Multiplexed fluorescence detection in microfabricated devices with both time-resolved and spectral-discrimination capabilities using near-infrared fluorescence

Electrophoretic Transport of Single DNA Nucleotides through Nanoslits: A Molecular Dynamics Simulation Study

There is potential for flight time based DNA sequencing involving disassembly into individual nucleotides which would pass through a nanochannel with two or more detectors. We performed molecular dynamics simulations of electrophoretic motion of single DNA nucleotides through 3 nm wide hydrophobic slits with both smooth and rough walls. The electric field (E) varied from 0.0 to 0.6 V/nm. The nucleotides adsorb and desorb from walls multiple times during their transit through the slit. The nucleotide-wall interactions differed due to nucleotide hydrophobicities and wall roughness which determined duration and frequency of nucleotide adsorptions and their velocities while adsorbed. Transient association of nucleotides with one, two, or three sodium ions occurred, but the mean association numbers (ANs) were weak functions of nucleotide type. Nucleotide-wall interactions contributed more to separation of nucleotide flight time distributions than ion association and thus indicate that nucleotide-wall interactions play a defining role in successfully discriminating between nucleotides on the basis of their flight times through nanochannels/slits. With smooth walls, smaller nucleotides moved faster, but with rough walls larger nucleotides moved faster due to fewer favorable wall adsorption sites. This indicates that roughness, or surface patterning, might be exploited to achieve better time-of-flight based discrimination between nucleotides.

Label-free analysis in chip electrophoresis applying deep UV fluorescence lifetime detection

Herein we introduce deep UV fluorescence lifetime detection in microfluidics applied for label-free detection and identification of various aromatic analytes in chip electrophoresis. For this purpose, a frequency quadrupled Nd:YAG (neodymium-doped yttrium aluminum garnet) picosecond laser at 266  nm was incorporated into an inverse fluorescence microscope setup with time-correlated single photon counting detection. This allowed recording of photon timing with sub-nanosecond precision. Thereby fluorescence decay curves are gathered on-the-fly and average lifetimes can be determined for each substance in the electropherogram. The aromatic compounds serotonin, propranolol, 3-phenoxy-1,2-propanediol and tryptophan were electrophoretically separated using a fused-silica microchip. Average lifetimes were independently determined for each compound via bi-exponential tail fitting. Time-correlated single photon counting also allows the discrimination of background fluorescence in the time domain. This results in improved signal-to-noise-ratios as demonstrated for the above model analytes. Microchip electrophoretic separations with fluorescence lifetime detection were also performed with a protein mixture containing lysozyme, trypsinogen and chymotrypsinogen emphasizing the potential for biopolymer analysis.

Modulation-frequency encoded multi-color fluorescent DNA analysis in an optofluidic chip

We introduce a principle of parallel optical processing to an optofluidic lab-on-a-chip. During electrophoretic separation, the ultra-low limit of detection achieved with our set-up allows us to record fluorescence from covalently end-labeled DNA molecules. Different sets of exclusively color-labeled DNA fragments-otherwise rendered indistinguishable by spatio-temporal coincidence-are traced back to their origin by modulation-frequency-encoded multi-wavelength laser excitation, fluorescence detection with a single ultrasensitive, albeit color-blind photomultiplier, and Fourier analysis decoding. As a proof of principle, fragments obtained by multiplex ligation-dependent probe amplification from independent human genomic segments, associated with genetic predispositions to breast cancer and anemia, are simultaneously analyzed.

A CTRW-based model of time-resolved fluorescence lifetime imaging in a turbid medium

We develop an analytic model of time-resolved fluorescent imaging of photons migrating through a semi-infinite turbid medium bounded by an infinite plane in the presence of a single stationary point fluorophore embedded in the medium. In contrast to earlier models of fluorescent imaging in which photon motion is assumed to be some form of continuous diffusion process, the present analysis is based on a continuous-time random walk (CTRW) on a simple cubic lattice, the object being to estimate the position and lifetime of the fluorophore. Such information can provide information related to local variations in pH and temperature with potential medical significance. Aspects of the theory were tested using time-resolved measurements of the fluorescence from small inclusions inside tissue-like phantoms. The experimental results were found to be in good agreement with theoretical predictions provided that the fluorophore was not located too close to the planar boundary, a common problem in many diffusive systems.

Dual-point dual-wavelength fluorescence monitoring of DNA separation in a lab on a chip

We present a simple approach in electrophoretic DNA separation and fluorescent monitoring that allows to identify the insertion or deletion of base-pairs in DNA probe molecules from genetic samples, and to perform intrinsic calibration/referencing for highly accurate DNA analysis. The principle is based on dual-point, dual-wavelength laser-induced fluorescence excitation using one or two excitation windows at the intersection of integrated waveguides and microfluidic channels in an optofluidic chip and a single, color-blind photodetector, resulting in a limit of detection of ~200 pM for single-end-labeled DNA molecules. The approach using a single excitation window is demonstrated experimentally, while the option exploiting two excitation windows is proposed theoretically.

Quantum dots versus organic dyes as fluorescent labels

Suitable labels are at the core of Luminescence and fluorescence imaging and sensing. One of the most exciting, yet also controversial, advances in label technology is the emerging development of quantum dots (QDs)--inorganic nanocrystals with unique optical and chemical properties but complicated surface chemistry--as in vitro and in vivo fluorophores. Here we compare and evaluate the differences in physicochemical properties of common fluorescent labels, focusing on traditional organic dyes and QDs. Our aim is to provide a better understanding of the advantages and limitations of both classes of chromophores, to facilitate label choice and to address future challenges in the rational design and manipulation of QD labels.

