我々は（PJS）は寛大（JPVに）陶器財団からの贈り物、（PJSへ）HealthGrant T32-CA079448の国立研究所、およびボール州立大学のスタートアップ資金を含め、当社の資金源に感謝したいと思います。資金提供者は、研究デザイン、データ収集と分析、公開することを決定、または原稿の準備で何の役割を持っていません。

<ol>
	<li>Qin, Y., Hurley, L. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structures,+folding+patterns,+and+functions+of+intramolecular+DNA+G-quadruplexes+found+in+eukaryotic+promoter+regions.">Structures, folding patterns, and functions of intramolecular DNA G-quadruplexes found in eukaryotic promoter regions.</a> Biochimie. 90 (8), 1149-1171 (2008).</li><li>Stegle, O., Payet, L., Mergny, J. L., MacKay, D. J., Leon, J. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Predicting+and+understanding+the+stability+of+G-quadruplexes.">Predicting and understanding the stability of G-quadruplexes.</a> Bioinformatics. 25 (12), i374-i382 (2009).</li><li>Todd, A. 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L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Re-evaluation+of+G-quadruplex+propensity+with+G4Hunter.">Re-evaluation of G-quadruplex propensity with G4Hunter.</a> Nucleic Acids Res. 44 (4), 1746-1759 (2016).</li><li>Mendoza, O., Bourdoncle, A., Boule, J. B., Brosh, R. M., Mergny, J. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=G-quadruplexes+and+helicases.">G-quadruplexes and helicases.</a> Nucleic Acids Res. 44 (5), 1989-2006 (2016).</li><li>Huppert, J. L., Balasubramanian, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=G-quadruplexes+in+promoters+throughout+the+human+genome.">G-quadruplexes in promoters throughout the human genome.</a> Nucleic Acids Res. 35 (2), 406-413 (2007).</li><li>Eddy, J., Maizels, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gene+function+correlates+with+potential+for+G4+DNA+formation+in+the+human+genome.">Gene function correlates with potential for G4 DNA formation in the human genome.</a> Nucleic Acids Res. 34 (14), 3887-3896 (2006).</li><li>Eddy, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=G4+motifs+correlate+with+promoter-proximal+transcriptional+pausing+in+human+genes.">G4 motifs correlate with promoter-proximal transcriptional pausing in human genes.</a> Nucleic Acids Res. 39 (12), 4975-4983 (2011).</li><li>Vaughn, J. P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+DEXH+protein+product+of+the+DHX36+gene+is+the+major+source+of+tetramolecular+quadruplex+G4-DNA+resolving+activity+in+HeLa+cell+lysates.">The DEXH protein product of the DHX36 gene is the major source of tetramolecular quadruplex G4-DNA resolving activity in HeLa cell lysates.</a> J Biol Chem. 280 (46), 38117-38120 (2005).</li><li>Booy, E. P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+RNA+helicase+RHAU+(DHX36)+unwinds+a+G4-quadruplex+in+human+telomerase+RNA+and+promotes+the+formation+of+the+P1+helix+template+boundary.">The RNA helicase RHAU (DHX36) unwinds a G4-quadruplex in human telomerase RNA and promotes the formation of the P1 helix template boundary.</a> Nucleic Acids Res. 40 (9), 4110-4124 (2012).</li><li>Creacy, S. D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=G4+resolvase+1+binds+both+DNA+and+RNA+tetramolecular+quadruplex+with+high+affinity+and+is+the+major+source+of+tetramolecular+quadruplex+G4-DNA+and+G4-RNA+resolving+activity+in+HeLa+cell+lysates.">G4 resolvase 1 binds both DNA and RNA tetramolecular quadruplex with high affinity and is the major source of tetramolecular quadruplex G4-DNA and G4-RNA resolving activity in HeLa cell lysates.</a> J Biol Chem. 283 (50), 34626-34634 (2008).</li><li>Giri, B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=G4+resolvase+1+tightly+binds+and+unwinds+unimolecular+G4-DNA.">G4 resolvase 1 tightly binds and unwinds unimolecular G4-DNA.</a> Nucleic Acids Res. 39 (16), 7161-7178 (2011).</li><li>Lattmann, S., Stadler, M. B., Vaughn, J. P., Akman, S. A., Nagamine, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+DEAH-box+RNA+helicase+RHAU+binds+an+intramolecular+RNA+G-quadruplex+in+TERC+and+associates+with+telomerase+holoenzyme.">The DEAH-box RNA helicase RHAU binds an intramolecular RNA G-quadruplex in TERC and associates with telomerase holoenzyme.</a> Nucleic Acids Res. 39 (21), 9390-9404 (2011).</li><li>Sexton, A. N., Collins, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+5'+guanosine+tracts+of+human+telomerase+RNA+are+recognized+by+the+G-quadruplex+binding+domain+of+the+RNA+helicase+DHX36+and+function+to+increase+RNA+accumulation.">The 5' guanosine tracts of human telomerase RNA are recognized by the G-quadruplex binding domain of the RNA helicase DHX36 and function to increase RNA accumulation.</a> Mol Cell Biol. 31 (4), 736-743 (2011).</li><li>Smaldino, P. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mutational+Dissection+of+Telomeric+DNA+Binding+Requirements+of+G4+Resolvase+1+Shows+that+G4-Structure+and+Certain+3'-Tail+Sequences+Are+Sufficient+for+Tight+and+Complete+Binding.">Mutational Dissection of Telomeric DNA Binding Requirements of G4 Resolvase 1 Shows that G4-Structure and Certain 3'-Tail Sequences Are Sufficient for Tight and Complete Binding.</a> PLoS One. 10 (7), e0132668 (2015).</li><li>Booy, E. P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+RNA+helicase+RHAU+(DHX36)+suppresses+expression+of+the+transcription+factor+PITX1.">The RNA helicase RHAU (DHX36) suppresses expression of the transcription factor PITX1.</a> Nucleic Acids Res. 42 (5), 3346-3361 (2014).</li><li>Huang, W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Yin+Yang+1+contains+G-quadruplex+structures+in+its+promoter+and+5'-UTR+and+its+expression+is+modulated+by+G4+resolvase+1.">Yin Yang 1 contains G-quadruplex structures in its promoter and 5'-UTR and its expression is modulated by G4 resolvase 1.</a> Nucleic Acids Res. 40 (3), 1033-1049 (2012).</li><li>Tran, H., Schilling, M., Wirbelauer, C., Hess, D., Nagamine, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Facilitation+of+mRNA+deadenylation+and+decay+by+the+exosome-bound,+DExH+protein+RHAU.">Facilitation of mRNA deadenylation and decay by the exosome-bound, DExH protein RHAU.</a> Mol Cell. 13 (1), 101-111 (2004).</li><li>Yoo, J. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DHX36+enhances+RIG-I+signaling+by+facilitating+PKR-mediated+antiviral+stress+granule+formation.">DHX36 enhances RIG-I signaling by facilitating PKR-mediated antiviral stress granule formation.</a> PLoS Pathog. 10 (3), e1004012 (2014).</li><li>Lai, J. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+DEAH-box+helicase+RHAU+is+an+essential+gene+and+critical+for+mouse+hematopoiesis.">The DEAH-box helicase RHAU is an essential gene and critical for mouse hematopoiesis.</a> Blood. 119 (18), 4291-4300 (2012).</li><li>Zhang, Z., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DDX1,+DDX21,+and+DHX36+helicases+form+a+complex+with+the+adaptor+molecule+TRIF+to+sense+dsRNA+in+dendritic+cells.">DDX1, DDX21, and DHX36 helicases form a complex with the adaptor molecule TRIF to sense dsRNA in dendritic cells.</a> Immunity. 34 (6), 866-878 (2011).</li><li>Kim, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Aspartate-glutamate-alanine-histidine+box+motif+(DEAH)/RNA+helicase+A+helicases+sense+microbial+DNA+in+human+plasmacytoid+dendritic+cells.">Aspartate-glutamate-alanine-histidine box motif (DEAH)/RNA helicase A helicases sense microbial DNA in human plasmacytoid dendritic cells.</a> Proc Natl Acad Sci U S A. 107 (34), 15181-15186 (2010).</li><li>Booy, E. P., McRae, E. K., McKenna, S. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biochemical+characterization+of+G4+quadruplex+telomerase+RNA+unwinding+by+the+RNA+helicase+RHAU.">Biochemical characterization of G4 quadruplex telomerase RNA unwinding by the RNA helicase RHAU.</a> Methods Mol Biol. 1259, 125-135 (2015).</li><li>Lattmann, S., Giri, B., Vaughn, J. P., Akman, S. A., Nagamine, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Role+of+the+amino+terminal+RHAU-specific+motif+in+the+recognition+and+resolution+of+guanine+quadruplex-RNA+by+the+DEAH-box+RNA+helicase+RHAU.">Role of the amino terminal RHAU-specific motif in the recognition and resolution of guanine quadruplex-RNA by the DEAH-box RNA helicase RHAU.</a> Nucleic Acids Res. 38 (18), 6219-6233 (2010).</li></ol>

