Analysis of DNA Replication by Optical Mapping in Nanochannels

DNA replication is essential to maintain genome integrity in S phase of the cell division cycle. Accumulation of stalled replication forks is a major source of genetic instability, and likely constitutes a key driver of tumorigenesis. The mechanisms of regulation of replication fork progression have therefore been extensively investigated, in particular with DNA combing, an optical mapping technique that allows the stretching of single molecules and the mapping of active region for DNA synthesis by fluorescence microscopy. DNA linearization in nanochannels has been successfully used to probe genomic information patterns along single chromosomes, and has been proposed to be a competitive alternative to DNA combing. Yet this conjecture remains to be confirmed experimentally. Here, two complementary techniques are established to detect the genomic distribution of tracks of newly synthesized DNA in human cells by optical mapping in nanochannels. Their respective advantages and limitations are compared, and applied them to detect deregulations of the replication program induced by the antitumor drug hydroxyurea. The developments here thus broaden the field of applications accessible to nanofluidic technologies, and can be used in the future as part for molecular diagnostics in the context of high throughput cancer drug screening.     

Flossing DNA in a Dual Nanopore Device

Solid‐state nanopores are a single‐molecule technique that can provide access to biomolecular information that is otherwise masked by ensemble averaging. A promising application uses pores and barcoding chemistries to map molecular motifs along single DNA molecules. Despite recent research breakthroughs, however, it remains challenging to overcome molecular noise to fully exploit single‐molecule data. Here, an active control technique termed “flossing” that uses a dual nanopore device is presented to trap a proteintagged DNA molecule and up to 100's of back‐and‐forth electrical scans of the molecule are performed in a few seconds. The protein motifs bound to 48.5 kb λ‐DNA are used as detectable features for active triggering of the bidirectional control. Molecular noise is suppressed by averaging the multiscan data to produce averaged intertag distance estimates that are comparable to their known values. Since nanopore feature‐mapping applications require DNA linearization when passing through the pore, a key advantage of flossing is that trans‐pore linearization is increased to >98% by the second scan, compared to 35% for single nanopore passage of the same set of molecules. In concert with barcoding methods, the dual‐pore flossing technique could enable genome mapping and structural variation applications, or mapping loci of epigenetic relevance.     

Fabrication of nanofluidic biochips with nanochannels for applications in DNA analysis

With the development of nanotechnology, great progress has been made in the fabrication of nanochannels. Nanofluidic biochips based on nanochannel structures allow biomolecule transport, bioseparation, and biodetection. The domain applications of nanofluidic biochips with nanochannels are DNA stretching and separation. In this Review, the general fabrication methods for nanochannel structures and their applications in DNA analysis are discussed. These representative fabrication approaches include conventional photolithography, interference lithography, electron-beam lithography, nanoimprint lithography and polymer nanochannels. Other nanofabrication methods used to fabricate unique nanochannels, including sub-10-nm nanochannels, single nanochannels, and vertical nanochannels, are also mentioned. These nanofabrication methods provide an effective way to form nanoscale channel structures for nanofluidics and biosensor devices for DNA separation, detection, and sensing. The broad applications of nanochannels and future perspectives are also discussed.     

Micrometer‐sized DNA–Single‐Fluorophore–DNA Supramolecule: Synthesis and Single‐Molecule Characterization

The synthesis of single‐fluorophore‐bis(micrometer‐sized DNA) triblock supramolecules and the optical and structural characterization of the construct at the single‐molecule level is reported. A fluorophore‐bis(oligodeoxynucleotide) triblock is synthesized via the amide‐coupling reaction. Subsequent protocols of DNA hybridization/ligation are developed to form the supramolecular triblock structure with λ‐DNA fragments on the micrometer length scale. The successful synthesis of the micrometer‐sized DNA–single‐fluorophore–DNA supramolecule is confirmed by agarose gel electrophoresis with fluorescence imaging under UV excitation. Single triblock structures are directly imaged by combined scanning force microscopy and single‐molecule fluorescence microscopy, and provide unambiguous confirmation of the existence of the single fluorophore inserted in the middle of the long DNA. This type of triblock structure is a step closer to providing a scaffold for single‐molecule electronic devices after metallization of the DNAs.     

Tuneable elastomeric nanochannels for nanofluidic manipulation

Fluidic transport through nanochannels offers new opportunities to probe fundamental nanoscale transport phenomena and to develop tools for manipulating DNA, proteins, small molecules and nanoparticles. The small size of nanofabricated devices and the accompanying increase in the effect of surface forces, however, pose challenges in designing and fabricating flexible nanofluidic systems that can dynamically adjust their transport characteristics according to the handling needs of various molecules and nanoparticles. Here, we describe the use of nanoscale fracturing of oxidized poly(dimethylsiloxane) to conveniently fabricate nanofluidic systems with arrays of nanochannels that can actively manipulate nanofluidic transport through dynamic modulation of the channel cross-section. We present the design parameters for engineering material properties and channel geometry to achieve reversible nanochannel deformation using remarkably small forces. We demonstrate the versatility of the elastomeric nanochannels through tuneable sieving and trapping of nanoparticles, dynamic manipulation of the conformation of single DNA molecules and in situ photofabrication of movable polymeric nanostructures.     