Toward nanoscale genome sequencing

This article reports on the state-of-the-art technologies that sequence DNA using miniaturized devices. The article considers the miniaturization of existing technologies for sequencing DNA and the opportunities for cost reduction that 'on-chip' devices can deliver. The ability to construct nano-scale structures and perform measurements using novel nano-scale effects has provided new opportunities to identify nucleotides directly using physical, and not chemical, methods. The challenges that these technologies need to overcome to provide a US$1000-genome sequencing technology are also presented.

Mechanical and chemical analysis of plasma and ultraviolet-ozone surface treatments for thermal bonding of polymeric microfluidic devices

Here we have demonstrated that radio frequency plasma and ultraviolet-ozone (UVO) surface modifications are effective treatments for enabling the thermal bonding of polymeric microfluidic chips at temperatures below the T(g) (glass transition temperature) of the polymer. The effects of UVO and plasma treatments on the surface properties of a cyclic polyolefin and polystyrene were examined with X-ray photoelectron spectroscopy (XPS), contact angle measurements, atomic force microscopy (AFM) surface roughness measurements and surface adhesion measurements with AFM force-distance data. Three-point bending tests using a dynamic mechanical analyzer (DMA) were used to characterize the bond strength of thermally sealed polymer parts and the cross-sections of the bonded microchannels were evaluated with scanning electron microscopy (SEM). The experimental results demonstrated that plasma and UVO surface treatments cause changes in the chemical and physical characteristics of the polymer surfaces, resulting in a decrease in T(g) at the surface, and thus allowing the microfluidic chips to be effectively bonded at temperatures lower than the T(g) of the bulk polymer without losing the intended channel geometry.

Surface modification of poly(methyl methacrylate) microfluidic devices for high-resolution separations of single-stranded DNA

While polymer-based microfluidic devices offer some unique opportunities in developing low-cost systems for a variety of application areas, the ability to sort electrophoretically with high efficiency a number of different targets has remained somewhat elusive with an example consisting of achieving single base resolution as required for DNA sequencing. While the reasons for this are many-fold, it is clear that some type of coating is required on the polymer substrate to suppress the EOF and/or minimize potential solute/wall interactions. To this end, we report on a simple grafting procedure to allow the formation of polymer coats, which in this example used linear polyarcylamides (LPAs), onto a poly(methyl methacrylate) (PMMA) microfluidic device. The procedure involved creating an amine-terminated PMMA surface by appropriately functionalizing the PMMA through either a chemical or photochemical process. The aminated surface could then be used to covalently anchor methacrylic acid, which was used as a scaffold to produce LPAs on the surface through radical polymerization of acrylamide. The resulting surfaces demonstrated EOFs that were nearly an order of magnitude smaller than native PMMA. In addition, these LPA-coated devices could produce highly reproducible migration times of over approximately 20 runs with plate numbers exceeding 10(5) m(-1). Using gel electrophoretic analysis of a single base track generated from an M13mp18 template using Sanger cycle sequencing and dye-primer chemistry, the resolution value obtained for bases 199 and 200 was 0.18 while for bases 208 and 209 it was 0.21. For the native PMMA, these bands were found to comigrate.

Emerging technologies in DNA sequencing

Demand for DNA sequence information has never been greater, yet current Sanger technology is too costly, time consuming, and labor intensive to meet this ongoing demand. Applications span numerous research interests, including sequence variation studies, comparative genomics and evolution, forensics, and diagnostic and applied therapeutics. Several emerging technologies show promise of delivering next-generation solutions for fast and affordable genome sequencing. In this review article, the DNA polymerase-dependent strategies of Sanger sequencing, single nucleotide addition, and cyclic reversible termination are discussed to highlight recent advances and potential challenges these technologies face in their development for ultrafast DNA sequencing.

Development of a two-color laser fluorescence detector. On-line detection of internal standards and unknowns by capillary electrophoresis within the same sample

A two-laser, two-color detector has been developed for the simultaneous detection of naturally occurring and recombinant (internal standards) cytokines within the same biological sample. The internal standards were labeled with Bimane and detected with a 408 nm laser while the natural cytokines were labeled with AlexaFluor633 and detected with a 633 nm laser. The two resulting electropherograms were plotted as overlaid traces and quantification of the natural materials determined by comparison with the standards. Using this system, recovery of all four cytokine standards was greater than 94% in both saline and cytokine-depleted plasma. These recoveries could be achieved with intra- and inter-assay coefficients of variance (c.v.) of less than 4.5 and 5.6, respectively. Application of this system to the examination of clinical samples demonstrated that measurement of the four pro-inflammatory cytokines could distinguish between normals, sub-clinical and clinical inflammation. An advantage of this approach is that direct calculation of unknowns by comparison to identical internal standards can shorten analytical time by eliminating the need for additional standard or calibration runs.

Color-blind fluorescence detection for four-color DNA sequencing

We present an approach called pulsed multiline excitation (PME) for measurements of multicomponent, fluorescence species and demonstrate its application in capillary electrophoresis for DNA sequencing. To fully demonstrate the advantages of PME, a fluorescent dye set has been developed whose absorption maxima span virtually the entire visible spectrum. Unlike emission wavelength-dependent approaches for identifying fluorescent species, the removal of the spectral component in PME confers a number of advantages including higher and normalized signals from all dyes present in the assay, the elimination of spectral cross-talk between dyes, and higher signal collection efficiency. Base-calling is unambiguously determined once dye mobility corrections are made. These advantages translate into significantly enhanced signal quality as illustrated in the primary DNA sequencing data and provide a means for achieving accurate base-calling at lower reagent concentrations.