On-site manipulation of single chromosomal DNA molecules by using optically driven microstructures

We report a novel method for manipulation of single giant DNA molecules under a video microscope. Using optically driven microstructures, we manipulated chromosomal DNA of length in the order of millimetres, extended by electroosmotic flow without DNA breakage in aqueous solution: we picked up DNA, using microfabricated hooks and wound it around microfabricated bobbins.     

Electrophoretic separation of DNA using a new matrix in uncoated capillaries

A new separation matrix, consisting of polymer poly(N-isopropylacrylamide) (PNIPAM) and small molecule additive mannitol, was used for double-stranded (ds) DNA and plasmid DNA separation by capillary electrophoresis. The matrix had a low viscosity, which made it very easy to handle. The additive mannitol dramatically enhanced the sieving performance of PNIPAM in TBE buffer. The optimal mannitol concentration 6% in polymer solution, was determined with the consideration of both speed and resolution. A resolution of 0.95 was achieved on the separation of 271/281 bp in the phiX174/HaeIII digest by using 1.5% PNIPAM + 6% mannitol, while the supercoiled, linear and nicked conformers of lambda plasmid were separated in 1% PNIPAM + 6% mannitol, demonstrating the potential use of this new matrix for effective DNA separations. The dramatic impact of mannitol on sieving performance of PNIPAM solution was investigated. pH dependent self-coating ability of PNIPAM was revealed. The presence of mannitol in TBE buffer decreased the pH of the buffer, which led to more efficient self-coating ability of PNIPAM probable due to the formation of hydrogen bonds between PNIPAM molecules and silanol groups at the silica wall.     

Electrophoretic separation of linear and supercoiled DNA in uncoated capillaries.

We report electrophoretic separation of supercoiled plasmids (2-16 kilo base pairs) and linear double-stranded DNA (0.6-23 kilo base pairs) in uncoated capillaries filled with dilute hydroxyethylcellulose. Because electroosmotic flow reverses the order of elution, long plasmids spend less time in the capillary and their bandwidths are narrower than observed in coated capillaries. However, resolution is similar to that obtained in coated capillaries, because it is governed by the distribution of unresolved topoisomers. In the presence of electroosmotic flow migration of supercoiled plasmids does not follow the elastic rod model that has been observed in coated capillaries.     

Compaction dynamics of single DNA molecules under tension

Using transverse magnetic tweezers, we studied the dynamics of DNA compaction induced by hexaammine cobalt chloride under constant forces. Discontinuous DNA compaction events were found for forces ranging from 0.5 to 1.7 pN, with approximately 270 nm DNA adsorbed in each compaction event. Forces larger than 6 pN were found able to unravel the toroid in a similar intermittent stepwise manner. The observations indicate that the folding/unfolding events are transitions between two metastable structural states which are separated by a tension-dependent energy barrier. Analysis of the waiting time revealed that the degree of the package ordering of DNA in a toroid depends on the compaction kinetics.     

Quantitative detection of single DNA molecules on DNA tetrahedron decorated substrates

A single DNA molecule detection method on DNA tetrahedron decorated substrates has been developed. DNA tetrahedra were introduced onto substrates for both preventing nonspecific adsorption and sensitive recognition of single DNA molecules.     

Nanofluidic system for the studies of single DNA molecules

Here, we describe a simple and low-cost lithographic technique to fabricate size-controllable nanopillar arrays inside the microfluidic channels for the studies of single DNA molecules. In this approach, nanosphere lithography has been employed to grow a single layer of well-ordered close-packed colloidal crystals inside the microfluidic channels. The size of the polymeric colloidal nanoparticles could be trimmed by oxygen plasma treatment. These size-trimmed colloidal nanoparticles were then used as the etching mask in a deep etching process. As a result, well-ordered size-controllable nanopillar arrays could be fabricated inside the microfluidic channels. The gap distance between the nanopillars could be tuned between 20 and 80 nm allowing the formation of nanofluidic system where the behavior of a single lambda-phage DNA molecule has been investigated. It was found that the lambda-phage DNA molecule could be fully stretched in the nanofluidic system formed by nanopillars with 50 nm gap distance at a field of 50 V/cm.     

