人的基因组及DNA序列分析──过去、现去及将来（上）

人的基因组研究已成为生命科学前沿领域中最热门的课题之一。ＤＮＡ序列分析是基因组研究的关键技术．本文对人的基因组分析及其对ＤＮＡ序列分析的要求进行了论述．对ＤＮＡ序列分析方法如板凝胶电泳自放射显影法、板凝胶电泳激光荧光法、毛细管电泳激光荧光法、阵列毛细管凝胶电泳激光荧光法。超薄层板在胶电泳激光荧光法作了详细评论．并对正在开发的不用凝胶电泳分离的直接测序新技术和新方法，如质谱法、原子探针法（扫描隧道显微镜、原子力显微镜）、杂交法、流动单分子荧光检测法等进行了评论。     

A liquid core waveguide fluorescence detector for multicapillary electrophoresis applied to DNA sequencing in a 91-capillary array

A new laser-induced fluorescence (LIF) detector for multicapillary electrophoresis is presented. The detection principle is based on waveguiding of the emitted fluorescence from the point of illumination to the capillary ends by total internal reflection (TIR) and imaging of the capillary ends. The capillaries themselves thus act as liquid core waveguides (LCWs). At the illumination point, the capillaries are arranged in a planar array, which allows clean and efficient illumination with a line-focused laser beam. The capillary ends are rearranged into a small, densely packed two-dimensional array, which is imaged end-on with high light collection efficiency and excellent image quality. Wavelength dispersion is obtained with a single prism. Intercapillary optical crosstalk is less than 0.5%, and rejection of stray light is very efficient. The detector is applied to four-color DNA sequencing by gel electrophoresis in a 91-capillary array, with simple fluorescein and rhodamine dyes as fluorophores. Since the imaged two-dimensional array is so compact, the detector has a high potential for very large-scale multiplexing.     

Side-entry excitation and detection of square capillary array electrophoresis for DNA sequencing.

In high throughput DNA sequencing based on capillary electrophoresis, efficient coupling of the laser to each capillary is a challenge. Our group previously reported two multiple point irradiation schemes. The present work describes a more efficient excitation and detection method in which the laser light propagates through the capillary array without undergoing a serious reduction in power. An array of square capillaries (340 microns O.D. x 75 microns I.D.) was sandwiched between two fused-silica plates with an index-matching solution in between. The light was directed into the channel across the capillary array from the side. DNA sequences of PGEM/U from 24 capillaries were obtained even with a relatively low-power laser. The excitation scheme can be scaled up to hundreds of capillaries to achieve high-speed, high-throughput DNA sequencing, genetic typing and drug screening.     

Construction and evaluation of a capillary array DNA sequencer based on a micromachined sheath-flow cuvette

A capillary array electrophoresis DNA sequencer is reported based on a micromachined sheath-flow cuvette as the detection chamber. This cuvette is equipped with a set of micromachined features that hold the capillaries in precise registration to ensure uniform spacing between the capillaries, in order to generate uniform hydrodynamic flow in the cuvette. A laser beam excites all of the samples simultaneously, and a microscope objective images fluorescence onto a set of avalanche photodiodes, which operate in the analog mode. A high-gain transimpedance amplifier is used for each photodiode, providing high duty-cycle detection of fluorescence.     

Two-color excitation system for fluorescence detection in DNA sequencing by capillary array electrophoresis

Two computer-controlled galvanometer scanners are adapted for two-dimensional step scanning across a 96-capillary array for laser-induced fluorescence detection. 488 nm and 514 nm laser lines from the same Ar(+) laser were alternately coupled for two-color excitation in each capillary. The signal at a single photomultiplier tube is temporally sorted to distinguish among the capillaries and the excitation wavelengths. Based on the differences in absorption spectra for the dyes, the peak-height ratios in the 488 nm and 514 nm excitation electropherograms were used for peak identification for multiplexed capillary electrophoresis. Successful base calling for 24-capillary DNA sequencing was achieved to 450 bp with 99% accuracy. Advantages include the efficient utilization of light due to the high duty-cycle of step scan, good detection performance due to the reduction of stray light, ruggedness due to the small mass of the galvanometer mirror, low cost due to the simplicity of components and flexibility due to the independent paths for excitation and emission.     