Perspectives and Challenges of Emerging Single‐Molecule DNA Sequencing Technologies

The growing demand for analysis of the genomes of many species and cancers, for understanding the role of genetic variation among individuals in disease, and with the ultimate goal of deciphering individual human genomes has led to the development of non‐Sanger reaction‐based technologies towards rapid and inexpensive DNA sequencing. Recent advancements in new DNA sequencing technologies are changing the scientific horizon by dramatically accelerating biological and biomedical research and promising an era of personalized medicine for improved human health. Two single‐molecule sequencing technologies based on fluorescence detection are already in a working state. The newly launched and emerging single‐molecule DNA sequencing approaches are reviewed here. The current challenges of these technologies and potential methods of overcoming these challenges are critically discussed. Further research and development of single‐molecule sequencing will allow researchers to gather nearly error‐free genomic data in a timely and inexpensive manner.

     

Dynamic Curvature Nanochannel‐Based Membrane with Anomalous Ionic Transport Behaviors and Reversible Rectification Switch

Biological nanochannels control the movements of different ions through cell membranes depending on not only those channels' static inherent configurations, structures, inner surface's physicochemical properties but also their dynamic shape changes, which are required in various essential functions of life processes. Inspired by ion channels, many artificial nanochannel‐based membranes for nanofluidics and biosensing applications have been developed to regulate ionic transport behaviors by using the functional molecular modifications at the inner surface of nanochannel to achieve a stimuli‐responsive layer. Here, the concept of a dynamic nanochannel system is further developed, which is a new way to regulate ion transport in nanochannels by using the dynamic change in the curvature of channels to adjust ionic rectification in real time. The dynamic curvature nanochannel‐based membrane displays the advanced features of the anomalous effect of voltage, concentration, and ionic size for applying simultaneous control over the curvature‐tunable asymmetric and reversible ionic rectification switching properties. This dynamic approach can be used to build smart nanochannel‐based systems, which have strong implications for flexible nanofluidics, ionic rectifiers, and power generators.     

Controlling DNA Tug‐of‐War in a Dual Nanopore Device

Methods for reducing and directly controlling the speed of DNA through a nanopore are needed to enhance sensing performance for direct strand sequencing and detection/mapping of sequence‐specific features. A method is created for reducing and controlling the speed of DNA that uses two independently controllable nanopores operated with an active control logic. The pores are positioned sufficiently close to permit cocapture of a single DNA by both pores. Once cocapture occurs, control logic turns on constant competing voltages at the pores leading to a “tug‐of‐war” whereby opposing forces are applied to regions of the molecules threading through the pores. These forces exert both conformational and speed control over the cocaptured molecule, removing folds and reducing the translocation rate. When the voltages are tuned so that the electrophoretic force applied to both pores comes into balance, the life time of the tug‐of‐war state is limited purely by diffusive sliding of the DNA between the pores. A tug‐of‐war state is produced on 76.8% of molecules that are captured with a maximum two‐order of magnitude increase in average pore translocation time relative to the average time for single‐pore translocation. Moreover, the translocation slow‐down is quantified as a function of voltage tuning and it is shown that the slow‐down is well described by a first passage analysis for a 1D subdiffusive process. The ionic current of each nanopore provides an independent sensor that synchronously measures a different region of the same molecule, enabling sequential detection of physical labels, such as monostreptavidin tags. With advances in devices and control logic, future dual‐pore applications include genome mapping and enzyme‐free sequencing.     

Cover Picture: Length‐Dependent Uptake of DNA‐Wrapped Single‐Walled Carbon Nanotubes (Adv. Mater. 7/2007)

Well‐defined length fractions of DNA‐wrapped single‐walled carbon nanotubes (SWNTs) of below 200 nm are taken up preferentially by IMR‐90 human lung fibroblasts, while longer DNA wrapped SWNTs are excluded from the cell interior (inset), report Matt Becker and coworkers on p. 939. The cover image construct includes overlaid images of the labeled cell membrane, the nuclei (blue), and the fluorescently labeled DNA wrapped SWNTs (red) that have gained access to the cell interior.     