All-optical manipulation of azo-dye molecules

A challenging issue in the field of the design of devices for photonic applications is to achieve complete manipulation of the molecular order. Azo-dye aromatic polymers have been shown to offer interesting prospects for material engineering using light matter interactions. Dual-frequency irradiation using appropriate combinations of circular beams polarizations are demonstrated to enable full control of the molecular polar rotation. More recent results on photoinduced surface-relief gratings have also opened the way of molecular translation control using optical fields. Understanding of the relevant parameters of molecular translation processes is a key issue for optimization of such an optomechanical effect: a simple model accounting qualitatively for the essential features of photoinduced surface-relief gratings will be presented.     

Simultaneous AFM manipulation and fluorescence imaging of single DNA strands.

We report combined atomic force and far-field fluorescence microscopic experiments which allow the simultaneous atomic force manipulation and optical observation of individual dye-labeled DNA molecules. A detailed understanding of the binding properties of DNA to different transparent surfaces is prerequisite for these investigations. Atomic force spectroscopy and fluorescence microscopy of single DNA strands yielded detailed insight into two different types of DNA binding onto transparent polylysine-coated and silanized glass surfaces. We subsequently demonstrate how the different binding can be exploited to perform two types of nanomanipulation experiments: On polylysine, strong electrostatic interactions over the whole length of the DNA strand enable the writing of micrometer-sized patterns. By contrast, the strong pointwise attachment of DNA to silanized surfaces allows horizontal stretching of single DNA strands to lengths exceeding 1.6 times the contour length of the DNA strand. With this new approach it is possible to directly observe the rupture of the strongly bonded DNA strand.     

Laser adiabatic manipulation of the bond length of diatomic molecules with a single chirped pulse

We propose and test numerically a scheme for controlling the bond distance in a diatomic molecule that requires the use of a single chirped pulse. The laser prepares a superposition state of both nuclear and electronic degrees of freedom, where the main character of the electronic wave function is that of an excited dissociative state. The main limitation of the scheme is the need of ultra broadband pulses, where the bandwidth must be of the order of the dissociation energy to achieve large bond elongations. The scheme can be used to deform the bond during the laser excitation to an arbitrary large and constant value, or to allow slow time-dependent bond elongations. Additionally, the scheme can be used to prepare highly excited vibrational wave packets in the ground potential after the pulse is switched off, at the expense of losing some population that dissociates. These wave packets are initially localized at the outer well of the potential, at energies controllable by the excitation process.     

Electrophoretic separation of environmentally important phenolic compounds using montomorillonite-coated fused-silica capillaries

This paper reports a simple procedure for coating fused-silica capillaries with poly(diallyldimethyl ammonium chloride) and montmorillonite. The coated capillaries were characterized by performing EOF measurements as a function of buffer pH, number of layers of coating, and number of runs (stability). The coated capillaries showed a highly stable mu(EOF) (run-to-run RSD less than 1.5%, n = 20), allowing continuous use for several days without conditioning. The coated capillaries were then used for the effective separation of nine environmentally important phenolic compounds showing a significant improvement in the resolution, when compared to bare fused-silica capillaries. The EOF of the coated capillaries was constant in alkaline solutions (pH > or = 7), allowing the optimization of the separation conditions of phenolic compounds without significantly affecting the mu(EOF).     