A cam-based laser-induced fluorescence scanner for capillary array electrophoresis

Capillary array electrophoresis (CAE) is an important high throughput analytical technique. Laser-induced fluorescence (LIF) has been the dominant detection method for CAE owing to its low limit of detection (LOD) and wide linear dynamic range (LDR). Linear LIF scanners were first used in CAE because linear motions of an objective match well with a common planar array of capillaries. A problem with linear scanners is that the motor is required accelerating/decelerating so that all capillaries can be properly scanned, which makes motion control complicated and reduces the duty cycle. Rotary scanners were developed to overcome this problem. While rotary scanners have been successfully applied in CAE, the capillaries have to be arranged in a circular format, which can be inconvenient in some cases. In this report, we describe a cam-based LIF scanner as an alternative technique for CAE detection. In this system, a rotary motor is mechanically linked with a capillary holder via a cam. During operation, the motor carries the cam in a rotary motion that drives an array of capillaries on the holder to move back and forth across the objective for fluorescence detection. Using this design, the capillaries can be parallel-arranged in a plane while the motor acceleration/deceleration is avoided. To demonstrate the feasibility of this approach, we constructed a prototype instrument with a constant-velocity scanning distance of ∼10 mm, a scanning frequency of 3 Hz and a duty cycle of ∼70%. The scanner exhibited a LOD of 69 pM of fluorescein and a LDR of 3.5 orders of magnitude. Multiplexed capillary SDS-PAGE was performed on this scanner for protein separations.     

Multiplex high-throughput solid-phase minisequencing by capillary electrophoresis and liquid core waveguide fluorescence detection

Minisequencing, solid-phase single-nucleotide primer extension reaction, is a robust method for performing multiplex single-nucleotide polymorphism (SNP) analysis. We have combined this technology with capillary gel electrophoresis in a multicapillary format, using liquid core waveguide (LCW) fluorescence detection. Polymerase chain reaction (PCR) amplification of multiple DNA targets is performed with one primer for each target biotinylated. Separation of the complementary strands, minisequencing and washing steps are carried out using streptavidin-coated magnetic beads. Dideoxynucleotides analogues labelled with different fluorophores are used for the extension of the minisequencing primers. The extended oligonucleotides, the length of which defines the position on the target and the color the identity of the polymorphism, are then separated in a gel-filled array of capillaries, coated on the outside with a layer of a fluoropolymer to provide the liquid core waveguide characteristics. The technology has a potential for extremely high throughputs when a combination of multiplex PCR-minisequencing is used together with a large array of capillaries, four-color detection and high-speed separation.     

Integrated circuit microchip system with multiplex capillary electrophoresis module for DNA analysis

In this paper, we describe the use of an integrated circuit (IC) microchip system as a detector in multiplex capillary electrophoresis (CE). This combination of multiplex capillary gel electrophoresis and the IC microchip technology represents a novel approach to DNA analysis on the microchip platform. Separation of DNA ladders using a multiplex CE microsystem of four capillaries was monitored simultaneously using the IC microchip system. The IC microchip-CE system has advantages such as low cost, rapid analysis, compactness, and multiplex capability, and has great potential as an alternative system to conventional capillary array gel electrophoresis systems based on charge-coupled device (CCD) detection.     

532nm激光诱导荧光毛细管阵列电泳仪的研制

基于共聚焦激光诱导荧光检测技术,研制了一台旋转扫描高效毛细管阵列电泳装置。以波长为532nm的半导体二极管激光器作为激发光源,多根毛细管阵列采用圆形布局,微型高速直流电机带动旋转反射镜进行激光扫描,加快了数据采集的速度;采用旋转编码器实现了毛细管的定位与位置读出,并触发数据采集系统进行荧光信号采集。以罗丹明6G和罗丹明B为分析样品,考察了16通道毛细管阵列电泳仪的基本性能。     

532 nm激光诱导荧光毛细管阵列电泳仪的研制

基于共聚焦激光诱导荧光检测技术,研制了一台旋转扫描高效毛细管阵列电泳装置.以波长为532nm的半导体二极管激光器作为激发光源,多根毛细管阵列采用圆形布局,微型高速直流电机带动旋转反射镜进行激光扫描,加快了数据采集的速度;采用旋转编码器实现了毛细管的定位与位置读出,并触发数据采集系统进行荧光信号采集.以罗丹明6G和罗丹明B为分析样品,考察了16通道毛细管阵列电泳仪的基本性能.     

