A single-fluor approach to DNA sequence determination using high performance capillary electrophoresis

Scale-up development of high-performance polymer matrix for DNA sequencing analysis

Linear polyacrylamide (LPA) has been widely used as a replaceable separation matrix in CE. An increase in the molecular weight of the separation medium favors the separation of larger DNA fragments. In order to obtain ultrahigh-molecular-weight (UHMW) LPA, a "frozen" method was developed to synthesize the LPA homopolymer. This approach has three major advantages when compared with other existing routes of LPA synthesis: (i) long LPA chains could be obtained easily, with their average molecular weight (MW) being in the high 10 MDa range; (ii) the desired MW could be adjusted over a broad range by controlling the temperature and the concentration of initiators during synthesis; (iii) the product solution contains only a tiny amount of impurity besides the solvent and LPA. Both static and dynamic laser light scattering measurements were carried out to characterize the synthesized LPA in the buffer solution. The DNA sequencing matrix prepared from LPA using this method was studied and the results were compared with the newly developed commercial product POP7 from Applied Biosystems. It should be noted that this approach can be applied to synthesize other water-soluble polymers, resulting in UHMW products because the chain transfer constant is smaller at lower temperatures.

Copolymer solutions as separation media for DNA capillary electrophoresis

A review on copolymers used as DNA separation media in capillary electrophoresis is presented. Copolymers can combine the desirable properties of different monomers, yielding many attractive features, such as high sieving ability, low viscosity, self-assembly behavior and dynamic coating ability. Copolymers with different molecular architecture, including block copolymers, random copolymers, and graft copolymers, have been developed and tested as DNA separation media with unique and tailored properties that cannot be achieved easily by using only homopolymers.

DNA sequencing by capillary electrophoresis using copolymers of acrylamide and N,N-dimethylacrylamide

Copolymers of acrylamide (AM) and N,N-dimethylacrylamide (DMA) with AM to DMA molar ratios of 3:1, 2:1 and 1:1 and molecular weights of about 2.2 MDa were synthesized. The polymers were tested as separation media in DNA sequencing analysis by capillary electrophoresis (CE). The dynamic coating ability of polydimethylacrylamide (PDMA) and the hydrophilicity of polyacrylamide (PAM) have been successfully combined in these random copolymers. A separation efficiency of over 10 million theoretical plates per meter has been reached by using the bare capillaries without the additional polymer coating step. Under optimized separation conditions for longer read length DNA sequencing, the separation ability of the copolymers decreased with decreasing AM to DMA molar ratio from 3:1, 2:1 and 1:1. In comparison with PAM, the copolymer with a 3:1 AM:DMA ratio showed a higher separation efficiency. By using a 2.5% w/v copolymer with 3:1 AM:DMA ratio, one base resolution of 0.55 up to 699 bases and 0.30 up to 963 bases have been achieved in about 80 min at ambient temperatures.

Fast DNA sequencing up to 1,000 bases by capillary electrophoresis using poly(N,N-dimethylacrylamide) as a separation medium

Poly(N,N-dimethylacrylamide) (PDMA) with a molecular mass of 5.2 x 10(6) g/mol has been synthesized and used in DNA sequencing analysis by capillary electrophoresis (CE). A systematic investigation is presented on the effects of different separation conditions, such as injection amount, capillary inner diameter, polymer concentration, effective separation length, electric field and temperature, on the resolution. DNA sequencing up to 800 bases with a resolution (R) limit of 0.5 (and 1,000 bases with a resolution limit of 0.3) and a migration time of 96 min was achieved by using 2.5% w/v polymer, 150 V/cm separation electric field, and 60 cm effective separation length at room temperature on a DNA sample prepared with FAM-labeled--21M13 forward primer on pGEM3Zf(+) and terminated with ddCTP. Ultrafast and fast DNA sequencing up to 420 and 590 bases (R > or = 0.5) were also achieved by using 3% w/v polymer and 40 cm effective separation length with a separation electric field of 525 and 300 V/cm, and a migration time of 12.5 and 31.5 min, respectively. PDMA has low viscosity, long shelf life and dynamic coating ability to the glass surface. The unique properties of PDMA make it a very good candidate as a separation medium for large-scale DNA sequencing by capillary array electrophoresis (CAE).

