Protein based approaches for further development of the pyrosequencing technology platform

Abstract: The innovation of DNA analysis techniques has enabled arevolution in the field of molecular biology. In the 70’s,first technologies for sequence determination of DNA wereinvented and these techniques enormously increased thepossibilities of genetic research. A large proportion ofmethods for DNA sequencing is based on enzymatic DNA synthesiswith chain termination followed by electrophoretic separationand detection. However, alternative approaches have beendeveloped and one example of this is the pyrosequencingtechnology, which a four-enzyme DNA sequencing method based onreal-time monitoring of DNA synthesis.Currently, the method is limited to analysis of short DNAsequences and therefore it has primarily been used for mutationdetection and single-nucleotide polymorphism analysis. In orderto expand the use of the pyrosequencing technology, the readlength obtained in the methods needs to be improved. However,it was previously shown that the data quality in pyrosequencingtechnology could be significantly increased by addition ofEscherichia coli single-stranded DNAbinding protein, SSB, tothe sequencing reaction. Since little was known about themechanism of this enhancement, we performed a systematic effortto analyse the effect of SSB on 103 clones randomly selectedfrom a cDNA library. We investigated the effect of SSB on theobtained read length in pyrosequencing and identified thecauses of low quality sequences. Moreover, the effciency ofprimer annealing and SSB binding for individual cDNA clones wasinvestigated by use of real-time biosensor analysis. Resultsfrom these experiments show that templates with highperformance in pyrosequencing without SSB possess effcientprimer annealing and low SSB affnity.To minimise the cost of the pyrosequencing system, effcientand scaleable procedures for production and isolation of theprotein components are required. Therefore, protocol foreffcient expression in E.coliand rapid isolation of native SSB was developed.Moreover, by use of a gene fusion strategy, Klenow polymerasewas produced in fusion with the Zbasic domain at high levels inE. coli. This highly charged protein handle enables selectiveand effcient ion exchange purification at physiological pH.Furthermore, active Apyrase was expressed in Methyltropic yeastPichia pastoris and purified by two chromatographic steps.Since pyrosequencing analysis mainly is performed in a96-sample plate format, an increase in sample capacity would bevery beneficial. One approach to achieve this would be to usemicromachined filter chamber arrays where nano-liter samplescan be monitored in real-time. However, to enable accuratepyrosequencing analysis of parallel samples, the produced lightshould preferable be docked to the correct DNA template.Therefore, two different gene fusion strategies were utilisedbased on directed immobilisation of the light-harvesting enzymeLuciferase on the DNA molecules. The thermostable variant ofthe enzyme was genetically fused to a DNA binding protein(either SSB or Klenow) and the Zbasic purification handle, which could beselectively removed by protease cleavage. A protocol wasdeveloped for effcient expression in E.coliand purification by Ion Exchange Chromatography.The proteins were analysed by complete extension of DNAtemplates immobilised on magnetic beadspyrosequencing monitoredby pyrosequencing chemistry. Results from these experimentsshow that the proteins bound selectively to the immobilised DNAand that their enzymatic domains were active.In summary, the work presented in this thesis pinpointsfeatures in the pyrosequencing technology that needs to befurther developed. Moreover, various protein-based strategiesare presented in order to overcome these limitations.Keywords:pyrosequencing, SSB, Zbasic, Klenow, Apyrase, expression, purification,Biacore, DNA template length, Luciferase, affnity, gene fusion,immobilisation.