著者らは、開示することは何もありません。

このプロトコルは、DHX36遺伝子産物、G4-Resolvase1（またラウとDHX36呼ばG4R1）（ 図1）を単離するための非常に効率的な発現、精製、および定量化スキームを表します。 G4-DNA複合化ビーズ上のHisタグの親和性コバルト親和性ビーズ上での精製と酵素精製：このプロトコルは、2つの精製工程を利用しています。後者のステップは、それがrG4R1はG4構造に持っているタイトな親和性、高特異性、および触媒巻き戻し活性を活用するという点で独特です。 G4構造のためのタイトな親和性（低pMの範囲のK d）は大幅に非特異的なタンパク質の存在を減少させる、G4のビーズから溶出前に（塩化ナトリウムの溶解度限界に近い）高塩洗浄を可能にします。 G4構造上G4R1の触媒活性は、ATPおよびMgCl 2の添加時にアクティブrG4R1の特定の溶出を可能にします。この二段階精製スキームが一貫して高純度の生成しますほとんどの生化学分析に適した量でrG4R1 13、触媒活性。 いくつかの重要なステップは、触媒活性、高純度rG4R1の良好な収率を保証します。最初は、細菌発現株でのHis-rG4R1の適切な誘導条件を確保することです。我々は、細胞は誘導の直前にせいぜい0.4〜0.6のOD 600まで増殖させたときに、組換えタンパク質の最高の収率が生じることを見出しました。このポイントを超えて細胞を成長させることはおそらく封入体へのrG4R1の取り込みに、タンパク質回収の全体的な損失をもたらすことがあります。第二に、我々はコバルト親和性ビーズを溶解物「直列結合」によって精製されたタンパク質の高濃度を得ました。例えば、我々はコバルト親和性ビーズに誘導された培養物の0.5 Lからの溶解物を結合させ、その後、同じコバルト親和性ビーズに文化の追加0.5 Lから別の溶解物の第二の結合を行いました。このステップコバルト親和性ビーズの全容量を利用するため、ビーズの所与の体積に結合rG4R1分子の数を増加させることにより、タンパク質のより濃縮された調製物を確実にします。第三に、G4ビーズにコバルトアフィニティー溶出を結合した後、高塩洗浄は、ビーズに結合するほぼすべての非特異的タンパク質が除去されることを保証します。第四に、ATP / MgCl 2を溶出工程は、ビーズから放出されるようにrG4R1を引き起こし、触媒的一本鎖にtetramolecular構造をほどくためにG4ビーズに結合rG4R1を可能にします。我々は完全にATPが競争ではなく、触媒の方法でrG4R1を溶出するという可能性を除外することはできません。我々は以前に非加水分解性ATP類似体13,18を結合する競合的には十分ではないことを示しているので、これは、ケースである可能性が低いです。解舒ためrG4R1、一本鎖DNAの親和性が少ないtより一桁です彼はtetramolecular G4-DNAを開始し、したがってrG4R1は、ビーズにバインドを再度べきではありません。この可能性を低減するために、しかし、この工程は37℃で行われるべきであり、溶出体積はできるだけ迅速にビーズから分離されるべきです。溶出工程は、最大の回復を確実にするために2回繰り返します。下流のアプリケーションは、DNAの汚れから保護するためにタンパク質が必要な場合は、我々は、精製された調製物が存在する場合、任意のビオチン化DNAを除去するために、ストレプトアビジンビーズに再結合している追加のクリーンアップ手順をお勧めします。 我々は、適切な条件は、プロトコルを通して維持されていない場合rG4R1が分解に感受性であることを見出しました。酵素の完全性及び活性を維持するために、我々は、以下の重要な保護手段を使用します。プロテアーゼ阻害剤は、精製工程全体にわたって存在保たれています。特に断りのない限り、プロトコルは、4°Cで行われます。タンパク質は、ラの存在下で精製されますctalbuminおよびβメルカプトエタノール。プロトコルは、（精製のために1日に）タイムリーに行われます。さらに、当社は、複数の凍結融解サイクルが負タンパク質の活性に影響を与えることを発見したので、私たちはへのタンパク質を分取、「1回の使用、 &quot;7μLアリコートを精製後、-80℃で保管してください。 製剤中のラクトアルブミンの存在が、タンパク質の完全性及び活性を維持するために必要とされるが、上述のように、我々は、これが下流のアプリケーションを妨げることができることを見出しました。精製rG4R1調製物中に存在している他の潜在的な干渉分子は、ATP、βメルカプトエタノール、および選抜本鎖DNAが含まれます。例えば、我々は、このタンパク質調製物は、緩衝液成分から高いバックグラウンド信号に起因BIACORE分析と互換性があることを見出しました。また、タンパク質調製物におけるラクトアルブミンの存在は、標準的なブラッドフォードの使用を妨げますそしてBCAタンパク質定量アッセイ。しかし、我々は、この制限を回避するための代替ゲルベースの定量法を開発しました。 