JP7438966B2 - ナノアレイおよびマイクロアレイを製造する方法 - Google Patents
ナノアレイおよびマイクロアレイを製造する方法 Download PDFInfo
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- JJGWLCLUQNFDIS-GTSONSFRSA-M sodium;1-[6-[5-[(3as,4s,6ar)-2-oxo-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]hexanoyloxy]-2,5-dioxopyrrolidine-3-sulfonate Chemical compound [Na+].O=C1C(S(=O)(=O)[O-])CC(=O)N1OC(=O)CCCCCNC(=O)CCCC[C@H]1[C@H]2NC(=O)N[C@H]2CS1 JJGWLCLUQNFDIS-GTSONSFRSA-M 0.000 description 1
- 238000003797 solvolysis reaction Methods 0.000 description 1
- 230000003595 spectral effect Effects 0.000 description 1
- 238000004544 sputter deposition Methods 0.000 description 1
- 238000010186 staining Methods 0.000 description 1
- 239000007858 starting material Substances 0.000 description 1
- 230000000707 stereoselective effect Effects 0.000 description 1
- 229940014800 succinic anhydride Drugs 0.000 description 1
- 229940124530 sulfonamide Drugs 0.000 description 1
- 238000006277 sulfonation reaction Methods 0.000 description 1
- 125000001174 sulfone group Chemical group 0.000 description 1
- 150000003457 sulfones Chemical class 0.000 description 1
- 125000000472 sulfonyl group Chemical group *S(*)(=O)=O 0.000 description 1
- 230000001502 supplementing effect Effects 0.000 description 1
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- 238000010189 synthetic method Methods 0.000 description 1
- 229920001059 synthetic polymer Polymers 0.000 description 1
- IEGYTTZAHJJGLG-UHFFFAOYSA-N tert-butyl n-[2-[[4-[[4-(3-azidopropoxy)phenyl]diazenyl]benzoyl]amino]ethyl]carbamate Chemical compound C1=CC(C(=O)NCCNC(=O)OC(C)(C)C)=CC=C1N=NC1=CC=C(OCCCN=[N+]=[N-])C=C1 IEGYTTZAHJJGLG-UHFFFAOYSA-N 0.000 description 1
- JTPJJKZSKWNWKK-UHFFFAOYSA-N tert-butyl n-pent-4-ynylcarbamate Chemical compound CC(C)(C)OC(=O)NCCCC#C JTPJJKZSKWNWKK-UHFFFAOYSA-N 0.000 description 1
- 150000003512 tertiary amines Chemical class 0.000 description 1
- FPGGTKZVZWFYPV-UHFFFAOYSA-M tetrabutylammonium fluoride Chemical compound [F-].CCCC[N+](CCCC)(CCCC)CCCC FPGGTKZVZWFYPV-UHFFFAOYSA-M 0.000 description 1
