Capturing the diversity of a target gene in environments using gene probes and magnetic beads

• Project/Area Number: 25550061
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Modeling and technologies for environmental conservation and remediation
• Research Institution: The University of Tokyo
• Principal Investigator: TOBINO TOMOHIRO 東京大学, 環境安全研究センター, 助教 (90624916)
• Project Period (FY): 2013-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000); Fiscal Year 2014: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000); Fiscal Year 2013: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
• Keywords: 遺伝子捕捉 / 環境遺伝子 / ハイブリダイゼーション / メタゲノム / 磁気ビーズ / 機能遺伝子 / アンモニア酸化遺伝子 / 遺伝子捕捉反応 / Gene capture metagenome / 遺伝子多様性

Outline of Final Research Achievements

A new method using DNA probes and magnetic beads has been developed to capture and enrich a target gene from environmental gene pools with covering a wide spectrum of the sequence diversity of the gene. Various conditions in the capture reaction were tested to see the effects on fold-enrichment and sequence-specific capturing bias. Trade-off always existed in any conditions between the fold-enrichment and sequence-specific capturing bias when an oligonucleotide probe was used, while the use of single stranded long DNA probe could achieve as high as >10,000 fold-enrichment without giving significant effects on sequence-specific capturing bias.