Bioinspired Smart Gating of Nanochannels Toward Photoelectric‐Conversion Systems

Learning from nature has inspired the creation of intelligent materials to better understand and imitate biology. Recent studies on bioinspired responsive surfaces that can switch between different states are shown, which open up new avenues for the development of smart materials in two dimensions. Based on this strategy, biomimetic nanochannel systems have been produced by introducing responsive molecules, which closely mimic the gating mechanism of biological nanochannels and show potential applications in many fields such as photoelectric‐conversion systems demonstrated in this paper.     

Non-planar nanofluidic devices for single molecule analysis fabricated using nanoglassblowing

A method termed 'nanoglassblowing' is presented for fabricating integrated microfluidic and nanofluidic devices with gradual depth changes and wide, shallow nanochannels. This method was used to construct fused silica channels with out-of-plane curvature of channel covers from over ten micrometers to a few nanometers, nanochannel aspect ratios smaller than 2 × 10(-5):1 (depth:width), and nanochannel depths as shallow as 7?nm. These low aspect ratios and shallow channel depths would be difficult to form otherwise without collapse of the channel cover, and the gradual changes in channel depth eliminate abrupt free energy barriers at the transition from microfluidic to nanofluidic regions. Devices were characterized with atomic force microscopy (AFM), white light interferometry, scanned height measurements, fluorescence intensity traces, and single molecule analysis of double-stranded deoxyribonucleic acid (DNA) velocity and conformation. Nanochannel depths and aspect ratios formed by nanoglassblowing allowed measurements of the radius of gyration, R(g), of single λ?DNA molecules confined to slit-like nanochannels with depths, d, ranging from 11?nm to 507?nm. Measurements of R(g) as a function of d agreed qualitatively with the scaling law R(g)∝d(-0.25) predicted by Brochard for nanochannel depths from 36?nm to 156?nm, while measurements of R(g) in 11?nm and 507?nm deep nanochannels deviated from this prediction.     

Lipid-based passivation in nanofluidics

Stretching DNA in nanochannels is a useful tool for direct, visual studies of genomic DNA at the single molecule level. To facilitate the study of the interaction of linear DNA with proteins in nanochannels, we have implemented a highly effective passivation scheme based on lipid bilayers. We demonstrate virtually complete long-term passivation of nanochannel surfaces to a range of relevant reagents, including streptavidin-coated quantum dots, RecA proteins, and RecA-DNA complexes. We show that the performance of the lipid bilayer is significantly better than that of standard bovine serum albumin-based passivation. Finally, we show how the passivated devices allow us to monitor single DNA cleavage events during enzymatic degradation by DNase I. We expect that our approach will open up for detailed, systematic studies of a wide range of protein-DNA interactions with high spatial and temporal resolution.     

Engineering of the Fluorescent‐Energy‐Conversion Arm of Phi29 DNA Packaging Motor for Single‐Molecule Studies

The bacteriophage phi29 DNA packaging motor contains a protein core with a central channel comprising twelve copies of re‐engineered gp10 protein geared by six copies of packaging RNA (pRNA) and a DNA packaging protein gp16 with unknown copies. Incorporation of this nanomotor into a nanodevice would be beneficial for many applications. To this end, extension and modification of the motor components are necessary for the linkage of this motor to other nanomachines. Here the re‐engineering of the motor DNA packaging protein gp16 by extending its length and doubling its size using a fusion protein technique is reported. The modified motor integrated with the eGFP‐gp16 maintains the ability to convert the chemical energy from adenosine triphosphate (ATP) hydrolysis to mechanical motion and package DNA. The resulting DNA‐filled capsid is subsequently converted into an infectious virion. The extended part of the gp16 arm is a fluorescent protein eGFP, which serves as a marker for tracking the motor in single‐molecule studies. The activity of the re‐engineered motor with eGFP‐gp16 is also observed directly with a bright‐field microscope via its ability to transport a 2‐µm‐sized cargo bound to the DNA.     

Identifying DNA methylation in a nanochannel

DNA methylation is a stable epigenetic modification, which is well known to be involved in gene expression regulation. In general, however, analyzing DNA methylation requires rather time consuming processes (24–96 h) via DNA replication and protein modification. Here we demonstrate a methodology to analyze DNA methylation at a single DNA molecule level without any protein modifications by measuring the contracted length and relaxation time of DNA within a nanochannel. Our methodology is based on the fact that methylation makes DNA molecules stiffer, resulting in a longer contracted length and a longer relaxation time (a slower contraction rate). The present methodology offers a promising way to identify DNA methylation without any protein modification at a single DNA molecule level within 2 h.     