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- JOXIMZWYDAKGHI-UHFFFAOYSA-N toluene-4-sulfonic acid Chemical class CC1=CC=C(S(O)(=O)=O)C=C1 JOXIMZWYDAKGHI-UHFFFAOYSA-N 0.000 description 1
- CRDAMVZIKSXKFV-UHFFFAOYSA-N trans-Farnesol Natural products CC(C)=CCCC(C)=CCCC(C)=CCO CRDAMVZIKSXKFV-UHFFFAOYSA-N 0.000 description 1
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- 230000001052 transient effect Effects 0.000 description 1
- 150000003918 triazines Chemical class 0.000 description 1
- YNJBWRMUSHSURL-UHFFFAOYSA-N trichloroacetic acid Chemical compound OC(=O)C(Cl)(Cl)Cl YNJBWRMUSHSURL-UHFFFAOYSA-N 0.000 description 1
- JXUKBNICSRJFAP-UHFFFAOYSA-N triethoxy-[3-(oxiran-2-ylmethoxy)propyl]silane Chemical compound CCO[Si](OCC)(OCC)CCCOCC1CO1 JXUKBNICSRJFAP-UHFFFAOYSA-N 0.000 description 1
- BDZBKCUKTQZUTL-UHFFFAOYSA-N triethyl phosphite Chemical compound CCOP(OCC)OCC BDZBKCUKTQZUTL-UHFFFAOYSA-N 0.000 description 1
- ILWRPSCZWQJDMK-UHFFFAOYSA-N triethylazanium;chloride Chemical compound Cl.CCN(CC)CC ILWRPSCZWQJDMK-UHFFFAOYSA-N 0.000 description 1
- 230000001960 triggered effect Effects 0.000 description 1
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- KZRMTEVIDYXWQW-CYCLDIHTSA-K trisodium;[[[(2r,3s,4r,5r)-5-(2-amino-6-oxo-3h-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-oxidophosphoryl] phosphate Chemical compound [Na+].[Na+].[Na+].C1=2NC(N)=NC(=O)C=2N=CN1[C@@H]1O[C@H](COP(O)(=O)OP([O-])(=O)OP([O-])([O-])=O)[C@@H](O)[C@H]1O KZRMTEVIDYXWQW-CYCLDIHTSA-K 0.000 description 1
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- HBOMLICNUCNMMY-XLPZGREQSA-N zidovudine Chemical compound O=C1NC(=O)C(C)=CN1[C@@H]1O[C@H](CO)[C@@H](N=[N+]=[N-])C1 HBOMLICNUCNMMY-XLPZGREQSA-N 0.000 description 1
Images
Classifications
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K1/00—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
- C07K1/04—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length on carriers
- C07K1/047—Simultaneous synthesis of different peptide species; Peptide libraries
-
- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
- G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
- G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
- G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
