JP2016512206A - 修飾ヌクレオシドまたは修飾ヌクレオチド - Google Patents
修飾ヌクレオシドまたは修飾ヌクレオチド Download PDFInfo
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Abstract
Description
発明の分野
本明細書に記載するいくつかの実施形態は、3’−ヒドロキシ保護基を含む修飾されたヌクレオチドまたはヌクレオシド、およびポリヌクレオチド配列決定方法における該ヌクレオチドまたはヌクレオシドの使用に関する。本明細書に記載するいくつかの実施形態は、3’−ヒドロキシ保護したヌクレオチドまたはヌクレオシドを調製する方法に関する。
分子の研究の進歩は、一部は、分子または分子の生物学的反応を特徴づけるのに使用される技術の改良によってもたらされてきた。特に、核酸であるDNAおよびRNAの研究は、配列分析におよびハイブリッド形成事象の研究に使用される技術を開発することによって利益を受けてきた。
可逆的保護基は、以前に記載されている。例えばMetzkerら(Nucleic Acids Research、22(20):4259〜4267、1994)は、8個の3’修飾した2−デオキシリボヌクレオシド5’−トリホスフェート(3’修飾したdNTP)の合成および使用、ならびに取り込み活性についての2つのDNAテンプレートアッセイにおける検査を開示している。WO2002/029003は、ポリメラーゼ反応において成長中のDNA鎖上で3’−OH基をキャッピングするためのアリル保護基の使用を含み得る配列決定方法を記載している。
加えて、本発明者らは、その全体が参照により本明細書により組み込まれる国際出願公開WO2004/018497号において、いくつかの可逆的保護基の開発、およびDNA適合条件下でそれらを脱保護する方法を既に報告した。
本明細書に記載するいくつかの実施形態は、プリン塩基またはピリミジン塩基と、3’−炭素原子に共有結合した構造−O−C(R)2N3を形成する除去可能な3’−ヒドロキシ保護基を有するリボースまたはデオキシリボースの糖部分とを含む、修飾されたヌクレオチド分子または修飾されたヌクレオシド分子に関し、ここで、
Rは、水素、−C(R1)m(R2)n、−C(=O)OR3、−C(=O)NR4R5、−C(R6)2O(CH2)pNR7R8および−C(R9)2O−Ph−C(=O)NR10R11からなる群から選択され、
各R1およびR2は、水素、任意に置換されたアルキル、またはハロゲンから独立して選択され、
R3は、水素または必要に応じて置換されたアルキルから選択され、
各R4およびR5は、水素、必要に応じて置換されたアルキル、必要に応じて置換されたアリール、必要に応じて置換されたヘテロアリール、または必要に応じて置換されたアラルキルから独立して選択され、
各R6およびR9は、水素、必要に応じて置換されたアルキル、またはハロゲンから選択され、
各R7、R8、R10およびR11は、水素、必要に応じて置換されたアルキル、必要に応じて置換されたアリール、必要に応じて置換されたヘテロアリール、または必要に応じて置換されたアラルキルから独立して選択され、
mは、0〜3の整数であり、かつ
nは、0〜3の整数であり、但し、m+nの合計は3に等しく、かつ
pは、0〜6の整数であり、但し、
R1およびR2は両方ともハロゲンであることはできず、かつ
少なくとも1つのRは水素ではない。
一実施形態は、3’−OH保護基を含む修飾されたヌクレオチドまたはヌクレオシドである。一実施形態において、3’−OH保護基は、モノフルオロメチル置換したアジドメチル保護基である。別の実施形態において、3’−OH保護基は、C−アミド置換したアジドメチル保護基である。さらに別の実施形態は、ジフルオロメチル置換したアジドメチル3’−OH保護基を有する修飾されたヌクレオチドに関する。
定義
Ac アセチル
Ac2O 無水酢酸
aq. 水性(aqueous)
Bn ベンジル
Bz ベンゾイル
BOCまたはBoc tert−ブトキシカルボニル
Bu n−ブチル
cat. 触媒的
Cbz カルボベンジルオキシ
