High molecular weight DNA purification instrument for metagenomics

描述（由申请人提供）：在自然界中观察到的所有微生物中，只有不到1%可以在实验室中培养，这使得研究人员无法在某些环境中研究超过99%的微生物——这些微生物有时具有独特的能力，例如合成可以用作新药或抗生素的化合物。宏基因组学是对不可培养微生物的基因组重建，是获取这些微生物未开发资源的有力新工具。在一种方法中，从含有不可培养微生物的样品中提取DMA的大片段，并将其克隆到大肠杆菌等宿主中，以产生宏基因组文库。然后筛选文库中表达的化合物的效用。虽然用这种方法已经发现了新的抗生素和酶，但要成功地生产由原始微生物合成的化合物，如抗生素，就面临着克隆足够长的片段以容纳长度通常超过100kb的基因簇编码的途径的困难挑战。现有的纯化技术倾向于将基因组DMA剪切为50kb或更小的片段。从土壤等困难样品中提取和纯化高分子量DMA的方法的发现将为宏基因组学提供一个突破，可能使许多未来的药物和抗生素的发现成为可能。我们最近展示了一种用于DMA浓度的非线性电泳方法，该方法能够在没有机械处理（如离心或移液）的情况下进行DMA操作和浓度。从细菌裂解液中提取DNA，并证明了4000倍的浓度因子。该方法是下一代从复杂样品（如土壤或体液）中提取DNA方法的绝佳候选方法。我们建议开发一种仪器来执行这种浓缩方法，验证其在土壤样品中提取高分子量DNA的性能，用于旨在发现新药和抗生素的宏基因组学研究。该技术将获得许可，以解决其他引人注目的应用，包括从体液中提取DNA用于癌症生物标志物和病原体检测。

DESCRIPTION (provided by applicant): Less than 1% of all microorganisms observed in nature can be cultured in the laboratory, leaving researchers unable to study more than 99% of microorganisms in some environments - microorganisms that sometimes have unique abilities such as synthesis of compounds that could find use as new drugs or antibiotics. Metagenomics, the genomic reconstruction of unculturable microorganisms , is a powerful new tool for accessing the untapped resources of these organisms. In one approach, large fragments of DMA from a sample containing unculturable microorganisms are extracted and cloned into a host such as E. coli to produce a metagenomics library. The library is then screened for utility of expressed compounds. Though new antibiotics and enzymes have been discovered with this method, successful production of compounds, such as antibiotics, synthesized by the original microorganism presents the difficult challenge of cloning fragments long enough to hold pathways encoded by gene clusters that are often over 100kb in length. Existing purification techniques tend to shear genomic DMA to fragments of 50kb or less. The discovery of a method to extract and purify high MW DMA from difficult samples such as soil will provide a breakthrough for metagenomics that may enable the discovery of many future drugs and antibiotics. We have recently demonstrated a non-linear electrophoretic method for DMA concentration that is capable of DMA manipulation and concentration without mechanical handling (such as centrifugation or pipetting). Extraction of DNA from bacterial lysate and 4,000 fold concentration factors have been demonstrated. This method is an excellent candidate for the next generation of methods for DNA extraction methods from complex samples such as soil or body fluids. We propose to develop an instrument to carry out this concentration method, validating its performance on extraction of high molecular weight DNA on soil samples for metagenomics studies aimed at discovery of new drugs and antibiotics. Licensing of this technology will be pursued to address other compelling applications including DNA extraction from body fluids for cancer biomarker and pathogen detection.