the lowest level of nonspecific binding (0.8% nonspecific binding relative to APTES), resulting from the combined effect of (i) DNA-blocking PEG and carboxylic acid groups and (ii) dense polymeric SAMs. Therefore, thin and dense polymeric SAMs may be effective in electrochemical detection and easy DNA immobilization along with low levels of nonspecific binding.

Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures

Optical nanostructures have enabled the creation of subdiffraction detection volumes for single-molecule fluorescence microscopy. Their applicability is extended by the ability to place molecules in the confined observation volume without interfering with their biological function. Here, we demonstrate that processive DNA synthesis thousands of bases in length was carried out by individual DNA polymerase molecules immobilized in the observation volumes of zero-mode waveguides (ZMWs) in high-density arrays. Selective immobilization of polymerase to the fused silica floor of the ZMW was achieved by passivation of the metal cladding surface using polyphosphonate chemistry, producing enzyme density contrasts of glass over aluminum in excess of 400:1. Yields of single-molecule occupancies of approximately 30% were obtained for a range of ZMW diameters (70-100 nm). Results presented here support the application of immobilized single DNA polymerases in ZMW arrays for long-read-length DNA sequencing.

Immobilization of Biomolecules on Cycloolefin Polymer Supports

Recent trends in the development of microfluidic and biodiagnostic chips favor polymer materials over glass, primarily for optical and economical reasons. Therefore, existing chemical methods to prepare biomolecule microarrays on glass slides have to be adapted or replaced in order to suit polymer substrates. Here we present a strategy to immobilize DNA and antibodies on cyclic polyolefin slides, like Zeonor. This polymer represents a class of new polymeric materials with excellent optical and mechanical properties. By plasma and liquid chemical treatment followed by coating with polyelectrolytes, we have succeeded in immobilizing DNA onto the polymer substrate, yielding stable and versatile biosensor surfaces. We demonstrate the stability and usage of the coated Zeonor substrates not only in DNA chip technology but also in protein chip technology with DNA-directed immobilization of proteins.