High molecular weight DNA purification instrument for metagenomics

用于宏基因组学的高分子量DNA纯化仪

• 批准号: 7048341
• 负责人: ANDRE MARZIALI
• 金额: $ 21.6万
• 依托单位: UNIVERSITY OF BRITISH COLUMBIA
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-03-01 至 2009-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7048341
• 关键词: DNA; antibiotics; molecular weight; nucleic acid purification; nucleic acids

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.

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，这使研究人员无法在某些环境中研究超过99％的微生物 - 有时具有独特能力的微生物，例如可以使用新药物或抗生素的化合物合成的独特能力。宏基因组学是无法培养的微生物的基因组重建，是一种用于访问这些生物未开发的资源的强大新工具。在一种方法中，从包含不可培养的微生物的样品中提取并将其克隆到大肠杆菌等宿主中以产生元基因组学库中的大量DMA片段。然后将库筛选以获取表达化合物的实用性。尽管已经通过这种方法发现了新的抗生素和酶，但是由原始微生物合成的化合物的成功产生（例如抗生素）提出了克隆片段的困难挑战，足以容纳经常长度超过100kb的基因簇编码的途径。现有的纯化技术倾向于将基因组DMA剪切到50KB或更少的片段。发现一种从困难的样品（例如土壤）中提取和净化高MW DMA的方法将为宏基因组学提供突破，这可能会发现许多未来的药物和抗生素。最近，我们证明了一种用于DMA浓度的非线性电泳方法，该方法能够在没有机械处理的情况下进行DMA操纵和浓度（例如离心或移液）。已经证明了从细菌裂解物中提取DNA和4,000倍浓度因子。该方法是从诸如土壤或体液等复杂样品中提取DNA提取方法的下一代方法的绝佳候选者。我们建议开发一种仪器来执行这种浓度方法，以验证其在旨在发现新药物和抗生素的元基因组学研究上提取土壤样品上的高分子重量DNA的表现。该技术的许可将被追求解决其他引人注目的应用，包括从体液中提取癌症生物标志物和病原体检测的DNA。