℃ 摂氏温度
dATP デオキシアデノシントリホスフェート
dCTP デオキシシチジントリホスフェート
dGTP デオキシグアノシントリホスフェート
dTTP デオキシチミジントリホスフェート
ddNTP(s) ジデオキシヌクレオチド(類)
DBU 1,8−ジアザビシクロ[5.4.0]ウンデカ−7−エン
DCA ジクロロ酢酸
DCE 1,2−ジクロロエタン
DCM 塩化メチレン
DIEA ジイソプロピルエチルアミン
DMA ジメチルアセトアミド
DME ジメトキシエタン
DMF N,N’−ジメチルホルムアミド
DMSO ジメチルスルホキシド
DPPA ジフェニルホスホリルアジド
Et エチル
EtOAc 酢酸エチル
ffN 完全機能性ヌクレオチド
g グラム
GPC ゲル浸透クロマトグラフィー
hまたはhr 時間
iPr イソプロピル
KPi pH7.0の10mMリン酸カリウム緩衝液
KPS 過硫酸カリウム
IPA イソプロピルアルコール
IMX 取り込み混合物
LCMS 液体クロマトグラフィー−質量分析
LDA ジイソプロピルアミドリチウム
mまたはmin 分
mCPBA メタ−クロロペルオキシ安息香酸
MeOH メタノール
MeCN アセトニトリル
Mono−F −CH2F
Mono−F ffN アジドメチル3’−OH保護基のメチレン位において置換した−CH2Fを有する修飾されたヌクレオチド
mL ミリリットル
MTBE メチルtert−ブチルエーテル
NaN3 アジ化ナトリウム
NHS N−ヒドロキシスクシンイミド
PG 保護基
Ph フェニル
ppt 沈殿物
rt 室温
SBS 合成による配列決定
TEA トリエチルアミン
TEMPO (2,2,6,6−テトラメチルピペリジン−1−イル)オキシル
TCDI 1,1’−チオカルボニルジイミダゾール
Tert、t 三級
TFA トリフルオロ酢酸
THF テトラヒドロフラン
TEMED テトラメチルエチレンジアミン
μL マイクロリットル
3’−OH保護基−C(R)2N3
3’−OH保護基の脱保護
検出可能な標識
リンカー
A.求電子的に切断されるリンカー
B.求核的に切断されるリンカー
C.光切断可能なリンカー
D.還元条件下での切断
E.酸化条件下での切断
F.セーフティーキャッチリンカー
G.脱離機構による切断
配列決定方法
実験手順
1H NMR (d6 DMSO, 400 MHz): δ, 0.95 (s, 9H, tBu), 2.16 − 2.28 (m, 2H, H-2’), 3.67 (s, OMe), 3.65 -3.85 (m, 2H, HH-5’), 3.77 (dd, J = 11.1, 4.5 Hz, 1H, HH-5’), 3.95-3.98 (m, 1H, H-4’), 4.04 (m, 2H, CH2F), 4.63-4.64 (m, 1H, H-3’), 5.01-5.32 (s, 1H, CH), 6.00 (m, 1H, H-1’), 6.72-6.87 (m, 3H, Ar), 7.35-7.44 (m, 7H, Ar), 7.55-7.60 (m, 4H, Ar), 7.88 (s, 1H, H-6), 9.95 (brt, 1H, NH), 11.70 (s, 1H, NH)
1H NMR (d6 DMSO, 400 MHz): δ 1.02 (s, 9H, tBu), 2.35 − 2.43 (m, 2H, H-2’), 3.76-3.80 (m, 1H, H-5’), 3.88 - 3.92 (m, 1H, H-5’), 4.10 - 4.12 (m, 1H, H-4’), 4.14 (d, J = 4.1 Hz 2H, NHCH2), 4.46-4.60 (m, 3H, H-3’, CH2F), 5.05-5.09 (m, 1H, CHN3), 6.11 (t, J = 6.1 Hz, 1H, H-1’), 7.47 - 7.51 (m, 6H, Ar), 7.64 - 7.68 (m, 4H, Ar), 7.97 (s, 1H, H-6), 10.03 (bt, 1H, J = 10.0 Hz, NH), 11.76 (s, 1H, NH). 19F NMR: -74.3 (CF3), -230.2 (CH2F)