- G01N33/543—Immunoassay; Biospecific binding assay; Materials therefor with an insoluble carrier for immobilising immunochemicals
- G01N33/54353—Immunoassay; Biospecific binding assay; Materials therefor with an insoluble carrier for immobilising immunochemicals with ligand attached to the carrier via a chemical coupling agent
-
- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
- G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
- G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
- G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
- G01N33/543—Immunoassay; Biospecific binding assay; Materials therefor with an insoluble carrier for immobilising immunochemicals
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6813—Hybridisation assays
- C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
- C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
Description
本出願は、2018年4月4日に出願された米国仮特許出願第62/652,849号の恩典を主張し、これは参照により本明細書に完全に組み入れられる。
マイクロアレイおよびナノアレイは、生物学的および化学的実体を評価するために使用され得る。ナノアレイおよびマイクロアレイの設計を特定の評価用に調整することが有益であり得る。
本明細書において言及される全ての刊行物、特許、および特許出願は、個々の刊行物、特許、および特許出願の各々が参照により組み入れられるために具体的かつ個々に示されているかのように同程度まで、参照により本明細書に組み入れられる。
固体支持体の表面にわたって空間的に分布しておりかつ該表面と安定的に相互作用している複数の分子を有するマイクロアレイおよびナノアレイは、バイオアナリシスおよび関連分野においてますます重要なツールとなりつつある。ポリペプチドおよびポリヌクレオチドの両方のマイクロアレイが開発され、遺伝子シーケンシング、遺伝子発現のモニタリング、遺伝子マッピング、細菌の同定、創薬、およびコンビナトリアルケミストリー等の様々な適用分野において用途が見出される。特にマイクロアレイが用途を見出す一つの領域は、遺伝子発現解析における領域である。
いくつかの場合において、生体分子または固体支持体のエポキシドまたはオキシランが、バイオコンジュゲーションのために利用され得る。例えば、生体分子のエポキシドまたはオキシラン基は、開環プロセスにおいて求核剤と反応し得る。反応は、第1級アミン、スルフヒドリル、またはヒドロキシル基と起こり得、それぞれ、第2級アミン、チオエーテル、またはエーテル結合を作る。
いくつかの場合において、低分子量モノマーの重合が、バイオコンジュゲーションのために利用され得る。重合は、2つの機構のうちの1つ、鎖成長または段階的成長のいずれかを介して進行すると分類され得る。鎖成長重合中、モノマーは成長中のポリマー鎖の「活性」末端で付加され、低変換でさえ高分子量材料の形成がもたらされる。段階的成長重合中、短いオリゴマー鎖がカップリングしてポリマー化学種を形成し、高分子量に達するために高変換を必要とする。両方の技術が生体分子-ポリマーコンジュゲートを形成するために使用され得る。アクリレートおよびメタクリレートモノマーの重合は、特に有益であると分かった。例えば、アクリレートおよびメタクリレート修飾ペプチドおよびグリカンは容易に重合され得る。同様に、合成オリゴヌクレオチドホスホロアミダイト構築ブロック「Acrydite」、フリーラジカル重合の利用可能性は、DNAおよびRNA官能化生体材料を形成するための最も一般的な方法のうちの1つのままである。コモノマーの存在下で重合を行うことによって、生体分子提示の密度は容易に調整され得、立体障害からの潜在的な困難が克服されることを可能にする。重合の開始は、熱、UVおよび可視光、酸化還元反応、ならびに電気化学を含む、多数の手段によって誘発され得る。アクリレート修飾タンパク質もまた、重合を受け、生物学的活性を保持しつつ機能材料を生成し得る。いくつかの場合において、リビングラジカル重合(LRP)がバイオコンジュゲーションのために利用され得る。例えば、バイオコンジュゲートの形成のための最も一般的に使用されるLRPとしては、原子移動ラジカル重合(ATRP)、可逆的付加開裂連鎖移動(RAFT)重合、およびニトロキシド媒介重合(NMP)が挙げられる。
