Separation of oligonucleotides in N-methyl-formamide-based polymer matrices by capillary electrophoresis

Combining liquid chromatography with multiplexed capillary gel electrophoresis for offline comprehensive analysis of complex oligonucleotide samples

Offline two dimensional liquid chromatography (LC)×capillary gel electrophoresis (CGE) and LC×(24) multiplexed-CGE methodologies were developed for the separation of oligonucleotides of therapeutic size. Both ion-pair chromatography (IPC) and ion-exchange chromatography (IEC) were studied as methods for the first dimension and single and multiplexed capillary electrophoresis methods in entangled polymer solutions were used for the second dimension separations. Electrokinetic and pressure injection were evaluated for the analysis of the collected LC fractions. The comprehensive separation was optimized with standard mixtures of poly adenosine, thymidine, cytosine and uracil homodeoxyoligonucleotides up to 35 bases long. Highly orthogonal methodologies and overall peak capacities of 6435 and 6993 for IPC×CGE and IEC×CGE, respectively, were obtained within a few hours analysis time.

Study on steady-state kinetics of nucleotide analogues incorporation by non-gel CE

A method for studying steady-state kinetics of nucleotide analogues incorporation into DNA strand by non-gel CE (NGCE) with LIF was developed. Nucleoside analogue is a kind of antiviral agent used to inhibit viral replication in infected cells, especially HIV. Steady-state parameter K(m) for nucleotide analogues is determined to imply the relationship between nucleoside analogues and the enzyme in the DNA chain elongation and predict the antiviral efficacy in vivo. Samples were prepared by single nucleotide incorporation assays catalyzed by Taq DNA polymerase at 58 degrees C and HIV reverse transcriptase (RT) at 37 degrees C, and then were separated using NGCE under optimized conditions: 25 mmol/L Tris-boric-EDTA buffer (pH 8.0) with 7 mmol/L urea in the presence of 20% w/v PEG 35000 at 30 degrees C and -20 kV. K(m(dTTP)), K(m(d4TTP)) and K(m(AZTTP)) were measured by NGCE for the first time and their values for Taq DNA polymerase were 0.29+/-0.04, 32.1+/-3.3 and 74.5+/-6.6 micromol/L, respectively. For HIV RT, the values were 0.15+/-0.05, 0.31+/-0.03 and 0.17+/-0.03 micromol/L, respectively. The trend of data for HIV RT measured by NGCE was consistent with that measured by PAGE. The reported method by NGCE for the K(m) determination was powerful, sensitive and fast, and required less amounts of reagents compared with PAGE. It be employed as a reliable alternative method and further applied in other relative studies of nucleoside analogue substrates and DNA polymerases or RTs.

Nanostructured copolymer gels for dsDNA separation by CE

Pluronics are triblock copolymers of poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) that are able to form many different ordered nanostructures at appropriate polymer concentrations and temperatures in selective solvents. These nanostructured "gels" showed desirable criteria when used as DNA separation media, especially in microchip electrophoresis, including dynamic coating and viscosity switching. A ternary system of F127 (E99P69E99)/TBE buffer/1-butanol was selected as a model system to test the sieving performance of different nanostructures in separating dsDNA by CE. The nanostructures and their lattice constants were determined by small-angle X-ray scattering. Viscosity measurements showed the sol-gel transition phenomena. In addition to the cubic structure, successful electrophoretic separation of dsDNA in 2-D hexagonally packed cylinders was achieved. Results showed that without further optimization, PhiX174 DNA-Hae III digest was well separated within 15 min in a 7-cm separation channel, by using F127/TBE/1-butanol gel with a 2-D hexagonal structure. A mechanism for DNA separations by those gels with both hydrophilic and hydrophobic domains is discussed.