JP7275301B2 - Dnaのコード化方法及びそのコード化方法の生命工学的応用 - Google Patents
Dnaのコード化方法及びそのコード化方法の生命工学的応用 Download PDFInfo
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Description
本発明は、DNAのそれぞれの分子量が小さい順に、C、T、A、Gの4つの塩基にそれぞれ00、01、10、11のコードを命名し、各塩基がGとC、及びAとTの塩基対を形成したとき、それぞれの分子量の和がコードの和の比率と一致するようにコードを命名する方法を提供する。
DNAの配列を決定する4つの塩基をコンピュータ言語である2進法の二桁の数で示し、コードに標準化するために各塩基の分子量を分析した後、これを図1に表記した。それぞれの塩基G、A、T、Cと1個のリン酸基とが連結されたデオキシリボヌクレオチド(deoxyribonucleotide)をそれぞれdGMP、dAMP、dTMP、dCMPと表記した。
DNAの各塩基の分子量によって質量が小さいものから大きいものの順にコードを指定したので、DNA断片のコードの総和は、各配列の分子量の比率を反映して計算した(図3)。コードの分子量反映の比率を確認し、6個の例示配列でコードの和と分子量を比較した。
5’ AGAGCTCGCGCCGGAGTTCTCAATGCAAGAGC 3’(配列番号1)
5’ GCGGCGGTGGCCTGAAGTCTGGCGGTGGCCCC 3’(配列番号2)
5’ GCGGCGGTGGCCAGAAGTCTCGCGGTGGCGGC 3’(配列番号3)
5’ GTGGAGGCGGTGGCCAGTCTCGCGGTGGCGGC 3’(配列番号4)
5’ GTGGCGGTGGCCAGCATAGTGGCGGTGGCCAG 3’(配列番号5)
5’ GTGGAGGCGGTGGCCGTGGAGGCGGAGGCCGC 3’(配列番号6)
DNA断片とアプタマーの配列を2進数の塩基コードに変換し、各配列を比較することによって、配列内に含まれている特定パターン及び2次構造(secondary structure)などを把握するために最適化した。これを把握するために、9個の塩基配列で構成されたDNA配列を例示配列として活用した(図4)。
5’ GCGGTGGCG 3’(配列番号7)
11 00 11 11 01 11 11 00 11(例示配列コード1)
DNA配列をコードに変換し、各配列のコードの和を比較することによって特定DNA断片の塩基配列への変異の有無を把握するために最適化した。SNP配列は、塩基1個が変異したDNA断片の配列であるので、コードをSNP配列に適用し、正常配列と比較することによって変異の存在有無及び位置を把握するのが容易になることを確認した。多様なSNP配列のうち一つであり、84%の乳癌患者から確認されるCD44遺伝子のSNP配列に適用し、コード標準化の効率性を確認した。[Zhou,J.,Nagarkatti,P.S.,Zhong,Y.,Creek,K.,Zhang,J.,& Nagarkatti,M.(2010)。Unique SNP in CD44 intron 1 and its role in breast cancer development.Anticancer research,30(4),1263-1272。]
Claims (2)
- コンピュータによって行われる下記のステップを含むDNAをコードに標準化する方法であって、
前記ステップは、
(a)特定DNA断片の塩基配列のC、T、A、Gである4つの塩基をそれぞれ00、01、10、11と命名するステップと、
(b)各塩基がGとCの塩基対を形成したときは、5’から3’方向にGとCの場合を1100と命名し、5’から3’方向にCとGの場合を0011と命名し、及び各塩基がAとTの塩基対を形成したときは、5’から3’方向にAとTの場合を1001と命名し、5’から3’方向にTとAの場合を0110とそれぞれ命名するステップと、
(c)前記(a)ステップの00、01、10、及び11の2進数の数配列を10進数に変形した後でその和を求め、正常配列の和と比較したときに1~3の差がある場合に変異が存在すると判断するステップを含む、DNAをコードに標準化する方法。 - コンピュータ可読媒体に格納され、コンピュータによって請求項1に記載の方法を行えるようにするためのコンピュータ可読媒体に格納されたコンピュータプログラム。
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KR10-2019-0025377 | 2019-03-05 | ||
KR1020190025377A KR102252977B1 (ko) | 2019-03-05 | 2019-03-05 | Dna 코드화 방법 및 그 코드화 방법의 의생명공학적 응용 |
PCT/KR2019/003570 WO2020179962A1 (ko) | 2019-03-05 | 2019-03-27 | Dna 코드화 방법 및 그 코드화 방법의 의생명공학적 응용 |
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JP2022525042A JP2022525042A (ja) | 2022-05-11 |
JP7275301B2 true JP7275301B2 (ja) | 2023-05-17 |
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US (1) | US20220139500A1 (ja) |
EP (1) | EP3937177A4 (ja) |
JP (1) | JP7275301B2 (ja) |
KR (1) | KR102252977B1 (ja) |
WO (1) | WO2020179962A1 (ja) |
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KR20230070674A (ko) * | 2021-11-15 | 2023-05-23 | 주식회사 넥스모스 | 신규한 압타머 및 그 압타머를 유효성분으로 포함하는 인지 기능 개선 및 항노화용 조성물 |