Cycling gradient capillary electrophoresis: a low-cost tool for high-throughput analysis of genetic variations

In the present work, we introduce a new type of DNA variation detection. This method represents a transfer of melting gel technique onto multicapillary electrophoresis DNA sequencing instrument with further improvements to achieve maximum sample throughput while maintaining a high performance. The main improvement comes from application of cycling (revolving) temporal temperature gradient in place of a single-sweep gradient, commonly used in similar gel-based techniques. This improvement enables utilization of multiple-injection technique, in which multiple samples are injected into the same capillary (or sets of capillaries) separated by predefined time intervals of partial electrophoresis. The periodic oscillation of the temperature results in identical separation conditions of all samples injected in such series. Using this novel approach, we demonstrate a dramatic increase in separation throughput by turning a standard commercial 96-capillary array instrument into a semicontinuous flow mutation detection system capable to screen over 15 000 samples in 24 h of operation on a single 96-capillary commercial instrument. This represents a 10-fold increase in sample throughput over the current comparable technology.     

A capillary-array electrophoresis system using side-entry on-column laser irradiation combined with glass rod lenses

We have developed a simple and high-throughput capillary-array electrophoresis system that uses side-entry on-column laser irradiation. The number of capillaries in an array is generally limited by laser-power attenuation along the array due to reflection and divergence. We overcame these problems by placing the capillaries in water and adding glass rod lenses between the capillaries. As a result, up to 45 capillaries could be simultaneously irradiated with a single laser beam and the fluorescence from all the capillaries could be detected with high sensitivity. We demonstrated the high throughput of 12 kbp/h with a 45 capillary array using this system.     

Detection of duck hepatitis B virus DNA fragments using on-column intercalating dye labeling with capillary electrophoresis-laser-induced fluorescence.

A rapid on-column DNA labeling technique is used to detect viral restriction DNA fragments by capillary electrophoresis-laser induced fluorescence detection. Intercalating dyes such as POPO3 or ethidium homodimer-2 are incorporated into the detection buffer. The cationic dyes migrate into the capillary during electrophoresis and bind to the oppositely migrating DNA fragments. A post-column sheath-flow fluorescence detector is used in the experiment. Excellent labeling efficiency is achieved at minimal background fluorescence by diluting the dyes to between 1 x 10(-7) M and 5 x 10(-7) M in a buffer with low ionic strength relative to the running buffer within the capillary. This dilute sheath-flow buffer allows stacking of dye molecules inside the capillary when an electric field is applied. Calibration curves using a series of DNA size markers (between 72 and 1353 base pairs) were linear over an order of magnitude in DNA concentration. Sensitivity also increased linearly with fragment length, and detection limits ranged from 4 x 10(-14) M to 5 x 10(-13) M for the size-standards. Analysis of cloned viral DNA using duck hepatitis B virus demonstrated a concentration detection limit of 3.9 x 10(-16) M. Last, the technique produced very high separation efficiency, 14 x 10(6) theoretical plates which is greater than 47 x 10(6) plates m-1, for the duck hepatitis B viral genome.     

Continuous, on-line DNA sequencing using a versatile infrared laser scanner/electrophoresis apparatus.

A new apparatus for continuously detecting fluorescently labeled DNA fragments is based on infrared fluorescence technology. This technology combines state-of-the-art developments in chemistry, laser technology, and detection, while achieving improved reliability, sensitivity, and flexibility for applications including DNA sequencing. DNA molecules labeled with a novel infrared fluorophore are detected during electrophoresis using a scanning infrared fluorescence microscope. The microscope consists of a laser diode for exciting the fluorophore and a silicon avalanche photodiode for detecting the infrared emission. Optimum conditions for detection and throughput are obtained by adjusting electrophoresis, scanning and imaging parameters. Typical DNA sequencing runs (test templates) allow identification of over 500 bases per sample with greater than 99% accuracy.     

High-performance genetic analysis using microfabricated capillary array electrophoresis microplates.