バイオコンジュゲーションについての粒子上の一般的な官能基または反応基
オリゴを最終濃度100uMになるようにdH20で戻した。ただし、伸長プライマーは500uM (2.9mg/ml)になるように戻した。伸長プライマーをDeep Red 200nmビーズにコンジュゲートさせた。
サーモサイクラー条件:
95℃で30秒間
0.1℃/sで50℃まで下げる
4℃で維持する
ローリングサークルテンプレートのライゲーション
100μLのNEB T4 DNAリガーゼ[400,000u/ml]を添加する
サーモサイクラー条件:
70℃で30秒間
0.1℃/sで40℃まで下げる
4℃で維持する
ナノ粒子を構築するためのローリングサークル増幅
ボルテックスして混合し、次いで以下を添加した:
プライミングされたローリングサークルテンプレート 300μL
ボルテックスして混合し、次いで以下を添加した:
NEB phi29ポリメラーゼ[10Ku/ml] 50μL
反転して混合した。反応混合物をPCRチューブ中に63μLアリコートへと等分した。
以下でインキュベートした:
30℃で120分間
65℃で10分間。
サンプルをプールし、90ulの250mM EDTAを添加した。
サンプルを4℃にて5分間12,500Gで遠心分離した。上澄みを回収し、白色ペレットを廃棄した。
サンプル(100ul)に対して1:100で連続希釈を行い(+1:10希釈)、2ulのSybr Gold (1×)を添加した。アミン表面処理スライド上に1ulスポットを加えて画像化した。図3および図4において見られるように、DNA SNAPが首尾よく形成され、DNA SNAPとDeep Redボールの間で高度の共局在が見られた。
いくつかの場合において、SNAPを、それらが結合しているチップまたはアレイ等の表面から取り外すことができる。SNAPの取り外しは、例えば、高量のアセトニトリル、高濃度の水酸化ナトリウム、または高濃度の塩によって媒介され得る。高量のアセトニトリルは、少なくとも約20%、30%、40%、50%、60%、70%、80%、90%、または100%アセトニトリルの最終パーセンテージであり得る。高量の水酸化ナトリウムは、少なくとも約0.1 M、0.5 M、1 M、2 M、3 M、4 M、5 M、6 M、7 M、8 M、9 M、または10 Mであり得る。高量の塩は、少なくとも約0.1 M、0.5 M、1 M、2 M、3 M、4 M、5 M、6 M、7 M、8 M、9 M、または10 Mであり得る。使用される塩は、例えばMgCl2またはNaClであり得る。いくつかの場合において、DMSOまたはホルムアミド等のカオトロピック試薬がSNAPの取り外しを媒介し得る。
さらなる例において、Epimark Taqポリメラーゼを使用して、SNAP生成を最適化した。SNAPテンプレートを、実施例1、段落[0071]~[0076]に記載の方法に従って調製した。Taqポリメラーゼは、phi29ポリメラーゼよりもSNAPサイズに対してより良い制御を有すると決定された。500μl反応混合物を、8683 ngテンプレートを使用して調製した。以下の試薬を1.5 ml PCRチューブ内で混合した:
PCRミックス:
PCRチューブ内でPCRミックスを短時間ボルテックスした。ボルテックスした後、2.5μlのEpimark TaqポリメラーゼをPCRミックスに添加した。PCRチューブを反転し、ポリメラーゼと他の試薬を混合した。PCRミックスをサーマルサイクラー中に置いた。最初にテンプレートDNAを94℃で30秒間変性させた。反応混合物を以下の熱的条件下で30サイクル増幅させた:
94℃で30秒間変性
53℃で60秒間アニーリング
68℃で30秒間伸長
最終熱サイクル後、SNAPを68℃でさらに5分間保持した。次に、PCRチューブを4℃まで冷却し、精製まで保持した。
SNAPのバッチは本明細書に記載されているように生成可能である。SNAPが生成されると、それらを精製することができる。SNAPを精製可能な3工程の例示的プロトコルを、以下に記載する。
高速タンパク質液体クロマトグラフィー(FPLC)陰イオン交換クロマトグラフィーを使用して、SNAPを精製した。ここでは、塩勾配を用いて、異なって帯電したDNA分子(SNAP)を収集のために分離した。3つのフラクション(下部、中央、上部)を分析のために収集した。