1H NMR (d6 DMSO, 400 MHz): δ 1.01 (s, 9H, tBu), 2.38 − 2.42 (m, 2H, H-2’), 3.74-3.78 (m, 1H, H-5’), 3.86-3.90 (m, 1H, H-5’), 4.00-4.05 (m, 1H, H-4’), 4.12 (d, J = 4.1 Hz 2H, NHCH2), 4.45-4.60 (m, 3H, H-3’, CH2F), 5.00-5.14 (m, 1H, CHN3), 6.09 (t, J = 6.1 Hz, 1H, H-1’), 7.41 - 7.50 (m, 6H, Ar), 7.63-7.66 (m, 4H, Ar), 7.95 (s, 1H, H-6), 10.01 (bs, 1H, NH), 11.74 (s, 1H, NH). 19F NMR: -74.5 (CF3), -230.4 (CH2F)
1H NMR (400 MHz, d6-DMSO): δ 2.24-2.35 (m, 2H, H-2’), 3.56-3.66 (m, 2H, H-5’), 3.96-4.00 (m, 1H, H-4’), 4.23 (s, 2H, CH2NH), 4.33-4.37 (m, 1H, H-3’), 4.43-4.51 (m, CH2F), 5.12 (br.s, 1H, CHN3), 5.23 (br.s, 1H, 5’-OH), 6.07 (t, J=6.7 Hz, 1H, H-1’), 8.26 (s, 1H, H-6), 10.11 (br s, 1H, NH), 11.72 (br s, 1H, NH). 19F NMR: -74.3 (CF3), -230.5 (CH2F)
1H NMR (400 MHz, d6-DMSO): δ 2.24-2.37 (m, 2H, H-2’), 3.57-3.70 (m, 2H, H-5’), 3.97-4.01 (m, 1H, H-4’), 4.23 (br.s, 2H, CH2NH), 4.33-4.37 (m, 1H, H-3’), 4.44-4.53 (m, CH2F), 5.11-5.21 (br.s, 1H, CHN3), 5.23 (br.s, 1H, 5’-OH), 6.07 (t, J=6.6 Hz, 1H, H-1’), 8.23 (s, 1H, H-6), 10.09 (br s, 1H, NH), 11.70 (br s, 1H, NH). 19F NMR: -74.1 (CF3), -230.1 (CH2F)
実験手順
実験手順
1H NMR (400 MHz, d6-DMSO): δ 2.24-2.35 (m, 2H, H-2’), 3.56-3.66 (m, 2H, H-5’), 3.96-4.00 (m, 1H, H-4’), 4.23 (s, 2H, CH2NH), 4.33-4.37 (m, 1H, H-3’), 4.85 (s, 2H, OCH2N3), 5.23 (t, J=5.1 Hz, 1H, 5’-OH), 6.07 (t, J=6.7 Hz, 1H, H-1’), 8.19 (s, 1H, H-6), 10.09 (br s, 1H, NH), 11.70 (br s, 1H, NH). 19F NMR: -74.4 (CF3), -131.6 (CH2F).
1H NMR (400 MHz, d6-DMSO): δ 2.27-2.44 (m, 2H, H-2’), 3.58-3.67 (m, 2H, H-5’), 4.00-4.02 (m, 1H, H-4’), 4.24 (d, J=4.1 Hz, 2H, CH2NH), 4.57-4.58 (m, 1H, H-3’), 5.24-5.29 (m, 2H, 5’-OH, OCHN3), 6.07-6.34 (m, 2H, H-1’, CHF2), 8.19 (s, 1H, H-6), 10.09 (br s, 1H, NH), 11.70 (br s, 1H, NH). 19F NMR: -74.2 (CF3), -131.4 (CH2F).