Processive replication of single DNA molecules in a nanopore catalyzed by phi29 DNA polymerase

Coupling nucleic acid processing enzymes to nanoscale pores allows controlled movement of individual DNA or RNA strands that is reported as an ionic current/time series. Hundreds of individual enzyme complexes can be examined in single-file order at high bandwidth and spatial resolution. The bacteriophage phi29 DNA polymerase (phi29 DNAP) is an attractive candidate for this technology, due to its remarkable processivity and high affinity for DNA substrates. Here we show that phi29 DNAP-DNA complexes are stable when captured in an electric field across the α-hemolysin nanopore. DNA substrates were activated for replication at the nanopore orifice by exploiting the 3'-5' exonuclease activity of wild-type phi29 DNAP to excise a 3'-H terminal residue, yielding a primer strand 3'-OH. In the presence of deoxynucleoside triphosphates, DNA synthesis was initiated, allowing real-time detection of numerous sequential nucleotide additions that was limited only by DNA template length. Translocation of phi29 DNAP along DNA substrates was observed in real time at ?ngstrom-scale precision as the template strand was drawn through the nanopore lumen during replication.     

An integrated optics microfluidic device for detecting single DNA molecules

A fluorescence-based integrated optics microfluidic device is presented, capable of detecting single DNA molecules in a high throughput and reproducible manner. The device integrates microfluidics for DNA stretching with two optical elements for single molecule detection (SMD): a plano-aspheric refractive lens for fluorescence excitation (illuminator) and a solid parabolic reflective mirror for fluorescence collection (collector). Although miniaturized in size, both optical components were produced and assembled onto the microfluidic device by readily manufacturable fabrication techniques. The optical resolution of the device is determined by the small and relatively low numerical aperture (NA) illuminator lens (0.10 effective NA, 4.0 mm diameter) that delivers excitation light to a diffraction limited 2.0 microm diameter spot at full width half maximum within the microfluidic channel. The collector (0.82 annular NA, 15 mm diameter) reflects the fluorescence over a large collection angle, representing 71% of a hemisphere, toward a single photon counting module in an infinity-corrected scheme. As a proof-of-principle experiment for this simple integrated device, individual intercalated lambda-phage DNA molecules (48.5 kb) were stretched in a mixed elongational-shear microflow, detected, and sized with a fluorescence signal to noise ratio of 9.9 +/-1.0. We have demonstrated that SMD does not require traditional high numerical aperture objective lenses and sub-micron positioning systems conventionally used in many applications. Rather, standard manufacturing processes can be combined in a novel way that promises greater accessibility and affordability for microfluidic-based single molecule applications.     

Motion of single long DNA molecules through arrays of magnetic columns

We present a videomicroscopy study of T4 DNA (169 kbp) in microfluidic arrays of posts formed by the self-assembly of magnetic beads. We observe DNA moving through an area of 10 000 microm(2), typically containing 100-600 posts. We determine the distribution of the contact times with the posts and the distribution of passage times across the field of view for hundreds of DNA per experiment. The contact time is well approximated by a Poisson process, scaling like the inverse of the field strength, independent of the density of the array. The distribution of passage times allows us to estimate the mean velocity and dispersivity of the DNA during its motion over distances long compared to our field of view. We compare these values with those computed from a lattice Monte Carlo model and geometration theory. We find reasonable quantitative agreement between the lattice Monte Carlo model and experiment, with the error increasing with increasing post density. The deviation between theory and experiment is attributed to the high mobility of DNA after disengaging from the posts, which leads to a difference between the contact time and the total time lost by colliding. Classical geometration theory furnishes surprisingly good agreement for the dispersivity, while geometration theory with a mean free path significantly overestimates the dispersivity.     

Confined plasmons in nanofabricated single silver particle pairs: experimental observations of strong interparticle interactions

We report on the optical properties of single isolated silver nanodisks and pairs of disks fabricated by electron beam lithography. By systematically varying the disk size and surface separation and recording elastic scattering spectra in different polarization configurations, we found evidence for extremely strong interparticle interactions. The dipolar surface plasmon resonance for polarization parallel to the dimer axis exhibited a red shift as the interdimer separation was decreased; as expected from previous work, an extremely strong shift was observed. The scattering spectra of single particles and pairs separated by more than one particle radius can be well described by the coupled dipole approximation (CDA), where the particles are approximated as point dipoles using a modified dipole polarizability for oblate spheroids. For smaller particle separations (d < 20 nm), the simple dipole model severely underestimates the particle interaction, indicating the importance of multipolar fields and finite-size effects. The discrete dipole approximation (DDA), which is a finite-element method, describes the experimental results well even at d < 20 nm, including particles that have metallic bridges.     