陰イオン交換クロマトグラフィーを行った後、標準的な透析プロトコルによって塩を除去した。簡潔には、透析は、半透膜を通しての選択および受動拡散によって溶液中の高分子(例えばSNAP)からの小さい不要な化合物(例えば塩)の除去を促進し得る分離技術である。塩の除去を必要とするSNAPを含む陰イオン交換精製されたサンプルと、緩衝液とを、膜の反対側に置いた。SNAPは膜のサンプル側に保持されたが、塩は膜を自由に通過することができた。塩はSNAPとは反対の膜の側に収集され、従って、サンプル中の塩の濃度は低下した。このようにして、サンプル中の塩等の小さな混入物質の濃度を、許容されるかまたは無視できるレベルまで低下させた。
標準的な真空遠心分離プロトコルを使用して、従来のアプローチと比較して最小限の損失でSNAPのバッチを濃縮した。
本明細書に記載されているようにSNAPを生成し、ナノ粒子サイズを測定した。
SNAPのバッチを、フィーチャーを有するアレイに別々に加え、標準的な画像化プロトコルを使用して画像化した。アレイ間の濃淡値の違いによって測定したところ、最大濃淡値は約12,000であり、SNAPを有する領域と有さない領域との濃淡値の差異は約6,000であった。このように、SNAPはアレイに結合することができ、コンジュゲートされたSNAPが検出可能である。
SNAPを濃縮した後、SNAPの濃度を測定することができる。例えば、アミンとコンジュゲートしたSNAPは、図12の左上に示されているようなo-フタルジアルデヒド(OPA)遊離アミン反応を使用して定量することができる。簡潔には、OPAはアミンと反応して蛍光検出を可能にし得、標準曲線(例えば、0~100μMのポリTアミン連続希釈液、図12の左下)が行われる場合、定量を可能にし得る。
SNAPへのアジド-AlexaFluor 586のクリックコンジュゲーションがチップ上で行われるように、実験を行った。DBCO-SNAP(488) (488 nmで蛍光を発することができる色素にコンジュゲートされたDBCO基を有するSNAP)をフローによってアレイ上に固定化し、488 nm(SNAPチャネル)および575 nm (アジド色素チャネル)で画像を取得した。次いで、568 nmで蛍光を発することができるアジド-568 (アジド-AlexaFluor 568)をアレイ上でインキュベートしてDBCOとアジドの間のコンジュゲーション反応を可能にし、インキュベーション後にアレイを洗浄した。このプロトコルに続いて、488 nmおよび575 nmで再び画像を取得し、DBCO-アジド反応の程度を評価した。インキュベーション後、アジド色素チャネルは、インキュベーション前と比べ得て有意により多い蛍光を示した。SNAPチャネル(対照)は反応前後で同様のシグナルを示した(図14)。これは、チップ(アレイ)上でDBCOとアジドの間のクリックコンジュゲーションが実行可能であり得ることを示している。
PEとコンジュゲートした(R-フィコエリトリンとコンジュゲートした)アジドのクリックコンジュゲーションがチップ上で行われるように、実験を行った。DBCOハンドルおよび488 nmで蛍光を発することができるヌクレオチドを用いて、SNAPを調製した。SNAPをチップ表面上に堆積し、1時間インキュベートしてチップ表面に結合させた。チップを、ブロッキング緩衝液と共に15分~30分間インキュベートし、1000×モル過剰量のPE SNAPが存在するように、アミン上にアジドハンドルを有するPE(1 mg/ml)をチップ上に放った。次いでチップを一晩インキュベートした。次いで、2% tweenを含むリン酸緩衝食塩水(PBST)でチャネルを洗浄し、画像化した。
DBCOハンドルで調製されたSNAPを、チップ表面上に堆積し、チップ表面に結合させるために十分に長くインキュベートさせることができる。次いで、チップをブロッキング緩衝液と共に15分~30分間インキュベートすることができる。
DNA折り紙SNAPは、例えばDBCOハンドルで調製され得、チップ表面上に堆積され、チップ表面に結合するために十分に長くインキュベートさせることができる。いくつかの場合において、DNA折り紙SNAPは、グリッド様の様式でアレイ上に堆積され得る。いくつかの場合において、折り紙SNAPは約300 nmであり得る。
SNAPをフローによってアレイ上に固定化した。SNAPの蛍光を、100×100ミクロン視野で標準的な画像化プロトコルを使用して検出した(図18Aおよび18D)。ビオチンハンドルを含む大腸菌溶解液をアレイに加え、タンパク質をSNAPに結合させた。対照として、ビオチンハンドルを欠く溶解液にSNAPを曝露し、これとコンジュゲートさせた。図18B(ビオチンハンドル)および18E(対照)において見られるように、100×100ミクロン視野で蛍光ストレプトアビジン(これは検出のためにビオチンに結合することができる)を使用する標準的な画像化プロトコルを使用して蛍光イメージングを行い、溶解液を検出した。固定化された溶解液はビオチンタグを含有しないため、タンパク質は蛍光ストレプトアビジンによって検出されない。この対照は、(B)で観察された検出シグナルが固定化タンパク質に特異的であること(即ち、アレイ表面へのストレプトアビジン検出試薬の非特異的結合は存在しないこと)を実証する。
