High molecular weight DNA purification instrument for metagenomics

描述(申请人提供)：在自然界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研究某些环境中超过99%的微生物--有时具有独特能力的微生物，如合成可用作新药或抗生素的化合物。元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强有力的新工具。在一种方法中，从含有不可培养微生物的样本中提取大片段的DMA，并将其克隆到宿主(如大肠杆菌)中，以产生元基因组文库。然后对文库进行筛选，以确定表达化合物的实用性。尽管用这种方法已经发现了新的抗生素和酶，但由原始微生物合成的化合物(如抗生素)的成功生产带来了艰巨的挑战，即克隆足够长的片段，以容纳通常超过100kb的基因簇编码的路径。现有的纯化技术倾向于将基因组DNA剪切成50kb或更小的片段。从土壤等难处理的样品中提取和纯化高相对分子质量的DMA的方法的发现，将为元基因组学提供突破，从而可能发现许多未来的药物和抗生素。我们最近展示了一种用于DMA浓缩的非线性电泳法，该方法能够在不需要机械处理(如离心法或移液法)的情况下操纵和浓缩DMA。从细菌裂解物中提取DNA，浓缩倍数达到4000倍。这种方法是从土壤或体液等复杂样品中提取DNA的下一代方法的极佳候选方法。我们建议开发一种仪器来实现这种浓缩方法，验证其在提取土壤样品中的高分子量DNA的性能，以用于元基因组学研究，旨在发现新药和抗生素。这项技术的许可将用于解决其他引人注目的应用，包括从体液中提取DNA用于癌症生物标记物和病原体检测。

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.