実施例4
3’−OH保護基の熱安定性試験
実施例5
3’−OH保護基の脱保護
実施例6
配列決定試験
2×400bpの配列決定をMiseq上で実施して、配列決定の品質改善についてのこれらのヌクレオチドの能力を評価した。配列決定ランを製造元(Illumina社、カリフォルニア州サンディエゴ市)の説明書に従って実施した。標準的な取り込み緩衝液をすべてのmono−FブロックしたFFN(各々は、個別の色素標識、すなわちffA−色素1(2uM)、ffT−色素2(1uM)、ffC−色素3(2uM)およびffG−色素4(5uM)を有する)を含有する取り込み緩衝液で置換した。使用したDNAライブラリは、B cereusゲノムDNAから標準的なTruSeqHTプロトコルに従って作製した。
Claims (35)
- プリン塩基またはピリミジン塩基と、3’−炭素原子に共有結合した構造−O−C(R)2N3を形成する除去可能な3’−ヒドロキシ保護基を有するリボースまたはデオキシリボースの糖部分とを含む修飾されたヌクレオチド分子または修飾されたヌクレオシド分子であって、ここで
Rは、水素、−C(R1)m(R2)n、−C(=O)OR3、−C(=O)NR4R5、−C(R6)2O(CH2)pNR7R8および−C(R9)2O−Ph−C(=O)NR10R11からなる群から選択され、
各R1およびR2は、水素、必要に応じて置換されたアルキル、またはハロゲンから独立して選択され、
R3は、水素または必要に応じて置換されたアルキルから選択され、
各R4およびR5は、水素、必要に応じて置換されたアルキル、必要に応じて置換されたアリール、必要に応じて置換されたヘテロアリール、または必要に応じて置換されたアラルキルから独立して選択され、
各R6およびR9は、水素、必要に応じて置換されたアルキル、またはハロゲンから選択され、
各R7、R8、R10およびR11は、水素、必要に応じて置換されたアルキル、必要に応じて置換されたアリール、必要に応じて置換されたヘテロアリール、または必要に応じて置換されたアラルキルから独立して選択され、
mは、0〜3の整数であり、
nは、0〜3の整数であり、但し、m+nの合計は3に等しく、かつ
pは、0〜6の整数であり、但し、
R1およびR2は両方ともハロゲンであることはできず、かつ
少なくとも1つのRは水素ではない、修飾されたヌクレオチド分子または修飾されたヌクレオシド分子。 - Rのうちの1つは水素であり、他方のRは−C(R1)m(R2)nである、請求項1に記載の修飾されたヌクレオチド分子または修飾されたヌクレオシド分子。
- −C(R1)m(R2)nが、−CHF2、−CH2F、−CHCl2または−CH2Clから選択される、請求項1または2に記載の修飾されたヌクレオチド分子または修飾されたヌクレオシド分子。
- −C(R1)m(R2)nが−CHF2である、請求項1〜3のいずれか一項に記載の修飾されたヌクレオチド分子または修飾されたヌクレオシド分子。
- −C(R1)m(R2)nが−CH2Fである、請求項1〜3のいずれか一項に記載の修飾されたヌクレオチド分子または修飾されたヌクレオシド分子。
- Rのうちの1つは水素であり、他方のRは−C(=O)OR3である、請求項1に記載の修飾されたヌクレオチド分子または修飾されたヌクレオシド分子。
- R3が水素である、請求項6に記載の修飾されたヌクレオチド分子または修飾されたヌクレオシド分子。
- Rのうちの1つは水素であり、他方のRは−C(=O)NR4R5である、請求項1に記載の修飾されたヌクレオチド分子または修飾されたヌクレオシド分子。
- R4およびR5が両方とも水素である、請求項1または8に記載の修飾されたヌクレオチド分子または修飾されたヌクレオシド分子。
- R4が水素であり、R5がC1−6アルキルである、請求項1または8に記載の修飾されたヌクレオチド分子または修飾されたヌクレオシド分子。
- R4およびR5が両方ともC1−6アルキルである、請求項1または8に記載の修飾されたヌクレオチド分子または修飾されたヌクレオシド分子。
- Rのうちの1つは水素であり、他方のRは−C(R6)2O(CH2)pNR7R8である、請求項1に記載の修飾されたヌクレオチド分子または修飾されたヌクレオシド分子。
- R6が両方とも水素である、請求項1または12に記載の修飾されたヌクレオチド分子または修飾されたヌクレオシド分子。