具体的には、それを精製する手段としてG4R1の酵素活性を活用この精製手順は、他の方法とは異なる、この方法を行います。例えば、他のグループは、ヒト細胞中で昆虫細胞中で15、25またはGSTタグrG4R1 26を FLAGタグ付きrG4R1を表明しているし、それぞれFLAG-またはGST-アフィニティークロマトグラフィーにより、それを精製しました。これらの方法は、細菌発現系と比較して、真核生物の発現系で行われるという利点を有します。 G4構造のための得られた精製GST-G4R1の推定K d値は、我々の報告K dは 12値より14高い大きさ、13のオーダーであることが見出されました。私たちは、THI属性Sの6xHisタグ対かさばるGST-タグに関連する差異にK d値の不一致は、これらの2つの精製スキームから得られた純度の違い、およびAN対細菌で取得した翻訳後修飾の程度や種類の違い昆虫発現系。このタンパク質の精製は、直接その酵素活性にかかっているので、我々のアプローチは、前述の選択肢を超える明確な利点を持っています。したがって、我々は主にその酵素の性質を維持するような方法で折り畳まれ、変更されている酵素を得ます。他の親和性タグおよび/またはサイズ排除技術は、酵素的に死んで酵素から活性酵素を分離することはできません。 15、25、26（ 即ち、ヒト又は昆虫細胞発現する他のグループの精製プロトコルの長所を組み合わせることが、将来のプロトコル開発のために有用であろう我々のプロトコル（ すなわち、触媒系の精製）の強度を有するイオン系）はさらに、この方法を改善します。 このプロトコルはG4R1に現在特異的であるが、それは簡単には、これらに限定されない、BLM、WRN、FANCJ、のhnRNPタンパク質、hPif1、および/またはChlR1 / DDX1含む任意のATP依存性、G4分解タンパク質に適合させることができます。ストレプトアビジンビーズに結合した核酸の配列を変更することによって、このプロトコルは、核酸ヘリカーゼを含む酵素反応の生成物がもはや酵素の基質であるため、他のATP依存性核酸酵素を精製するために適合させることができますヌクレアーゼ。

G4構造は、DNAやRNAのグアニンリッチ領域内に形成安定性の高い核酸の二次構造です。 G4構造は、フーグスティーン結合相互作用を介して安定化され、大幅G4構造1、2の顕著な熱安定性に貢献する一価の陽イオン（ すなわち 、K +およびNa +）と中央の空洞内に配位結合しています。初期のバイオインフォマティクス研究は、ヒトゲノムは&gt; 375,000 &quot;潜在的なG4形成モチーフ「3、4含まれていることを示唆しました。さらに最近の研究で推定値は、別の研究は、ヒトゲノム6の716310の異なる潜在的なG4形成配列を予測しながら、G4モチーフの数は、2-5 5倍高いことを示唆しています。 G4形成配列は、進化的に保存し、ランダムに分散されていませんゲノム。 G4のモチーフは、遺伝子コード領域に濃縮され、そしてすべての遺伝子プロモーターの40％の上方には、G4モチーフ7を含んでいます 。興味深いことに、遺伝子G4モチーフの富化の程度は、遺伝子の機能を示唆することが実証されています。例えば、開発に関与するプロトオンコジーンおよび遺伝子は、腫瘍抑制遺伝子8,9よりG4構造の有意に高い濃縮度を有しています。 高い熱安定性により、ゲノム全体でほぼユビキタスプレゼンス、および大幅に主要な細胞プロセスに影響を与える可能性、細胞がこれらの構造を管理するために酵素を進化させたことを見つけるために驚くべきことではありません。 、我々はヒト（HeLa細胞）細胞10内tetramolecular G4-DNA解消活性の大部分のソースとして特徴づけ; 1つのこのような酵素はG4 Resolvase1（また、ラウとDHX36呼ばG4R1）です。それ以来、それが示されているTHAトンG4R1はしっかりと結合し、触媒G4結合タンパク質11、12、13のための最も厳しい報告KDSとtetramolecularと単分子G4-DNAとG4-RNAを巻き戻します。さらに、G4R1のG4分解活性は、テロメア/テロメラーゼ生物学11、14、15、16、転写及びスプライシング17、18、19、20、現像21、造血を含む生化学的および細胞プロセスの広い範囲に関与しています21、及び免疫調節22、23。 G4シーケンスが優勢と特異的にゲノムと多様な細胞のp全域にG4R1は最近表現し、効率的に高活性rG4R1を精製する能力は、このタンパク質の生化学的メカニズムや行動を解明するために最も重要なのだろう、と関与することが示唆されていることをrocesses。 ここでは、効率的に活性酵素を単離するためにrG4R1のATP依存性、G4分解活性を利用して新規発現および精製スキーム（ 図1）を示しています。このスキームは、酵素反応の生成物は、もはやG4R1の場合のように、結合のための基質であるため、他のATP依存性核酸酵素を精製するために適合させることができます。