DNA sequencing by capillary electrophoresis

Capillary electrophoresis has been under development for DNA sequencing since 1990. This development has traveled down two parallel tracks. The first track studied the details of DNA separation by gel electrophoresis. Early work stressed rapid separations at high electric fields, which reached the extreme of a 3.5 min sequencing run at 1200 V/cm. While fast separations are useful in clinical resequencing applications for mutation detection, long read-length is important in genomic sequencing. Unfortunately, sequence read-length degrades as electric field and sequencing speed increases; this tradeoff between read-length and sequencing speed appears to be a fundamental result of the physics of DNA separations in a polymer. The longest sequence sequencing read-lengths have been obtained at modest electric fields, high temperature, and with low concentration noncrosslinked polymers. In parallel with our understanding of DNA separations, the second track of DNA sequencing development considered the design of large-scale capillary instruments, wherein hundreds of DNA samples can be sequenced in parallel. Real-world application of these very high throughput capillary electrophoresis systems will require significant investment in sample preparation technology.

Microdialysis-immunoaffinity capillary electrophoresis studies on neuropeptide-induced lymphocyte secretion

A micro-sampling procedure has been developed for studying lymphocyte secretion of biologically important peptides in low cell density cultures. The technique is based on microdialysis recovery of the analytes of interest coupled with immunoaffinity capillary electrophoresis separation of the microdialysis samples and laser-induced fluorescence detection. Although the technique is able to recover secreted materials only at the 5-10 cell level, the detection system has a limit of detection (LOD) in the attomole (10(-18) M) range. This degree of sensitivity indicates that the system has the potential to measure secreted products at the single cell level. An added advantage of this system over other sampling techniques is that the microdialysis probe allows continuous sampling over time.

Activation energy of the separation of DNA sequencing fragments in denaturing noncross-linked polyacrylamide by capillary electrophoresis

We present the mobility of DNA sequencing fragments as a function of temperature in 5%T, 0%C noncross-linked polyacrylamide and at an electric field of 150 V/cm. The mobility of the fragments follows the Arrhenius equation. The activation energy for migration of a fragment through the polymer decreases monotonically with fragment length. The data were also analyzed in terms of the biased reptation model; the onset of biased reptation with stretching occurs for longer fragments as the temperature increase. These results are quite different from those observed for separation of DNA in cross-linked gels and represent a fundamental difference in the physics of the cross-linked and noncross-linked polyacrylamide.

The limiting mobility of DNA sequencing fragments for both cross-linked and noncross-linked polymers in capillary electrophoresis: DNA sequencing at 1200 V cm-1

The mobility of DNA sequencing fragments was measured in Long-Ranger gels at an electric field ranging from 200 to 1200 V cm-1 and in noncross-linked polyacrylamide at electric fields ranging from 100 to 300 V cm-1. In both cases, N*, the fragment length that denotes the onset of biased reptation with orientation, is inversely proportional to electric field. The inverse dependence of N* is inconsistent with the original biased reptation model but is consistent with modern models of DNA migration. While separation speed increases dramatically with electric field, the number of bases determined in a separation decreases in proportion to field strength. We present a DNA sequencing run at an electric field of 1200 V cm-1. Roughly 200 bases of sequence are determined in 3.5 min.