- R7およびR8が両方とも水素である、請求項1、12および13のいずれか一項に記載の修飾されたヌクレオチド分子または修飾されたヌクレオシド分子。
- pが0である、請求項1および12〜14のいずれか一項に記載の修飾されたヌクレオチド分子または修飾されたヌクレオシド分子。
- pが6である、請求項1および12〜14のいずれか一項に記載の修飾されたヌクレオチド分子または修飾されたヌクレオシド分子。
- Rのうちの1つは水素であり、他方のRは−C(R9)2O−Ph−C(=O)NR10R11である、請求項1に記載の修飾されたヌクレオチド分子または修飾されたヌクレオシド分子。
- R9が両方とも水素である、請求項1または17に記載の修飾されたヌクレオチド分子または修飾されたヌクレオシド分子。
- R10およびR11が両方とも水素である、請求項1、17および18のいずれか一項に記載の修飾されたヌクレオチド分子または修飾されたヌクレオシド分子。
- R10が水素であり、R11がアミノ置換アルキルである、請求項1、17および18のいずれか一項に記載の修飾されたヌクレオチド分子または修飾されたヌクレオシド分子。
- 前記3’−ヒドロキシ保護基が、ホスフィンを用いた脱保護反応において除去される、請求項1〜14のいずれか一項に記載の修飾されたヌクレオチド分子または修飾されたヌクレオシド分子。
- 前記ホスフィンが、トリス(ヒドロキシメチル)ホスフィン(THP)である、請求項21に記載の修飾されたヌクレオチド分子または修飾されたヌクレオシド分子。
- 前記塩基が、切断可能なリンカーまたは切断不可能なリンカーを介して検出可能な標識に結合している、請求項1〜22のいずれか一項に記載の修飾されたヌクレオチド分子または修飾されたヌクレオシド分子。
- 前記3’−ヒドロキシ保護基が、切断可能なリンカーまたは切断不可能なリンカーを介して検出可能な標識に結合している、請求項1〜22のいずれか一項に記載の修飾されたヌクレオチド分子または修飾されたヌクレオシド分子。
- 前記リンカーが切断可能である、請求項23または24に記載の修飾されたヌクレオチド分子または修飾されたヌクレオシド分子。
- 前記検出可能な標識がフルオロフォアである、請求項23〜25のいずれか一項に記載の修飾されたヌクレオチド分子または修飾されたヌクレオシド分子。
- 前記リンカーは、酸に不安定であるか、光に不安定であるか、またはジスルフィド結合を含有する、請求項23〜26のいずれか一項に記載の修飾されたヌクレオチド分子または修飾されたヌクレオシド分子。
- 配列決定反応における標的一本鎖ポリヌクレオチドと相補的な成長中のポリヌクレオチドを調製する方法であって、請求項1〜27のいずれか一項に記載の修飾されたヌクレオチド分子を該成長中の相補的なポリヌクレオチドに取り込む工程を含み、ここで、該修飾されたヌクレオチドの取り込みは、該成長中の相補的なポリヌクレオチドへのいかなるその後のヌクレオチドの導入も防止する、方法。
- 前記修飾されたヌクレオチド分子の組み込みが、末端トランスフェラーゼ、末端ポリメラーゼまたは逆転写酵素によって達成される、請求項28に記載の方法。
- 標的一本鎖ポリヌクレオチドの配列を決定するための方法であって、
相補的なヌクレオチドの連続的な取り込みをモニターする工程であって、ここで、取り込まれる少なくとも1つの相補的なヌクレオチドが、請求項23〜27のいずれか一項に記載の修飾されたヌクレオチド分子である工程、および
該修飾されたヌクレオチド分子のアイデンティティーを検出する工程
を含む、方法。 - 前記修飾されたヌクレオチドのアイデンティティーが、前記塩基に結合した前記検出可能な標識を検出することによって判定される、請求項30に記載の方法。
- 前記3’−ヒドロキシ保護基および前記検出可能な標識が、次の相補的なヌクレオチドを導入する前に除去される、請求項30または31に記載の方法。
- 前記3’−ヒドロキシ保護基および前記検出可能な標識が、単一工程の化学反応において除去される、請求項32に記載の方法。
- 請求項1〜27のいずれか一項に記載の複数の修飾されたヌクレオチド分子または修飾されたヌクレオシド分子と、そのための包装材料とを含む、キット。
- 酵素と、該酵素の作用に適した緩衝液とをさらに含む、請求項34に記載のキット。
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