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>TriEx4-DHX36 plasmid</td>
			<td>Addgene</td>
			<td>68368</td>
			<td></td>
		</tr>
		<tr>
			<td>Rosetta2(DE3)plysS competent cells</td>
			<td>Novagen</td>
			<td>71403-4</td>
			<td></td>
		</tr>
		<tr>
			<td>S.O.C medium</td>
			<td>Thermo Fisher Scientific</td>
			<td>15544034&#160;</td>
			<td></td>
		</tr>
		<tr>
			<td>Difco Terrific Broth</td>
			<td>Becton Dickinson</td>
			<td>243820</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycerol</td>
			<td>Sigma-Aldrich</td>
			<td>G5516</td>
			<td></td>
		</tr>
		<tr>
			<td>Chloramphenicol</td>
			<td>Sigma-Aldrich</td>
			<td>C1919</td>
			<td>35 &#181;g/ml in bacterial plates/large cultures</td>
		</tr>
		<tr>
			<td>Carbenicillin (plant cell culture tested)</td>
			<td>Sigma-Aldrich</td>
			<td>C3416</td>
			<td>50 &#181;g/ml in bacterial plates/large cultures</td>
		</tr>
		<tr>
			<td>Isopropyl &#946;-D-1-thiogalactopyranoside (IPTG)</td>
			<td>Sigma-Aldrich</td>
			<td>I6758</td>
			<td></td>
		</tr>
		<tr>
			<td>Lysozyme (from chicken egg white)</td>
			<td>Sigma-Aldrich</td>
			<td>L6876</td>
			<td></td>
		</tr>
		<tr>
			<td>1 M Tris-HCl pH=8</td>
			<td>Universal Scientific Supply Co.&#160;</td>
			<td>1963-B</td>
			<td>or From standard source</td>
		</tr>
		<tr>
			<td>1 M Tris-HCl pH=7</td>
			<td>Universal Scientific Supply Co.&#160;</td>
			<td>1966</td>
			<td>or From standard source</td>
		</tr>
		<tr>
			<td>1.5 M Tris-HCl, pH=8.8</td>
			<td></td>
			<td></td>
			<td>For casting resolving gel (for protein quantitation gel); From standard source</td>
		</tr>
		<tr>
			<td>1 M Tris-HCl, pH=6.8</td>
			<td></td>
			<td></td>
			<td>For casting stacking gel (for protein quantitation gel); From standard source</td>
		</tr>
		<tr>
			<td>1 M Tris-Acetate, pH=7.8</td>
			<td>Universal Scientific Supply Co.&#160;</td>
			<td>1981</td>
			<td>or From standard source</td>
		</tr>
		<tr>
			<td>70% Ethanol</td>
			<td></td>
			<td></td>
			<td>From standard source</td>
		</tr>
		<tr>
			<td>Magnesium chloride (1 M solution)</td>
			<td>Life Technologies</td>
			<td>AM9530G</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium chloride</td>
			<td>Sigma-Aldrich</td>
			<td>S7653</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium acetate</td>
			<td>Sigma-Aldrich</td>
			<td>S8750</td>
			<td></td>
		</tr>
		<tr>
			<td>20x SSC</td>
			<td>Universal Scientific Supply Co.&#160;</td>
			<td>1665</td>
			<td>or From standard source</td>
		</tr>
		<tr>
			<td>&#946;-mercaptoethanol (2-BME)</td>
			<td>Sigma-Aldrich</td>
			<td>63689</td>
			<td></td>
		</tr>
		<tr>
			<td>Protease inhibitor cocktail</td>
			<td>Sigma-Aldrich</td>
			<td>P8849</td>
			<td></td>
		</tr>
		<tr>
			<td>Leupeptin hemisulfate</td>
			<td>Sigma-Aldrich</td>
			<td>L8511</td>
			<td></td>
		</tr>
		<tr>
			<td>Streptavidin paramagnetic beads</td>
			<td>Promega</td>
			<td>Z5482</td>
			<td></td>
		</tr>
		<tr>
			<td>0.5 M EDTA, pH=8&#160;</td>
			<td>Universal Scientific Supply Co.&#160;</td>
			<td>0718</td>
			<td>or From standard source</td>
		</tr>
		<tr>
			<td>0.2 M EDTA, pH=6</td>
			<td>Universal Scientific Supply Co.&#160;</td>
			<td></td>
			<td>From standard source; initially adjust pH with NaOH, then adjust pH back down with HCl.&#160;&#160;</td>
		</tr>
		<tr>
			<td>A-lactalbumin (Type 1 from bovine milk)</td>
			<td>Sigma-Aldrich</td>
			<td>L5385</td>
			<td></td>
		</tr>
		<tr>
			<td>Cobalt metal affinity beads</td>
			<td>Clonetech</td>
			<td>635502</td>
			<td></td>
		</tr>
		<tr>
			<td>L-Histidine</td>
			<td>Sigma-Aldrich</td>
			<td>H8000</td>
			<td></td>
		</tr>
		<tr>
			<td>Acetic acid, glacial</td>
			<td>Fisher Scientific</td>
			<td>A38-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Adenosine 5&#39;-Triphosphate (from bacterial source)</td>
			<td>Sigma</td>
			<td>A7699</td>
			<td></td>
		</tr>
		<tr>
			<td>40% acrylamide/Bis solution (37.5:1)</td>
			<td>Biorad</td>
			<td>161-0148</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycine</td>
			<td>Sigma-Aldrich</td>
			<td>50046</td>
			<td>to make protein gel running buffer (192 mM glycine, 25 mM Tris Base, 0.1% SDS)</td>
		</tr>
		<tr>
			<td>10 % Sodium dodecyl sulfate&#160;</td>
			<td>Universal Scientific Supply Co.&#160;</td>
			<td>1667</td>
			<td>to make protein gel running buffer (192 mM glycine, 25 mM Tris Base, 0.1% SDS); or From standard source</td>
		</tr>
		<tr>
			<td>10x TBE&#160;</td>
			<td>Sigma-Aldrich</td>
			<td>11666703001</td>
			<td>or From standard source</td>
		</tr>
		<tr>
			<td>Tris base</td>
			<td>Fisher Scientific</td>
			<td>BP152-1</td>
			<td>to make protein gel running buffer (192 mM glycine, 25 mM Tris Base, 0.1% SDS); From standard source</td>
		</tr>
		<tr>
			<td>TEMED</td>
			<td>Sigma-Aldrich</td>
			<td>411019</td>
			<td></td>
		</tr>
		<tr>
			<td>Ammonium persulfate</td>
			<td>Sigma-Aldrich</td>
			<td>A3678</td>
			<td></td>
		</tr>
		<tr>
			<td>Broad Range Protein MW markers</td>