Adsorption of single DNA molecules at the water/fused-silica interface

We applied total internal reflection fluorescence microscopy (TIRFM) to study intermolecular interactions at the water/fused-silica interface at the single-molecule level. Real-time molecular motion at the interface was recorded to reveal adsorption behavior and conformational dynamics of three DNAs with sticky ends of different numbers of unpaired bases. Features of DNA motion at the interface, such as evanescent-field residence time, linear velocity and frequency of adsorption/desorption events were measured to assess the relative affinities of the oligonucleotides for the surface. The general trend of stronger interaction with the surface for longer sticky ends confirmed hydrophobic interaction and hydrogen bonding as the driving forces of DNA adsorption to fused-silica at pH 5. For DNAs of different sizes, different conformational dynamics and the accessibility of sticky ends give rise to a nonlinear relationship with respect to affinity. Such information may prove valuable for chromatography studies as well as for the design of DNA microarrays and drug delivery systems.     

Electrophoretic capture of circular DNA in gels

Results on electrophoretic capture of circular DNA in porous gels are reviewed. Processes which cause arrest of circular forms of DNA during electrophoresis can provide very efficient separation mechanism for the purification of plasmids and bacterial artificial chromosomes if the corresponding linear form is not trapped and therefore removed by the electric field. Two types of such topological traps have been proposed, impalement and lobster traps, and we here review the present experimental support for the existence of these two circle-specific mechanisms. Experiments designed to characterize the traps are discussed, regarding the concentration of the traps as well as their efficiency and capacity to trap both relaxed and supercoiled circular DNA. Studies of the dynamics of the capture process show that the average capture time is on the order of 10 s at 20 V/cm, by which time the circles have migrated several hundred micrometers and have passed hundreds of traps. We also review results on attempts to improve the capacity and efficiency of the trapping process by modification of the gels either by enzymatic treatment or by cogelation of neutral polymers.     

Toward room-temperature optical manipulation of small molecules

Room-temperature optical manipulation of small molecules is a challenging issue in the field of material science. To increase optical force for a single molecule trapping, it has been recognized that resonant excitation of molecules should be controlled under the light illumination. Strongly interacting molecules with solid surfaces at electrified interfaces show the exotic behavior of electronic excitation by localized surface plasmon. In this review, we emphases that surface-enhanced Raman scattering can be used to evaluate the resonant excitation of target molecules at interfaces. Under such excitation, the diffusion of small molecules can be controlled by the optical force generated by the intensity gradient of a highly localized electric field.     

Attractive mode manipulation of covalently bound molecules

We have investigated the manipulation of C₆₀ molecules on Si(1 0 0)-2×1 using the tip of a scanning tunnelling microscope. An attractive mode of manipulation has been identified in which molecules hop across the Si(1 0 0)-2×1 surface in steps of two lattice constants. An abrupt transition to repulsive manipulation occurs as the tip is lowered towards the surface. The attractive interaction is attributed to chemical forces between the tip and molecule.     

Photobleaching of asymmetric cyanines used for fluorescence imaging of single DNA molecules

The photobleaching of the cyanine dyes YO and YOYO has been investigated for both free and DNA-bound dyes, using absorption and fluorescence spectroscopy coupled with fluorescence microscopy. For the free dyes, the nature of the reactive species involved in the photodegradation process is different for the monomer and the dimer, as shown by scavenger studies. For DNA-bound dyes, photoinduced fading of the visible absorption band occurs by different pathways depending on the drug binding mode and can be attenuated by appropriate scavengers. However, none of these scavengers were found to have any significant effect on the photobleaching of dye fluorescence. It appears that the reduction of fluorescence intensity comes from a quenching of the dye fluorescence by modified DNA bases, possibly 8-oxo-7,8-dihydro-2'-deoxyguanosine.