Fabrication of Metallized Nanopores in Silicon Nitride Membranes for Single‐Molecule Sensing

The fabrication and characterization of a metallized nanopore structure for the sensing of single molecules is described. Pores of varying diameters (>10 nm) are patterned into free‐standing silicon nitride membranes by electron‐beam lithography and reactive ion etching. Structural characterization by transmission electron microscopy (TEM) and tomography reveals a conical pore shape with a 40° aperture. Metal films of Ti/Au are vapor deposited and the pore shape and shrinking are studied as a function of evaporated film thickness. TEM tomography analysis confirms metalization of the inner pore walls as well as conservation of the conical pore shape. In electrical measurements of the transpore current in aqueous electrolyte solution, the pores feature very low noise. The applicability of the metallized pores for stochastic sensing is demonstrated in real‐time translocation experiments of single λ‐DNA molecules. We observe exceptionally long‐lasting current blockades with a fine structure of distinct current levels, suggesting an attractive interaction between the DNA and the PEGylated metallic pore walls.     

Surface Modification of Solid‐State Nanopores for Sticky‐Free Translocation of Single‐Stranded DNA

Nanopore technology is one of the most promising approaches for fast and low‐cost DNA sequencing application. Single‐stranded DNA detection is primary objective in such device, while solid‐state nanopores remain less explored than their biological counterparts due to bio‐molecule clogging issue caused by surface interaction between DNA and nanopore wall. By surface coating a layer of polyethylene glycol (PEG), solid‐state nanopore can achieve long lifetime for single‐stranded DNA sticky‐free translocation at pH 11.5. Associated with elimination of non‐specific binding of molecule, PEG coated nanopore presents new surface characteristic as less hydrophility, lower 1/f noise, and passivated surface charge responsiveness on pH. Meanwhile, conductance blockage of single‐stranded DNA is found to be deeper than double‐stranded DNA, which can be well described by a string of blobs model for a quasi‐equilibrium state polymer in constraint space.     

Nanoplumbing with 2D Metamaterials

Complex manipulations of DNA in a nanofluidic device require channels with branches and junctions. However, the dynamic response of DNA in such nanofluidic networks is relatively unexplored. Here, the transport of DNA in a 2D metamaterial made by arrays of nanochannel junctions is investigated. The mechanism of transport is explained as Brownian motion through an energy landscape formed by the combination of the confinement free energy of DNA and the effective potential of hydrodynamic flow, which both can be tuned independently within the device. For the quantitative understanding of DNA transport, a dynamic mean‐field model of DNA at a nanochannel junction is proposed. It is shown that the dynamics of DNA in a nanofluidic device with branched channels and junctions is well described by the model.     

Modulation of Interparticle Distance in Discrete Gold Nanoparticle Dimers and Trimers by DNA Single‐Base Pairing

Self‐assembled structures of metallic nanoparticles with dynamically changeable interparticle distance hold promise for the regulation of collective physical properties. This paper describes gold nanoparticle dimers and trimers that exhibit spontaneous and reversible changes in interparticle distance. To exploit this property, a gold nanoparticle is modified with precisely one long DNA strand and approximately five short DNA strands. The long DNA serves to align the nanoparticles on a template DNA via hybridization, while the short DNAs function to induce the interparticle distance changes. The obtained dimer and trimer are characterized with gel electrophoresis, dynamic light scattering measurements, and transmission electron microscopy (TEM). When the complementary short DNA is added to form the fully matched duplexes on the particle surface in the presence of MgCl₂, spontaneous reduction of the interparticle distance is observed with TEM and cryo‐electron microscopy. By contrast, when the terminal‐mismatched DNA is added, no structural change occurs under the same conditions. Therefore, the single base pairing/unpairing at the outermost surface of the nanoparticle impacts the interparticle distance. This unique feature could be applied to the regulation of structures and properties of various DNA‐functionalized nanoparticle assemblies.     

Cross‐Talk Between Ionic and Nanoribbon Current Signals in Graphene Nanoribbon‐Nanopore Sensors for Single‐Molecule Detection

Nanopores are now being used not only as an ionic current sensor but also as a means to localize molecules near alternative sensors with higher sensitivity and/or selectivity. One example is a solid‐state nanopore embedded in a graphene nanoribbon (GNR) transistor. Such a device possesses the high conductivity needed for higher bandwidth measurements and, because of its single‐atomic‐layer thickness, can improve the spatial resolution of the measurement. Here measurements of ionic current through the nanopore are shown during double‐stranded DNA (dsDNA) translocation, along with the simultaneous response of the neighboring GNR due to changes in the surrounding electric potential. Cross‐talk originating from capacitive coupling between the two measurement channels is observed, resulting in a transient response in the GNR during DNA translocation; however, a modulation in device conductivity is not observed via an electric‐field‐effect response during DNA translocation. A field‐effect response would scale with GNR source–drain voltage (V_ds), whereas the capacitive coupling does not scale with V_ds. In order to take advantage of the high bandwidth potential of such sensors, the field‐effect response must be enhanced. Potential field calculations are presented to outline a phase diagram for detection within the device parameter space, charting a roadmap for future optimization of such devices.