蛍光標識されたSNAPをフローによってアレイ上に固定化した。当該SNAPに小さなペプチド(HHH*)をコンジュゲートさせた。対照として、SNAPをチップに固定化し、当該SNAPにはペプチドをコンジュゲートさせなかった。小さなHHHペプチドに特異的な蛍光アプタマーを加えた。SNAPの蛍光を、35×35ミクロン視野で標準的な画像化プロトコルを使用して検出した(図19Aおよび19D)。この視野はチップ上の1つのサブアレイの隅を示し得る。固定化されたSNAPは、アレイ上の不連続スポットとして見られ得る(これらのスポットの各々は直径が300 nmである)。
一態様において、本発明は以下を提供する。
(項目1)
タンパク質に共有結合している構造化核酸粒子(structured nucleic acid particle)(SNAP)を含む、組成物。
(項目2)
前記SNAPが固体支持体に結合している、項目1記載の組成物。
(項目3)
前記SNAPが固体支持体に共有結合している、項目2記載の組成物。
(項目4)
前記SNAPが固体支持体に非共有結合している、項目2記載の組成物。
(項目5)
生体分子に共有結合している核酸SNAPを含む、組成物。
(項目6)
前記SNAPが固体支持体に結合している、項目5記載の組成物。
(項目7)
前記SNAPが固体支持体に共有結合している、項目6記載の組成物。
(項目8)
前記SNAPが固体支持体に非共有結合している、項目6記載の組成物。
(項目9)
複数の構造化核酸粒子(SNAP)に結合している固体支持体を含む組成物であって、該複数のSNAPの各々が生体分子に結合している、組成物。
(項目10)
前記複数のSNAPがアレイ状に配置されている、項目9記載の組成物。
(項目11)
単一のタンパク質を固体支持体上の結合部位に結合させる方法であって、
該結合部位が該タンパク質より大きく;
該方法が、
該タンパク質を構造化核酸粒子(SNAP)に共有結合させる工程であって、該SNAPの直径が少なくとも該結合部位の直径と同じ大きさである、工程;および
該核酸SNAPを該結合部位に結合させる工程
を含む、方法。
(項目12)
各結合部位が単一のタンパク質に結合するように、複数の前記タンパク質の各々が前記固体支持体上の結合部位に結合する、項目11記載の方法。
(項目13)
固体支持体に結合している複数の生体分子を含む生体分子アレイであって、該複数の生体分子の各生体分子がリンカーに共有結合しており、該リンカーが該固体支持体に結合しており、かつ各リンカーが該複数の生体分子のうちの一つの生体分子のみに結合しており、各リンカーが少なくとも50nmの直径を有する、生体分子アレイ。
(項目14)
複数のタンパク質から空間的に分離されているタンパク質のアレイを製造する方法であって、該複数のタンパク質の各タンパク質を、構造化核酸粒子(SNAP)を構成する核酸分子の末端に共有結合させる工程、該SNAPを固体支持体に結合させる工程を含み、それによって空間的に分離されているタンパク質のアレイを製造する、方法。
(項目15)
タンパク質、構造化核酸粒子(SNAP)、および固体支持体を含む組成物であって、該タンパク質が該SNAPに共有結合しており、かつ該タンパク質が該固体支持体に接触していない、組成物。
(項目16)
空間的に分離されている生物学的または化学的実体のアレイを製造する方法であって、
結合部位を有する固体支持体を得る工程、
複数の生物学的または化学的実体を含むサンプルを得る工程、
各々が官能基を有するシードを得る工程、
該複数の生物学的または化学的実体の各生物学的または化学的実体を、該官能基を介して単一のシードに共有結合させる工程、
結合した各シードを所望のサイズの構造化核酸粒子(SNAP)へと成長させる工程、
該SNAPを該アレイの結合部位に結合させる工程
を含み、
それによって、空間的に分離されている生物学的または化学的実体のアレイを製造する、方法。
(項目17)
前記固体支持体がガラス支持体である、項目16記載の方法。
(項目18)
前記固体支持体がシリカ支持体である、項目16記載の方法。
(項目19)
前記固体支持体がプラスチック支持体である、項目16記載の方法。
(項目20)
前記固体支持体がシリコン支持体である、項目16記載の方法。
(項目21)
前記固体支持体が金支持体である、項目16記載の方法。
(項目22)
前記固体支持体が金属支持体である、項目16記載の方法。
(項目23)
前記固体支持体がクロム支持体である、項目16記載の方法。
(項目24)
前記固体支持体がチタン支持体である、項目16記載の方法。
(項目25)
前記固体支持体が酸化チタン支持体である、項目16記載の方法。
(項目26)
前記固体支持体がスズ支持体である、項目16記載の方法。
