JP2009519717A - 位相を固定した配列決定のための方法およびシステム - Google Patents
位相を固定した配列決定のための方法およびシステム Download PDFInfo
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- G01N21/62—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light
- G01N21/63—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
- G01N21/64—Fluorescence; Phosphorescence
- G01N21/6428—Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes"
- G01N2021/6432—Quenching
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Abstract
Description
本出願は、分子解析に関し、より具体的には単一分子の核酸配列決定に関する。
DNA配列決定は、特定のDNA断片のヌクレオチド配列の決定を可能にする。多くの従来のDNA配列決定法では、DNA配列決定反応の観測を容易にするためにフルオロフォアが使用される。塩基すなわちDNA分子の構成単位である4つのヌクレオチドまたはdNTPは、識別可能な蛍光色素で標識され、異なるヌクレオチドから放出される蛍光シグナルを使用して、これらの識別が可能となる。近年想定されたリアルタイムの単一分子の酵素による配列決定法において、dNTP塩基を、テンプレートの一本鎖DNA分子に結合する伸長オリゴヌクレオチドプライマーに1つずつ加える際に、単一ポリメラーゼ分子または酵素を観測する試みが行われている。参考として本明細書で援用される、Levene等の特許文献1を参照されたい。リアルタイムの単一分子の酵素によるDNA配列決定は、Fred Sangerが開発したジデオキシ配列決定法のような、純粋な配列の生成に複合サンプルの調製を必要とする従来のDNA配列決定法に比べると、費用が抑えられ得る。
本開示内容は単一分子核酸配列決定法、核酸の再配列決定および/もしくは検出、ならびに/または、遺伝子発現を含む一塩基多型の特性解析(SNP解析)に関する装置、システム、および方法を提供する。
前述の要約および後述の種々の実施形態における説明は、典型的かつ説明的であるのみであって本教示を限定するものではないことが理解されるべきである。本出願において、特に他の明示がない限り単数の使用は複数を含むものとする。また、他に明示されない限り「または」の使用は「および/または」を意味するものとする。同様に、「含む(comprise)」、「含む(comprises)」、「含む(comprising)」、および「含む(including)」は、これによって制限されることを意図しない。
AR(T)=BE(t)[1−ER(T)]、
図7のトレース730で示すように、閾値時間を使用してdNTPが取り込まれたかどうかを判断することによって得た、最良の配列決定データの精度は、閾値時間が2.1ミリ秒に設定された時に起こるが、この最良の精度は約55%未満である。
Claims (2)
- 標的核酸分子を配列決定するための装置であって、蛍光標識されたヌクレオチド塩基を含む溶液を保持し、それぞれが単一標的核酸分子および単一核酸重合酵素を含む少なくとも1つの単一分子検体を分離および限定するように構成された試料ホルダー;前記試料ホルダーに向ける励起光を生成するように構成された少なくとも1つの第一の光源であって、前記励起光がそれぞれの限定された検体周辺に少量を照射する、光源;ならびに、光パルスを生成して、少なくとも1つの検体で起こる取り込み反応のタイミングを制御するように構成された第二の光源、を備える、装置。
- 標的核酸分子を配列決定する方法であって、蛍光標識されたヌクレオチド塩基を含む溶液中の少なくとも1つの限定された単一分子検体を提供する工程であって、それぞれの単一分子検体が、単一の標的核酸分子および単一の核酸重合酵素を含む、工程;少なくとも1つの光源から少なくとも1つの検体に励起光を向ける工程であって、前記励起光が各検体周辺に少量を照射する、工程;ならびに、少なくとも1つの検体に向けて一連の光パルスを投影して、少なくとも1つの検体で起こる取り込み反応のタイミングを制御する工程、を含む、方法。
Applications Claiming Priority (2)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US75124405P | 2005-12-16 | 2005-12-16 | |
PCT/US2006/062156 WO2007070869A2 (en) | 2005-12-16 | 2006-12-15 | Method and system for phase-locked sequencing |
Publications (1)
Publication Number | Publication Date |
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JP2009519717A true JP2009519717A (ja) | 2009-05-21 |
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JP2008545988A Pending JP2009519717A (ja) | 2005-12-16 | 2006-12-15 | 位相を固定した配列決定のための方法およびシステム |
Country Status (4)
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US (1) | US20070154921A1 (ja) |
EP (1) | EP1963851A4 (ja) |
JP (1) | JP2009519717A (ja) |
WO (1) | WO2007070869A2 (ja) |
Cited By (3)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
JP2011525111A (ja) * | 2008-06-16 | 2011-09-15 | ピーエルシー ダイアグノスティクス, インコーポレイテッド | フェーズ合成による核酸配列決定システム及び方法 |
JP2019522463A (ja) * | 2016-05-16 | 2019-08-15 | ナノストリング テクノロジーズ,インコーポレイティド | サンプル中の標的核酸を検出する方法 |
US11821026B2 (en) | 2016-11-21 | 2023-11-21 | Nanostring Technologies, Inc. | Chemical compositions and methods of using same |
Families Citing this family (12)
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EP2100971A3 (en) * | 2000-07-07 | 2009-11-25 | Visigen Biotechnologies, Inc. | Real-time sequence determination |
US20070172866A1 (en) * | 2000-07-07 | 2007-07-26 | Susan Hardin | Methods for sequence determination using depolymerizing agent |
WO2002044425A2 (en) | 2000-12-01 | 2002-06-06 | Visigen Biotechnologies, Inc. | Enzymatic nucleic acid synthesis: compositions and methods for altering monomer incorporation fidelity |
WO2007072415A2 (en) * | 2005-12-22 | 2007-06-28 | Koninklijke Philips Electronics N.V. | Luminescence sensor operating in reflection mode |
US9423397B2 (en) | 2006-03-10 | 2016-08-23 | Indx Lifecare, Inc. | Waveguide-based detection system with scanning light source |
US9976192B2 (en) | 2006-03-10 | 2018-05-22 | Ldip, Llc | Waveguide-based detection system with scanning light source |
US8288157B2 (en) | 2007-09-12 | 2012-10-16 | Plc Diagnostics, Inc. | Waveguide-based optical scanning systems |
US7951583B2 (en) | 2006-03-10 | 2011-05-31 | Plc Diagnostics, Inc. | Optical scanning system |