			<td>Promega</td>
			<td>V8491</td>
			<td></td>
		</tr>
		<tr>
			<td>Biotinylated Z33 oligo (&#34;Z33-Bio&#34;)</td>
			<td>Oligos Etc</td>
			<td></td>
			<td>5&#8217; AAA GTG ATG GTG GTG GGG GAA GGA TTC GGA CCT-biotin 3&#8217;</td>
		</tr>
		<tr>
			<td>TAMRA-Z33 oligo (&#34;Z33-TAM&#34;)</td>
			<td>Oligos Etc</td>
			<td></td>
			<td>5&#8217; TAMRA-AAA GTG ATG GTG GTG GGG GAA GGA TTC GGA CCT 3&#8217;</td>
		</tr>
		<tr>
			<td>Fluor-coated TLC plate</td>
			<td>Life Technologies</td>
			<td>AM10110</td>
			<td></td>
		</tr>
		<tr>
			<td>Ficoll</td>
			<td>Sigma-Aldrich</td>
			<td>F2637</td>
			<td>30% in H2O</td>
		</tr>
		<tr>
			<td>Coomassie R-250</td>
			<td>Sigma-Aldrich</td>
			<td>27816</td>
			<td></td>
		</tr>
		<tr>
			<td>Methanol</td>
			<td>Fisher Scientific</td>
			<td>A412</td>
			<td></td>
		</tr>
		<tr>
			<td>Multiband UV lamp</td>
			<td></td>
			<td></td>
			<td>Capable of emitting UV light at 365 nm</td>
		</tr>
		<tr>
			<td>Table-top centrifuge (with swinging bucket rotor)</td>
			<td></td>
			<td></td>
			<td>Capable of being cooled to 4 &#176;C</td>
		</tr>
		<tr>
			<td>Microcentrifuge</td>
			<td></td>
			<td></td>
			<td>Capable of being cooled to 4 &#176;C</td>
		</tr>
		<tr>
			<td>Digital Sonfier</td>
			<td>Branson</td>
			<td></td>
			<td>Or equivalent capable of delivering sonication pulses (30% amplitude, 2s ON 2s OFF)</td>
		</tr>
		<tr>
			<td>50 &#176;C water bath</td>
			<td></td>
			<td></td>
			<td>For formation of Z33 into quadruplex</td>
		</tr>
		<tr>
			<td>37 &#176;C incubator for bacteria</td>
			<td></td>
			<td></td>
			<td>For bacterial transformations and initial overnight growth of large cultures of Rosetta2 E. coli transformed with TriEx4-DHX36</td>
		</tr>
		<tr>
			<td>37 &#176;C/14&#160; &#176;C shaking incubator for bacteria</td>
			<td></td>
			<td></td>
			<td>For growth and protein induction of large cultures of Rosetta2 E. coli transformed with TriEx4-DHX36</td>
		</tr>
		<tr>
			<td>Spectrophotometer</td>
			<td></td>
			<td></td>
			<td>capable of reading OD600; capable of reading oligomer concentrations based on base sequence (such as Biorad SmartSpec 3000)</td>
		</tr>
		<tr>
			<td>Thermometer</td>
			<td></td>
			<td></td>
			<td>From standard source</td>
		</tr>
		<tr>
			<td>PCR strip tubes</td>
			<td></td>
			<td></td>
			<td>From standard source</td>
		</tr>
		<tr>
			<td>15- and 50-ml centrifuge tubes (polypropylene)</td>
			<td></td>
			<td></td>
			<td>From standard source</td>
		</tr>
		<tr>
			<td>Microcentrifuge tubes (2.0 ml)</td>
			<td></td>
			<td></td>
			<td>From standard source</td>
		</tr>
		<tr>
			<td>500 ml centrifuge bottles (polypropylene)</td>
			<td>Thermo Scientific</td>
			<td>3141-0500</td>
			<td></td>
		</tr>
		<tr>
			<td>Standard array of pipet tips and serological pipettes</td>
			<td></td>
			<td></td>
			<td>From standard source</td>
		</tr>
		<tr>
			<td>Gel-loading tips</td>
			<td></td>
			<td></td>
			<td>From standard source</td>
		</tr>
		<tr>
			<td>Automatic repeating pipette</td>
			<td></td>
			<td></td>
			<td>For quick aliquoting of rG4R1; From standard source</td>
		</tr>
		<tr>
			<td>Thermal cycler</td>
			<td></td>
			<td></td>
			<td>From standard source</td>
		</tr>
		<tr>
			<td>Liquid Nitrogen</td>
			<td></td>
			<td></td>
			<td>From standard source</td>
		</tr>
		<tr>
			<td>Dry ice</td>
			<td></td>
			<td></td>
			<td>From standard source</td>
		</tr>
		<tr>
			<td>Laemlli sample buffer&#160;</td>
			<td>Biorad</td>
			<td>161-0737</td>
			<td></td>
		</tr>
		<tr>
			<td>Apparatus for running large slab gels</td>
			<td>Biorad</td>
			<td></td>
			<td>We have used the Protean II xi cell apparatus from Biorad</td>
		</tr>
		<tr>
			<td>Magnet</td>
			<td>Life Technologies</td>
			<td>12301D</td>
			<td>We use a magnet from One Lambda (Now a Thermo Fisher Scientific brand); and Life is also a subsidiary of Thermo, and thus the magnet listed here should be a suitable replacement</td>
		</tr>
		<tr>
			<td>Razor blades</td>
			<td></td>
			<td></td>
			<td>From standard source</td>
		</tr>
		<tr>
			<td>Filter paper and funnel</td>
			<td></td>
			<td></td>
			<td>From standard source</td>
		</tr>
		<tr>
			<td>Glass casserole dish</td>
			<td></td>
			<td></td>
			<td>From standard source</td>
		</tr>
		<tr>
			<td>Orbital shaker</td>
			<td></td>
			<td></td>
			<td>From standard source</td>
		</tr>
		<tr>
			<td>Kimwipes</td>
			<td></td>
			<td></td>
			<td>From standard source</td>
		</tr>
		<tr>
			<td>Clear sheet protectors</td>
			<td></td>
			<td></td>
			<td>From standard source</td>
		</tr>
		<tr>
			<td>Scanner and associated TWAIN software</td>
			<td></td>
			<td></td>
			<td>From standard source</td>
		</tr>
		<tr>
			<td>Image analysis software</td>
			<td></td>
			<td></td>
			<td>Such as Fuji Multiguage, or equivalent</td>
		</tr>
		<tr>
			<td>Microsoft Excel</td>
			<td></td>
			<td></td>
			<td>Or equivalent&#160;</td>
		</tr>
	</tbody>
</table>