Separation of DNA sequencing fragments using an automated capillary electrophoresis instrument

Rapid, high-resolution separation of DNA sequencing fragments by capillary gel electrophoresis using an automated, commercially available instrument is presented. The effect of column lengths and electric field strength on the resolution of sequencing fragments as well as the sensitivity of laser-induced fluorescence (LIF) detection was investigated. Using a short capillary of 20 cm length, which results in a U-shape of the capillary in the capillary cartridge, very high separation efficiency, up to 17 x 10(6) theoretical plates per m, is obtained. Analysis of the band broadening factors revealed that the resolution on the short column is predominantly determined by axial diffusion and to a minor extent by detection zone width. Presumably due to the coiling of longer capillaries in the capillary cartridge, increasing the capillary length does not increase the separation efficiency as predicted for diffusion-limited separation. The concentration limit of detection (signal-to-noise ratio = 2) is 0.2 x 10(-12) M of fluorescein-labeled oligonucleotide primer under the separating conditions for DNA sequencing samples. Increasing the electric field strength from 100 to 175 V/cm improved resolution and at the same time approximately doubled the sequencing speed. Fragments up to 500 nucleotides in length are resolved in less than 50 min.

Sodium dodecyl sulfate-gel electrophoresis of proteins employing short capillaries

The performance of capillary gel-sodium dodecyl sulfate (SDS) electrophoresis for molecular-mass-dependent separation of proteins has been examined employing cross-linked polyacrylamide gels and untreated fused-silica capillaries of short length. An apparatus for capillary electrophoresis has been constructed, combining a UV detector equipped with a capillary holder, a power supply, and a micromanipulator for sample loading. The apparatus is capable of accommodating gel capillaries of different lengths and can be operated with two methods of sample loading: manual injection on top of the gel or electrokinetic injection. Standard proteins have been separated according to their molecular mass (ranging from 17000 to 116000) within 30 min, employing gel capillaries of effective lengths shorter than 10 cm and polyacrylamide gels ranging from 2.4 to 4.8%T (5%C). The results confirmed that gel capillaries of effective length less than 10 cm can be used for protein size-separation by SDS electrophoresis, with much higher performance than is achieved in rod gel-SDS electrophoresis.

Sequencing of antisense DNA analogues by capillary gel electrophoresis with laser-induced fluorescence detection

A method using capillary gel electrophoresis with laser-induced fluorescence detection is described which permits complete sequence determination of antisense DNA analogues of unknown sequence. This method, originally created as a tool to confirm the sequence of antisense oligonucleotides being developed as therapeutic drugs, utilizes data collected under a range of experimental conditions described by the Ogston model as applied to gel electrophoresis. A linear relationship independent of experimental conditions between the relative electrophoretic migration time and the oligonucleotide base number was observed and is shown to be consistent with a simplified version of this model and can be used to facilitate the sequence determination.

Spatial and temporal depletion of ions from noncrosslinked denaturing polyacrylamide in capillary electrophoresis

Electrical conductivity across a polyacrylamide-filled capillary decreases during the separation of DNA sequencing fragments. This conductivity decrease is localized to the first few centimeters at the injection (negative) end of the capillary; no conductivity change is noted at the detection (positive) end of the capillary. The zone of decreased conductivity extends further into the capillary as the separation proceeds. The zone is most important for freshly prepared capillaries; capillaries used nine days after polymerization generate an insignificant current drop. The data are consistent with ionic depletion due to differences in transport numbers between the separation medium and the buffer reservoirs.

Characterization of digoxigenin-labeled B-phycoerythrin by capillary electrophoresis with laser-induced fluorescence. Application to homogeneous digoxin immunoassay

A laser-induced fluorescence (LIF) immunoassay technique based on capillary electrophoretic (CE) separation is demonstrated. The analysis of digoxin in serum at clinically useful concentration levels of 10(-9) to 10(-10) M is achieved using this technique. The chemistry presented here using digoxigenin-labeled B-phycoerythrin was selected as a convenient model for the exploration of CE-LIF-based immunoassays. The LIF system described here exhibits detection limits in the low 10(-11) M range for several common fluorophores. The data presented in this report are one of the first examples of nanomolar quantitative analysis in a human serum matrix by CE.