US9528939B2 (en) | 2006-03-10 | 2016-12-27 | Indx Lifecare, Inc. | Waveguide-based optical scanning systems |
AU2010241641B2 (en) | 2009-04-29 | 2015-05-14 | Ldip, Llc | Waveguide-based detection system with scanning light source |
US10018566B2 (en) | 2014-02-28 | 2018-07-10 | Ldip, Llc | Partially encapsulated waveguide based sensing chips, systems and methods of use |
WO2016138427A1 (en) | 2015-02-27 | 2016-09-01 | Indx Lifecare, Inc. | Waveguide-based detection system with scanning light source |
Citations (3)
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WO2003021212A1 (en) * | 2001-08-28 | 2003-03-13 | Baylor College Of Medicine | Pulsed-multiline excitation for color-blind fluorescence detection |
WO2005084367A2 (en) * | 2004-03-03 | 2005-09-15 | The Trustees Of Columbia University In The City Of New York | Photocleavable fluorescent nucleotides for dna sequencing on chip constructed by site-specific coupling chemistry |
JP2008520975A (ja) * | 2004-11-16 | 2008-06-19 | ヘリコス バイオサイエンシーズ コーポレイション | Tirf単分子分析および核酸を配列決定する方法 |
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US6232075B1 (en) * | 1998-12-14 | 2001-05-15 | Li-Cor, Inc. | Heterogeneous assay for pyrophosphate detection |
US7056661B2 (en) * | 1999-05-19 | 2006-06-06 | Cornell Research Foundation, Inc. | Method for sequencing nucleic acid molecules |
US6917726B2 (en) * | 2001-09-27 | 2005-07-12 | Cornell Research Foundation, Inc. | Zero-mode clad waveguides for performing spectroscopy with confined effective observation volumes |
CA2425112C (en) * | 2000-10-06 | 2011-09-27 | The Trustees Of Columbia University In The City Of New York | Massive parallel method for decoding dna and rna |
CA2482767A1 (en) * | 2002-04-22 | 2003-10-30 | Joseph F. Lawler, Jr. | Reagents for monitoring nuclei acid amplification and methods of using same |
US7169560B2 (en) * | 2003-11-12 | 2007-01-30 | Helicos Biosciences Corporation | Short cycle methods for sequencing polynucleotides |
US7315019B2 (en) * | 2004-09-17 | 2008-01-01 | Pacific Biosciences Of California, Inc. | Arrays of optical confinements and uses thereof |
AU2006211150A1 (en) * | 2005-01-31 | 2006-08-10 | Pacific Biosciences Of California, Inc. | Use of reversible extension terminator in nucleic acid sequencing |
-
2006
- 2006-12-15 WO PCT/US2006/062156 patent/WO2007070869A2/en active Application Filing
- 2006-12-15 JP JP2008545988A patent/JP2009519717A/ja active Pending
- 2006-12-15 EP EP06846641A patent/EP1963851A4/en not_active Withdrawn
- 2006-12-15 US US11/611,339 patent/US20070154921A1/en not_active Abandoned
Patent Citations (3)
Publication number | Priority date | Publication date | Assignee | Title |
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WO2003021212A1 (en) * | 2001-08-28 | 2003-03-13 | Baylor College Of Medicine | Pulsed-multiline excitation for color-blind fluorescence detection |
WO2005084367A2 (en) * | 2004-03-03 | 2005-09-15 | The Trustees Of Columbia University In The City Of New York | Photocleavable fluorescent nucleotides for dna sequencing on chip constructed by site-specific coupling chemistry |
JP2008520975A (ja) * | 2004-11-16 | 2008-06-19 | ヘリコス バイオサイエンシーズ コーポレイション | Tirf単分子分析および核酸を配列決定する方法 |
Non-Patent Citations (3)
Title |
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PROC.NATL.ACAD.SCI.USA.,VOL.102,NO.15(2005.APR.)P.5346-5351, JPN6011007430, ISSN: 0001847031 * |
PROC.NATL.ACAD.SCI.USA.,VOL.102,NO.17(2005.APR.)P.5926-5931, JPN6011007432, ISSN: 0001847032 * |
PROC.NATL.ACAD.SCI.USA.,VOL.102,NO.17(2005.APR.)P.5932-5937, JPN6011007434, ISSN: 0001847033 * |
Cited By (3)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
JP2011525111A (ja) * | 2008-06-16 | 2011-09-15 | ピーエルシー ダイアグノスティクス, インコーポレイテッド | フェーズ合成による核酸配列決定システム及び方法 |
JP2019522463A (ja) * | 2016-05-16 | 2019-08-15 | ナノストリング テクノロジーズ,インコーポレイティド | サンプル中の標的核酸を検出する方法 |
US11821026B2 (en) | 2016-11-21 | 2023-11-21 | Nanostring Technologies, Inc. | Chemical compositions and methods of using same |
Also Published As
Publication number | Publication date |
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EP1963851A2 (en) | 2008-09-03 |
WO2007070869A2 (en) | 2007-06-21 |
US20070154921A1 (en) | 2007-07-05 |
WO2007070869A3 (en) | 2008-02-28 |
EP1963851A4 (en) | 2009-07-29 |
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