This review focuses on some recent advances in realizing microfabricated capillary array electrophoresis (microCAE). In particular, the development of a novel rotary scanning confocal fluorescence detector has facilitated the high-speed collection of sequencing and genotyping data from radially formatted microCAE devices. The concomitant development of a convenient energy-transfer cassette labeling chemistry allows sensitive multicolor labeling of any DNA genotyping or sequencing analyte. High-performance hereditary haemochromatosis and short tandem repeat genotyping assays are demonstrated on these devices along with rapid mitochondrial DNA sequence polymorphism analysis. Progress in supporting technology such as robotic fluid dispensing and batched data analysis is also presented. The ultimate goal is to develop a parallel analysis platform capable of integrated sample preparation and automated electrophoretic analysis with a throughput 10-100 times that of current technology.     

Electrophoretically mediated microanalysis of a nicotinamide adenine dinucleotide-dependent enzyme and its facile multiplexing using an active pixel sensor UV detector

An electrophoretically mediated microanalysis (EMMA) method has been developed for yeast alcohol dehydrogenase and quantification of reactant and product cofactors, NAD and NADH. The enzyme substrate ethanol (1% (v/v)) was added to the buffer (50 mM borate, pH 8.8). Results are presented for parallel capillary electrophoresis with a novel miniature UV area detector, with an active pixel sensor imaging an array of two or six parallel capillaries connected via a manifold to a single output capillary in a commercial CE instrument, allowing conversions with five different yeast alcohol dehydrogenase concentrations to be quantified in a single experiment.     

人体基因组课题（HGP）计划给分析化学带来的挑战与机会

本文综述了在ＤＮＡ测序方面分析化学的最新进展，包括电泳，毛细管电泳（ＣＥ），质谱（ＭＳ），电喷雾电离－质谱（ＥＳＩ－ＭＳ），荧光光谱、共振离子谱（ＲＩＳ）和单分子测定，同时还叙述了两维技术和多段测序方法的进展。     

Voltage‐programming‐based capillary gel electrophoresis for the fast detection of angiotensin‐converting enzyme insertion/deletion polymorphism with high sensitivity

A voltage‐programming‐based capillary gel electrophoresis method with a laser‐induced fluorescence detector was developed for the fast and highly sensitive detection of DNA molecules related to angiotensin‐converting enzyme insertion/deletion polymorphism, which has been reported to influence predisposition to various diseases such as cardiovascular disease, high blood pressure, myocardial infarction, and Alzheimer's disease. Various voltage programs were investigated for fast detection of specific DNA molecules of angiotensin‐converting enzyme insertion/deletion polymorphism as a function of migration time and separation efficiency to establish the effect of voltage strength to resolution. Finally, the amplified products of the angiotensin‐converting enzyme insertion/deletion polymorphism (190 and 490 bp DNA) were analyzed in 3.2 min without losing resolution under optimum voltage programming conditions, which were at least 75 times faster than conventional slab gel electrophoresis. In addition, the capillary gel electrophoresis method also successfully applied to the analysis of real human blood samples, although no polymorphism genes were detected by slab gel electrophoresis. Consequently, the developed voltage‐programming capillary gel electrophoresis method with laser‐induced fluorescence detection is an effective, rapid analysis technique for highly sensitive detection of disease‐related specific DNA molecules.     

Light-emitting diode induced fluorescence (LED-IF) detection design for a pen-shaped cartridge based single capillary electrophoresis system

CGE is a well-established separation technique for the analysis of biologically important molecules such as nucleic acids. The inherent high resolving power, rapid analysis times, excellent detection sensitivity, and quantification capabilities makes this method favorable compared to conventional manual polyacrylamide and agarose slab gel electrophoresis techniques. In this paper we introduce a novel single-channel capillary gel electrophoresis system with LED-induced fluorescence detection also utilizing a compact pen-shaped capillary cartridge design for automatic analysis of samples from a 96-well plate. To evaluate the suitability of the system, 1000 genomic DNA(gDNA) samples were analyzed in gel filled capillaries and detected by the microball ended excitation and emission optical fiber based LED-induced fluorescence detection system. Excellent migration time reproducibility of RSD <0.75% was obtained over the course of 1000 runs. The system rapidly distinguished between intact and degraded gDNA samples, therefore provided important information if they could be used for downstream quantitative PCR processing where high-quality intact gDNA was key. We envision that this novel system design will rapidly find new applications in both research and clinical diagnostic laboratories as a highly sensitive and easy to use bio-analytical approach.