CN116092575A (zh) * | 2023-02-03 | 2023-05-09 | 中国科学院地理科学与资源研究所 | 基于gmns法则的g-dna结构判别方法 |
Citations (3)
Publication number | Priority date | Publication date | Assignee | Title |
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JP2004240975A (ja) | 2003-02-03 | 2004-08-26 | Samsung Electronics Co Ltd | Dna配列符号化装置及び方法 |
US20050187916A1 (en) | 2003-08-11 | 2005-08-25 | Eugene Levin | System and method for pattern recognition in sequential data |
US20160259886A1 (en) | 2013-07-05 | 2016-09-08 | Academy Of Mathematics And System Science, Chinese Academy Of Sciences | Method and system of mapping sequencing reads |
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KR100537523B1 (ko) * | 2003-02-03 | 2005-12-19 | 삼성전자주식회사 | Dna 서열 부호화 장치 및 방법 |
KR20130068185A (ko) * | 2011-12-14 | 2013-06-26 | 한국전자통신연구원 | 염기서열 맵핑 장치 및 그것의 염기서열 맵핑 방법 |
KR20160001455A (ko) | 2014-06-27 | 2016-01-06 | 한국생명공학연구원 | 데이터 저장용 dna 메모리 기술 |
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2019
- 2019-03-05 KR KR1020190025377A patent/KR102252977B1/ko active IP Right Grant
- 2019-03-27 US US17/434,122 patent/US20220139500A1/en active Pending
- 2019-03-27 JP JP2021553075A patent/JP7275301B2/ja active Active
- 2019-03-27 WO PCT/KR2019/003570 patent/WO2020179962A1/ko unknown
- 2019-03-27 EP EP19918443.3A patent/EP3937177A4/en not_active Withdrawn
Patent Citations (3)
Publication number | Priority date | Publication date | Assignee | Title |
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JP2004240975A (ja) | 2003-02-03 | 2004-08-26 | Samsung Electronics Co Ltd | Dna配列符号化装置及び方法 |
US20050187916A1 (en) | 2003-08-11 | 2005-08-25 | Eugene Levin | System and method for pattern recognition in sequential data |
US20160259886A1 (en) | 2013-07-05 | 2016-09-08 | Academy Of Mathematics And System Science, Chinese Academy Of Sciences | Method and system of mapping sequencing reads |
Non-Patent Citations (2)
Title |
---|
SANCHEZ, R.,A genetic code Boolean structure. I. The meaning of Boolean deductions,Bulletin of Mathematical Biology,2005年,p.1-14,DOI : 10.1016/j.bulm.2004.05.005 |
SUNTHORNWAT, R.,Detecting and classifying mutations in genetic code with an application to β-thalassaemia,ScienceAsia [online],2011年,p.51-61,[retrieved on 2022.10.27] URL : http://www.scienceasia.org/2011.37.n1/scias37_51.pdf,DOI : 10.2306/scienceasia1513-1874.2011.37.051 |
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WO2020179962A1 (ko) | 2020-09-10 |
EP3937177A1 (en) | 2022-01-12 |
JP2022525042A (ja) | 2022-05-11 |
EP3937177A4 (en) | 2022-12-07 |
US20220139500A1 (en) | 2022-05-05 |
KR102252977B1 (ko) | 2021-05-17 |
KR20200106761A (ko) | 2020-09-15 |
CN113614834A (zh) | 2021-11-05 |
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