a g-quadruplex dna-affinity approach for purification of enzymatically active g4 resolvase1

高次核酸構造は、両方のDNAおよびRNAのグアニンリッチ領域に形成することができ、G四重鎖（G4において、G4構造）と呼ばれ、非常に熱的に安定です。そこヒトゲノム中に375,000の推定上のG4形成配列が&gt;であり、それらは、プロモーター領域、非翻訳領域（UTR）、およびテロメア反復内で濃縮されています。このような複製および転写などの細胞プロセスに影響を与えるために、これらの構造のための潜在的に、細胞は、それらを管理するために酵素を進化してきました。 1つのこのような酵素は生化学的に我々の研究室と長嶺らが共同で特徴付けられたG4リゾルバーゼ1（G4R1）、です。そして、G4-DNAとG4-RNA（低pMの範囲内の K d）の両方に非常に強固に結合することが判明。 G4R1は、HeLa細胞溶解物中のG4分解活性の大部分の原因であるとからテロメア代謝、リンパ開発、遺伝子転写、造血および免疫監視において役割を果たすことが示唆されています。 EFする能力ficiently表現し、触媒活性G4R1がG4構造とG4分解酵素の動力学的相互作用にさらなる洞察を得ることに興味を持って研究室のために重要である浄化。ここでは、組換えG4R1（rG4R1）の精製のための詳細な方法について説明します。説明する手順は、C末端ヒスチジンタグ付き酵素の伝統的な親和性に基づく精製は、ATPで活性の高い酵素を精製するために、G4-DNAに結合し、くつろぐのにrG4R1の能力の活用でヒト・コドン最適化された細菌において発現組み込ん依存溶出工程。プロトコルはまたrG4R1の酵素活性は、G4-DNAをほどくする精製酵素の能力を調べることによって測定される品質管理ステップを含みます。この方法はまた、精製rG4R1の定量化を可能にすることが記載されています。このプロトコルの代替適応が議論されています。

このプロトコル（ 図1）は、日常的にほぼ純粋な、触媒活性rG4R1をもたらします。 rG4R1 0.013μLの範囲（ 図上に概説G4活性アッセイによってアッセイし、 - TAMRA標識tetramolecular G4-DNAの0.2ピコモルの50％が0.2の範囲内の単量体に変換される酵素活性の尺度として、それは、典型的に観察され2）。精製rG4R1のクマシー染色は、G4-DNAビーズを結合し、ATP依存性に溶出するために、その能力を維持していることrG4R1を切り捨てとなることができる〜75kDaの、でマイナー汚染バンドで、予想される120 kDaのサイズで単一のバンドを示し、方法（ 図3）。目的のバンドは、タンパク質標準曲線に対して定量化、およびこのプロトコルは、一般的に、細菌培養物1リットルあたり20から100 nMの精製酵素の200μLを取得しています。 <img alt="図1" src="/files/ftp_upload/55496/55496fig1.jpg" /> 図1：G4R1の2ステップ精製の概略図。 6xHisタグrG4R1は、最初に結合するとCo 2+から溶出することにより、 大腸菌溶解物からバルク精製されたビーズを抱合。 G4-DNA複合化磁気ビーズへの結合ステップは以下の通りです。最後に、ATP依存性の溶出工程は、比較的純粋で酵素的に活性なrG4R1を得る必要があります。 <a href="https://ecsource-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/55496/55496fig1large.jpg" target="_blank">この図の拡大版をご覧になるにはこちらをクリックしてください。</a> <img alt="図2" src="/files/ftp_upload/55496/55496fig2.jpg" /> 図2：品質制御G4-DNA巻き戻しアッセイ。レーン1から6：TAMRA標識tetramolecular G4-DNAの一定濃度を3.9μL、0.83μL、0.2μL、0.05μL、0.013μLを表す精製したrG4R1の4倍連続希釈液の存在下で30分間37℃でインキュベートしました、0<html>それぞれ0.003μL、。レーン7：rG4R1の不在下でのtetramolecular G4-DNA。レーン8：rG4R1の非存在下でのモノマーにG4構造を減らすためにゆでtetramolecular G4-DNA。 <a href="https://ecsource-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/55496/55496fig2large.jpg" target="_blank">この図の拡大版をご覧になるにはこちらをクリックしてください。</a> <img alt="図3" src="/files/ftp_upload/55496/55496fig3.jpg" /> 図3：精製rG4R1濃度の定量化。 6、それぞれ、タンパク質濃度の標準曲線を作成するために使用した - レーン1 500、250、125、62.5、31.3、15.7 NG：広域MWタンパク質マーカーは、以下の量で充填しました。レーン7は、rG4R1の35μLを表します。この特定のゲルは、62±22 nMの標準偏差の平均タンパク質濃度が得られ、ゲルの三重セットの一部として、定量化した（SD、N = 9）。.COM /ファイル/ ftp_upload / 55496 / 55496fig3large.jpg &quot;ターゲット=&quot; _空白 &quot;&gt;この図の拡大版をご覧になるにはこちらをクリックしてください。

Watch this Scientific Journal Video about A G-quadruplex DNA-affinity Approach for Purification of Enzymatically Active G4 Resolvase1 at JoVE.com

A G-quadruplex DNA-affinity Approach for Purification of Enzymatically Active G4 Resolvase1

G4 Resolvase1はG4結合タンパク質のための最も厳しい報告親和性でG-四重鎖（G4）の構造に結合し、HeLa細胞におけるG4-DNA巻き戻し活性の大部分を表しています。我々は、具体的には、触媒活性組換えG4R1を精製するための親和性およびG4-Resolvase1のATP依存性巻き戻し活性を活かした新たなプロトコルを記述します。