(項目27)
前記固体支持体が酸化スズ支持体である、項目16記載の方法。
(項目28)
前記固体支持体が光学的に不透明である、項目16記載の方法。
(項目29)
前記固体支持体が光学的に透明である、項目16記載の方法。
(項目30)
前記固体支持体が、正電荷を有するように修飾されている、項目16記載の方法。
(項目31)
前記固体支持体が、負電荷を有するように修飾されている、項目16記載の方法。
(項目32)
前記固体支持体が、前記SNAPに結合し得る官能基を有するように修飾されている、項目16記載の方法。
(項目33)
前記固体支持体が、周囲の表面とは異なるように修飾されている結合部位を含む、項目16記載の方法。
(項目34)
前記固体支持体が結合部位のアレイを含む、項目27記載の方法。
(項目35)
各結合部位が、他の結合部位の各々から少なくとも70nm離れている、項目34記載の方
法。
(項目36)
各結合部位が、他の結合部位の各々から少なくとも25nm離れている、項目34記載の方法。
(項目37)
任意の2つの結合部位の端部間の距離が、使用される前記SNAPの半径よりも大きい、項目34記載の方法。
(項目38)
任意の2つの結合部位の端部間の距離が、使用される前記SNAPの直径よりも大きい、項目34記載の方法。
(項目39)
前記分子がタンパク質である、項目16記載の方法。
(項目40)
前記シードがオリゴヌクレオチドである、項目16記載の方法。
(項目41)
前記オリゴヌクレオチドの3'末端が官能基で修飾されている、項目40記載の方法。
(項目42)
前記オリゴヌクレオチドの5'末端が官能基で修飾されている、項目40記載の方法。
(項目43)
前記官能基が、アミン、チオール、カルボン酸、三重結合、二重結合、エポキシド、アルキン、アルケン、シクロアルキン、アジド、シクロオクチン、シクロアルキン、ノルボルネン、テトラジン、シクロオクタン、エポキシド、およびヒドロキシルからなる群より選択される、項目41または42のいずれか一項記載の方法。
(項目44)
前記オリゴヌクレオチドが、光切断可能な結合を含むように修飾されている、項目40記載の方法。
(項目45)
前記SNAPがローリングサークル増幅によって形成される、項目16記載の方法。
(項目46)
前記SNAPがデンドリマーである、項目16記載の方法。
(項目47)
前記デンドリマーが正に帯電している、項目46記載の方法。
(項目48)
前記アレイ上の結合部位が負に帯電している、項目47記載の方法。
(項目49)
前記デンドリマーが負に帯電している、項目46記載の方法。
(項目50)
前記アレイ上の結合部位が正に帯電している、項目49記載の方法。
(項目51)
前記SNAPがおよそ100nmの直径を有する、項目50記載の方法。
(項目52)
前記SNAPがおよそ300nmの直径を有する、項目45記載の方法。
(項目53)
前記SNAPが約10nm~500μmの直径を有する、項目45記載の方法。
(項目54)
前記SNAPが約10nm~50μmの直径を有する、項目45記載の方法。
(項目55)
前記SNAPが約10nm~5μmの直径を有する、項目45記載の方法。
(項目56)
前記SNAPが約100nm~500nmの直径を有する、項目45記載の方法。
(項目57)
前記SNAPが、静電相互作用を通じて前記固体支持体に付着する、項目45記載の方法。
(項目58)
分子の空間的分離を達成する方法であって、
複数の分子を得る工程、
各々が官能基を有するシードを得る工程、
該複数の分子の各々を、該官能基を介して単一のシードに共有結合させる工程、
結合した各シードを、所望のサイズの構造化核酸粒子(SNAP)へと成長させる工程、
該SNAPを固体支持体に結合させる工程
を含み、
それによって単一分子の空間的分離を達成する、方法。
(項目59)
単一分子のアレイであって、各単一分子が所望のサイズの構造化核酸粒子(SNAP)に結合しており、該SNAPが該結合部位を介してアレイに結合している、単一分子のアレイ。
(項目60)
単一分子のアレイを製造するためのキットであって、
結合部位を有するアレイ、
各シードが単一の結合部位を有する、シード、および
該シードを構造化核酸粒子(SNAP)へと成長させるための試薬
を含む、キット。
(項目61)
固体支持体;および
該固体支持体に直接結合しているポリマーベースの分子であって、該ポリマーベースの分子が、実質的に該固体支持体の反対側に配置されているタンパク質部分を含み、かつ、該タンパク質部分が親和性試薬にアクセス可能である、ポリマーベースの分子
を含む、組成物。
(項目62)
アレイ上で生物学的または化学的実体を隔離する方法であって、
複数の構造化核酸粒子(SNAP)を作製する工程;
単一の生物学的または化学的実体を該複数のSNAPの各々にカップリングさせる工程;
該複数のSNAPをアレイに結合させる工程であって、該生物学的または化学的実体が実質的に該アレイの反対側にある、工程