High-speed and high-accuracy DNA sequencing by capillary gel electrophoresis in a simple, low cost instrument. Two-color peak-height encoded sequencing at 40 degrees C

A low-cost DNA sequencer was constructed based on a single helium-neon laser. The two-color peak-height encoded sequencing protocol, based on the use of T7 DNA polymerase in a manganese buffer, was used to generate samples. Two termination reactions were performed. In the first, a TAMRA (applied Biosystems)-labeled primer was extended in the presence of ddATP and ddCTP. The amounts of dideoxynucleotides were adjusted to produce a 3:1 peak height ratio. Similarly, a ROX (Applied Biosystems)-labeled primer was extended in the presence of ddGTP and ddTTP; the amounts of dideoxynucleotides was adjusted to produce a 3:1 peak height ratio. The pooled fragments were separated on a 4% T LongRanger gel operated at 39 degrees C. Over 500 bases of sequence were generated in 50 min.

The relative separation efficiencies of highly concentrated, uncrosslinked or low-crosslinked polyacrylamide gels compared to conventional gels of moderate concentration and crosslinking

The joint report [1] has shown that the separation of heteroduplex DNA from homoduplex DNA can be achieved by uncrosslinked polyacrylamide gels or gels of a very low degree of crosslinking (0.15%) with N,N'-methylenebisacrylamide (Bis), while conventional polyacrylamide gels of 2-5% crosslinking with Bis are incapable of such a separation in the absence of added denaturing agents. This result raised the question whether in application to other separation problems the same superiority of uncrosslinked or low-crosslinked polyacrylamide existed. To test that question, Ferguson plots were determined for the members of a DNA ladder (50 to 1000 bp) in polyacrylamide with 0, 0.1, 0.2, 0.3, 0.5% C (Bis), and the separation efficiency function, S, was evaluated in comparison with that in conventional 2-5% C (Bis) gels. S was found to be lower, not higher, in gels of low crosslinking at the respective maximally effective gel concentrations. However, the range of gel concentrations in which gels of low or no crosslinking were effective extended over a range of at least 10% T, while conventionally crosslinked gels were most effective over a range of 3 to 1 units of %T.

Semiconductor laser-induced fluorescence detection in capillary electrophoresis using a cyanine dye

Cy5, an activated carboxyl cyanine fluorophore, was characterized by capillary electrophoresis (CE) using a semiconductor laser at 652 nm to induce fluorescence. Hydrolysis of the activated Cy5 in the presence of ammonia results in the formation of a mono- and diamide and a dicarboxylic acid. A Cy5-labeled oligonucleotide M13 primer for DNA sequencing (M13mp18 template) was synthesized with a purity of better than 95%. The labeled primer was analyzed by liquid chromatography, using UV-visible detection, and by CE, monitored by laser-induced fluorescence (LIF) detection. Analysis of the Cy5-labeled oligonucleotide primer by CE-LIF in a 9% polyacrylamide gel-filled capillary indicated the purity of the major Cy5-oligonucleotide primer was greater than 90%. The detection sensitivity for Cy5-based CE-LIF detection system with a 2.5-mW red semiconductor laser is about 10(-10) M.

Contribution of secondary structure to DNA mobility in capillary gels

Intramolecular base pairing at the 3' end of single-stranded DNA molecules can cause increased electrophoretic mobility. In DNA sequencing separations this can result in compressions, where multiple oligomers differing in length by one base comigrate, which complicate sequence analysis. Using a novel approach to the application of capillary electrophoresis to DNA sequencing, incorporation of formamide into capillary gels, different separation field strengths, and external heating of the capillary are examined for their ability to resolve compressions. The identity of the 3' terminal nucleotide has also been observed to influence oligomer mobility in cross-linked acrylamide slab gels. We utilize automated data collection from DNA sequencing separations to show that a similar effect is also present in linear acrylamide capillary gels run at high field strengths. We also demonstrate the ability of capillary electrophoresis to separate synthetic oligos of the same length but differing in composition by one base, or of the same base composition but different sequence.