酵素的に活性G4 Resolvase1の精製のためのG-四重鎖DNA親和性のアプローチ

Higher-order nucleic acid structures called G-quadruplexes (G4s, G4 structures) can form in guanine-rich regions of both DNA and RNA and are highly ...

a-g-quadruplex-dna-affinity-approach-for-purification-enzymatically

Nanyang Technological University

Research

JoVE Journal

Biochemistry

9.5K ビュー.  Wake Forest School of Medicine.  G4 Resolvase1はG4結合タンパク質のための最も厳しい報告親和性でG-四重鎖（G4）の構造に結合し、HeLa細胞におけるG4-DNA巻き戻し活性の大部分を表しています。我々は、具体的には、触媒活性組換えG4R1を精製するための親和性およびG4-Resolvase1のATP依存性巻き戻し活性を活かした新たなプロトコルを記述します。 

ビデオ: A G-quadruplex DNA-affinity Approach for Purification of Enzymatically Active G4 Resolvase1

Directed Protein Packaging within Outer Membrane Vesicles from Escherichia coli: Design, Production and Purification

An increasing interest in applying synthetic biology techniques to program outer membrane vesicles (OMV) are leading to some very interesting and unique applications for OMV where traditional nanoparticles are proving too difficult to synthesize. To date, all Gram-negative bacteria have been shown to produce OMV demonstrating packaging of a variety of cargo that includes small molecules, peptides, proteins and genetic material. Based on their diverse cargo, OMV are implicated in many biological processes ranging from cell-cell communication to gene transfer and delivery of virulence factors depending upon which bacteria are producing the OMV. Only recently have bacterial OMV become accessible for use across a wide range of applications through the development of techniques to control and direct packaging of recombinant proteins into OMV. This protocol describes a method for the production, purification, and use of enzyme packaged OMV providing for improved overall production of recombinant enzyme, increased vesiculation, and enhanced enzyme stability. Successful utilization of this protocol will result in the creation of a bacterial strain that simultaneously produces a recombinant protein and directs it for OMV encapsulation through creating a synthetic linkage between the recombinant protein and an outer membrane anchor protein. This protocol also details methods for isolating OMV from bacterial cultures as well as proper handling techniques and things to consider when adapting this protocol for use for other unique applications such as: pharmaceutical drug delivery, medical diagnostics, and environmental remediation.

Directed Protein Packaging within Outer Membrane Vesicles from Escherichia coli: Design, Production and Purification

A protocol for the production, purification, and use of enzyme packaged outer membrane vesicles (OMV) providing for enhanced enzyme stability for implementation across diverse applications is presented.

からの外膜小胞内の指向性タンパク質包装<em&gt;エシェリヒア・コリ</em&gt;：デザイン、生産および精製

An increasing interest in applying synthetic biology techniques to program outer membrane vesicles (OMV) are leading to some very interesting and unique ...

生化学

A Facile and Efficient Approach for the Production of Reversible Disulfide Cross-linked Micelles

Nanomedicine is an emerging form of therapy that harnesses the unique properties of particles that are nanometers in scale for biomedical application. Improving drug delivery to maximize therapeutic outcomes and to reduce drug-associated side effects are some of the cornerstones of present-day nanomedicine. Nanoparticles in particular have found a wide application in cancer treatment. Nanoparticles that offer a high degree of flexibility in design, application, and production based on the tumor microenvironment are projected to be more effective with rapid translation into clinical practice. The polymeric micellar nano-carrier is a popular choice for drug delivery applications.
In this article, we describe a simple and effective protocol for synthesizing drug-loaded, disulfide cross-linked micelles based on the self-assembly of a well-defined amphiphilic linear-dendritic copolymer (telodendrimer, TD). TD is composed of polyethylene glycol (PEG) as the hydrophilic segment and a thiolated cholic acid cluster as the core-forming hydrophobic moiety attached stepwise to an amine-terminated PEG using solution-based peptide chemistry. Chemotherapy drugs, such as paclitaxel (PTX), can be loaded using a standard solvent evaporation method. The O2-mediated oxidation was previously utilized to form intra-micellar disulfide cross-links from free thiol groups on the TDs. However, the reaction was slow and not feasible for large-scale production. Recently, an H2O2-mediated oxidation method was explored as a more feasible and efficient approach, and it was 96 times faster than the previously reported method. Using this approach, 50 g of PTX-loaded, disulfide cross-linked nanoparticles have been successfully produced with narrow particle size distribution and high drug loading efficiency. The stability of the resulting micelle solution is analyzed using disrupting conditions such as co-incubation with a detergent, sodium dodecyl sulfate, with or without a reducing agent. The drug-loaded, disulfide cross-linked micelles demonstrated less hemolytic activity when compared to their non-cross-linked counterparts.

To deliver cancer drugs to tumor sites with high specificity and reduced side effects, new methods based on nanoparticles are required. Here, we describe disulfide cross-linked micelles that can be easily prepared by hydrogen peroxide-mediated oxidation and are able to dissociate efficiently under a reducing tumor environment to release payloads.

リバーシブルジスルフィド架橋ミセルの生産のための簡便かつ効率的なアプローチ

Nanomedicine is an emerging form of therapy that harnesses the unique properties of particles that are nanometers in scale for biomedical application. ...

Expression, Purification, and Antimicrobial Activity of S100A12

Calgranulin proteins are important mediators of innate immunity and are members of the S100 class of the EF-hand family of calcium binding proteins. Some S100 proteins have the capacity to bind transition metals with high affinity and effectively sequester them away from invading microbial pathogens in a process that is termed "nutritional immunity". S100A12 (EN-RAGE) binds both zinc and copper and is highly abundant in innate immune cells such as macrophages and neutrophils. We report a refined method for the expression, enrichment and purification of S100A12 in its active, metal-binding configuration. Utilization of this protein in bacterial growth and viability analyses reveals that S100A12 has antimicrobial activity against the bacterial pathogen, Helicobacter pylori. The antimicrobial activity is predicated on the zinc-binding activity of S100A12, which chelates nutrient zinc, thereby starving H. pylori which requires zinc for growth and proliferation.

