Analysis of plasmid-DNA and cell protein of recombinant Escherichia coli using capillary gel electrophoresis

Bioprocess monitoring and computer control: key roots of the current PAT initiative

This review article has been written for the journal, Biotechnology and Bioengineering, to commemorate the 70th birthday of Daniel I.C. Wang, who served as doctoral thesis advisor to each of the co-authors, but a decade apart. Key roots of the current PAT initiative in bioprocess monitoring and control are described, focusing on the impact of Danny Wang's research as a professor at MIT. The history of computer control and monitoring in biochemical processing has been used to identify the areas that have already benefited and those that are most likely to benefit in the future from PAT applications. Past applications have included the use of indirect estimation methods for cell density, expansion of on-line/at-line and on-line/in situ measurement techniques, and development of models and expert systems for control and optimization. Future applications are likely to encompass additional novel measurement technologies, measurements for multi-scale and disposable bioreactors, real time batch release, and more efficient data utilization to achieve process validation and continuous improvement goals. Dan Wang's substantial contributions in this arena have been one key factor in steering the PAT initiative towards realistic and attainable industrial applications.

Progress in monitoring, modeling and control of bioprocesses during the last 20 years

The paper gives a review on the recent development of bioprocess engineering. It includes monitoring of product formation processes by flow injection analysis, various types of chromatographic and spectroscopic methods as well as by biosensors. The evaluation of mycelial morphology and physiology by digital image analysis is discussed also. It deals with advanced control of indirectly evaluated process variables by means of state estimation/observer, with the use of structured and hybrid models, expert systems and pattern recognition for process optimization and gives a short report on the state of the art of metabolic flux analysis and metabolic engineering.

Off-line quantitative monitoring of plasmid copy number in bacterial fermentation by capillary electrophoresis

Capillary electrophoresis (CE) is an effective instrumental alternative to conventional slab gel electrophoresis in the determination of plasmid copy number during recombinant protein formation processes. This analytical setup provides efficient separation of different species of linearized plasmid molecules and quantification by UV detection. Both fused silica and gel-filled capillaries are assessed with respect to peak resolution and reproducibility. The application of coated capillaries eliminates the electroosmatic flow to a large extent, resulting in excellent separation of DNA fragments. The application of UV detection enables the analysis of linearized plasmid DNA with a conventional laboratory CE device. All investigated plasmids show good peak resolution due to their significant differences in molecular size, which is essential for sufficient separation of individual DNA molecules.

High-resolution capillary electrophoretic separation of supercoiled plasmid DNAs and their conformers in dilute hydroxypropylmethyl cellulose solutions containing no intercalating agent

The three conformers of plasmid pBR322, linear, supercoiled and nicked circular forms, were separated by capillary electrophoresis (CE) in 0.1% hydroxypropylmethyl cellulose (HPMC) solution in the absence of intercalating agents and the migration order was confirmed by co-migration of enzymatically prepared corresponding DNAs. The previously observed broad peaks of supercoiled DNAs in CE are results of unresolved peaks of topoisomers which differ only in the degrees of twisting. We have demonstrated the separation of an artificial topoisomer ladder made from pBR322 and topoisomerase I. The population of topoisomers of a supercoiled DNA is dependent on sample matrices and separation conditions.

Analysis of laser-induced plasmic DNA photolysis by capillary electrophoresis

Capillary electrophoresis (CE) was used to monitor the laser-induced conversion of supercoiled pKOL8UV5 plasmid DNA into nicked conformers. The plasmid samples (0.1 mg/ml) were incubated in the absence or presence of 110 mumol/l ethidium bromide (EB) and then exposed to 100 J of argon laser radiation (488 nm). The nicked, open circular conformers were separated from the supercoiled DNA by a 15% increase in retention time. Approximately 90% of the control DNA was in the supercoiled form. Laser radiation in the presence of EB caused complete conversion of the supercoiled plasmid DNA into nicked conformers. Laser-induced fluorescence CE (LIF-CE) was about 100-fold more sensitive than UV-CE in the detection of these conformers. Agarose gel electrophoresis confirmed these findings and showed the presence of the nicked plasmid conformers. Based on these comparisons, CE is an efficient analytical tool for the identification of laser-induced conformational changes in plasmid DNA.

An improvement of restriction analysis of bacteriophage DNA using capillary electrophoresis in agarose solution

Seven representatives of the serogroup B Staphylococcus aureus bacteriophages, 29, 53, 55, 83A, 85, phi 11 and 80 alpha, were examined by capillary electrophoresis (CE) for genomic homology using DNA restriction analysis. Genomic DNA of individual bacteriophages was cleaved by HindIII restriction endonuclease, and the resulting restriction fragments were separated by standard horizontal agarose slab gel electrophoresis (SGE) as well as by CE in low-melting-point agarose solutions. The number and size of restriction fragments identified by both methods were compared. The high separation power of CE makes it possible to extend the restriction fragment patterns. In most of the restriction patterns, some additional restriction fragments as small as 150 bp, not identified by SGE, were detected. With respect to speed, high separation efficiency, low sample consumption and automation, CE offers a simple procedure for processing of multiple samples cost-effectively in a reasonable time. The comparison of the complemented restriction patterns of the different phage strains and the subsequent identification of their common fragments leads to a deeper understanding of their phylogenetic relationships. The genome homologies expressed for individual phage pairs in terms of coefficient F values ranged from 15 to 69%. These values are in good accordance with the degree of DNA homology of these phages as determined by DNA hybridization studies and thermal denaturation analysis of DNA by other authors. The total size of each phage genome was estimated by adding the sizes of individual restriction fragments.

The use of coated and uncoated capillaries for the electrophoretic separation of DNA in dilute polymer solutions

We show that both uncoated and polyacrylamide-coated capillaries provide separation of large DNA restriction fragments (2.0-23.1 kbp) by capillary electrophoresis in dilute cellulosic polymer solutions. Uncoated capillaries, however, provide significantly better resolution of DNA fragments, particularly when ultra-dilute polymer solutions are used. This is because electroosmotic flow in uncoated capillaries increases the residence time of DNA in the capillary, without significantly contributing to band-broadening. At a given field strength and polymer concentration in the buffer, the electrophoretic mobilities of DNA restriction fragments in coated capillaries are virtually identical to those previously measured in uncoated capillaries. It is concluded that the fused silica surface of the capillary does not play a significant role in the mechanism of DNA separation by capillary electrophoresis in uncrosslinked polymer solutions. Thus, the separation of large DNA which has been observed to occur in ultra-dilute polymer solutions arises primarily from entanglement interactions between the cellulosic polymers and DNA restriction fragments which occur within the bulk of the polymer solution.