を含み、
それによって、該複数のSNAPの各々の各生物学的または化学的実体を、該複数のSNAPの各SNAPのサイズに基づく距離だけ隔離する、方法。
(項目63)
分子を分離する方法であって、各分子をより大きな荷電分子に変換する工程を含む、方法。
(項目64)
各分子をより大きな荷電分子に変換する工程が、所望のサイズへと成長することができるバイオポリマーに該分子をコンジュゲートさせることを含む、項目63記載の方法。
(項目65)
各分子をより大きな荷電分子に変換する工程が、各分子を10倍大きい分子に変換することを含む、項目63記載の方法。
(項目66)
各分子をより大きな荷電分子に変換する工程が、各分子をより大きな荷電分子にコンジュゲートさせることを含む、項目63記載の方法。
(項目67)
空間的に分離されている生物学的または化学的実体のアレイを製造する方法であって、
結合部位を有する固体支持体を得る工程、
複数の生物学的または化学的実体を含むサンプルを得る工程、
各々が官能基を有する構造化核酸粒子(SNAP)を得る工程、
該複数の生物学的または化学的実体の各生物学的または化学的実体を単一のSNAPに共有結合させる工程、
該SNAPを該アレイの該結合部位に結合させる工程、
を含み、
それによって、空間的に分離されている生物学的または化学的実体のアレイを製造する、方法。
(項目68)
前記SNAPがローリングサークル増幅産物である、前記項目のいずれか一項記載の組成物。
(項目69)
前記SNAPがプラスミドである、前記項目のいずれか一項記載の組成物。
(項目70)
前記SNAPがDNA折り紙分子である、前記項目のいずれか一項記載の組成物。
(項目71)
前記SNAPが核酸クラスターである、前記項目のいずれか一項記載の方法。
(項目72)
前記SNAPがローリングサークル増幅産物である、前記項目のいずれか一項記載の方法。
(項目73)
前記SNAPがプラスミドである、前記項目のいずれか一項記載の方法。
(項目74)
前記SNAPがDNA折り紙分子である、前記項目のいずれか一項記載の方法。
(項目75)
前記SNAPが核酸クラスターである、前記項目のいずれか一項記載の方法。
(項目76)
前記SNAPがローリングサークル増幅産物である、前記項目のいずれか一項記載のキット。
(項目77)
前記SNAPがプラスミドである、前記項目のいずれか一項記載のキット。
(項目78)
前記SNAPがDNA折り紙分子である、前記項目のいずれか一項記載のキット。
(項目79)
前記SNAPが核酸クラスターである、前記項目のいずれか一項記載のキット。
Claims (14)
- 単一のタンパク質を固体支持体上の1つの結合部位に結合させる方法であって、
該方法が、
該単一のタンパク質を、核酸折り紙を含む構造化核酸粒子(SNAP)に共有結合させる工程であって、該SNAPの直径が少なくとも該結合部位の直径と同じ大きさである、工程;および
各単一のタンパク質が該SNAPの1つに結合しており、該1つのSNAPが前記1つの結合部位に結合するように、該SNAPを該結合部位に結合させる工程
を含む、方法。 - 前記固体支持体がガラス支持体、シリカ支持体、プラスチック支持体、シリコン支持体、金支持体、金属支持体、クロム支持体、チタン支持体、酸化チタン支持体、スズ支持体、または酸化スズ支持体である、請求項1記載の方法。
- 前記固体支持体が光学的に不透明または透明である、請求項2記載の方法。
- 前記固体支持体が、正電荷または負電荷を有するように修飾されている、請求項2記載の方法。
- 前記固体支持体が、前記SNAPを前記結合部位に結合させる前に不動態化されている、請求項2記載の方法。
- 前記固体支持体が結合部位のアレイを含む、請求項1記載の方法。
- 各結合部位が、他の結合部位の各々から少なくとも70nmまたは少なくとも25nm離れている、請求項6記載の方法。
- 任意の2つの結合部位の端部間の距離が、前記SNAPの半径または直径よりも大きい、請求項6記載の方法。
- 前記SNAPが、光切断可能な結合を含む、請求項1記載の方法。
- 前記核酸折り紙がデオキシリボ核酸(DNA)またはリボデオキシリボ核酸(RNA)を含む、請求項1記載の方法。
- 前記SNAPがおよそ100nmまたはおよそ300nmの直径を有する、請求項1記載の方法。
- 前記SNAPが約10nm~500μmの直径を有する、請求項1記載の方法。
- 前記SNAPが、静電相互作用を通じて前記固体支持体に付着する、請求項1記載の方法。
- 前記SNAPが、リンカーにより前記単一のタンパク質に共有結合されており、該リンカーがPEG、DNA、短いカルボキシル、炭素鎖、ペプトイド、スペーサー、グリセル(glycer)から選択されるものを含んでもよい、請求項1に記載の方法。
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