Here, we present a method to express and purify S100A12 (calgranulin C). We describe a protocol to measure its antimicrobial activity against the human pathogen H. pylori.

S100A12の発現、精製および抗菌活性

Calgranulin proteins are important mediators of innate immunity and are members of the S100 class of the EF-hand family of calcium binding proteins. Some ...

Brain Membrane Fractionation: An Ex Vivo Approach to Assess Subsynaptic Protein Localization

Assessing the synaptic protein composition and function constitutes an important challenge in neuroscience. However, it is not easy to evaluate neurotransmission that occurs within synapses because it is highly regulated by dynamic protein-protein interactions and phosphorylation events. Accordingly, when any method is used to study synaptic transmission, a major goal is to preserve these transient physiological modifications. Here, we present a brain membrane fractionation protocol that represents a robust procedure to isolate proteins belonging to different synaptic compartments. In other words, the protocol describes a biochemical methodology to carry out protein enrichment from presynaptic, postsynaptic, and extrasynaptic compartments. First, synaptosomes, or synaptic terminals, are obtained from neurons that contain all synaptic compartments by means of a discontinuous sucrose gradient. Of note, the quality of this initial synaptic membrane preparation is critical. Subsequently, the isolation of the different subsynaptic compartments is achieved with light solubilization using mild detergents at differential pH conditions. This allows for separation by gradient and isopycnic centrifugations. Finally, protein enrichment at the different subsynaptic compartments (i.e., pre-, post- and extrasynaptic membrane fractions) is validated by means of immunoblot analysis using well-characterized synaptic protein markers (i.e., SNAP-25, PSD-95, and synaptophysin, respectively), thus enabling a direct assessment of the synaptic distribution of any particular neuronal protein.

Brain Membrane Fractionation: An Ex Vivo Approach to Assess Subsynaptic Protein Localization

Here, we present a brain membrane fractionation protocol that represents a robust procedure to isolate proteins belonging to different synaptic compartments.

脳膜分画：<em&gt; Ex Vivo</em&gt; Subsynaptic Protein Localizationを評価するアプローチ

Assessing the synaptic protein composition and function constitutes an important challenge in neuroscience. However, it is not easy to evaluate ...

Method for Efficient Refolding and Purification of Chemoreceptor Ligand Binding Domain

Identification of natural ligands of chemoreceptors and structural studies aimed at elucidation of the molecular basis of the ligand specificity can be greatly facilitated by the production of milligram amounts of pure, folded ligand binding domains. Attempts to heterologously express periplasmic ligand binding domains of bacterial chemoreceptors in Escherichia coli (E. coli) often result in their targeting into inclusion bodies. Here, a method is presented for protein recovery from inclusion bodies, its refolding and purification, using the periplasmic dCACHE ligand binding domain of Campylobacter jejuni (C. jejuni) chemoreceptor Tlp3 as an example. The approach involves expression of the protein of interest with a cleavable His6-tag, isolation and urea-mediated solubilisation of inclusion bodies, protein refolding by urea depletion, and purification by means of affinity chromatography, followed by tag removal and size-exclusion chromatography. The circular dichroism spectroscopy is used to confirm the folded state of the pure protein. It has been demonstrated that this protocol is generally useful for production of milligram amounts of dCACHE periplasmic ligand binding domains of other bacterial chemoreceptors in a soluble and crystallisable form.

A procedure is presented for the refolding of the dCACHE periplasmic ligand binding domain of Campylobacter jejuni chemoreceptor Tlp3 from inclusion bodies and the purification to yield milligram quantities of protein.

高効率巻き戻しと受容体リガンド結合領域の浄化法

Identification of natural ligands of chemoreceptors and structural studies aimed at elucidation of the molecular basis of the ligand specificity can be ...

Purification and Reconstitution of TRPV1 for Spectroscopic Analysis

Polymodal ion channels transduce multiple stimuli of different natures into allosteric changes; these dynamic conformations are challenging to determine and remain largely unknown. With recent advances in single-particle cryo-electron microscopy (cryo-EM) shedding light on the structural features of agonist binding sites and the activation mechanism of several ion channels, the stage is set for an in-depth dynamic analysis of their gating mechanisms using spectroscopic approaches. Spectroscopic techniques such as electron paramagnetic resonance (EPR) and double electron-electron resonance (DEER) have been mainly restricted to the study of prokaryotic ion channels that can be purified in large quantities. The requirement for large amounts of functional and stable membrane proteins has hampered the study of mammalian ion channels using these approaches. EPR and DEER offer many advantages, including determination of the structure and dynamic changes of mobile protein regions, albeit at low resolution, that might be difficult to obtain by X-ray crystallography or cryo-EM, and monitoring reversible gating transition (i.e., closed, open, sensitized, and desensitized). Here, we provide protocols for obtaining milligrams of functional detergent-solubilized transient receptor potential cation channel subfamily V member 1 (TRPV1) that can be labeled for EPR and DEER spectroscopy.

This article describes specific methods to obtain biochemical quantities of detergent-solubilized TRPV1 for spectroscopic analysis. The combined protocols provide biochemical and biophysical tools that can be adapted to facilitate structural and functional studies for mammalian ion channels in a membrane-controlled environment.

精製と TRPV1 の分光学的解析のための再構成

Polymodal ion channels transduce multiple stimuli of different natures into allosteric changes; these dynamic conformations are challenging to determine ...

Anaerobic Protein Purification and Kinetic Analysis via Oxygen Electrode for Studying DesB Dioxygenase Activity and Inhibition

Oxygen-sensitive proteins, including those enzymes which utilize oxygen as a substrate, can have reduced stability when purified using traditional aerobic purification methods. This manuscript illustrates the technical details involved in the anaerobic purification process, including the preparation of buffers and reagents, the methods for column chromatography in a glove box, and the desalting of the protein prior to kinetics. Also described are the methods for preparing and using an oxygen electrode to perform kinetic characterization of an oxygen-utilizing enzyme. These methods are illustrated using the dioxygenase enzyme DesB, a gallate dioxygenase from the bacterium Sphingobium sp. strain SYK-6.

Here we present a protocol for anaerobic protein purification, anaerobic protein concentration, and subsequent kinetic characterization using an oxygen electrode system. The method is illustrated using the enzyme DesB, a dioxygenase enzyme which is more stable and active when purified and stored in an anaerobic environment.

嫌気性蛋白質の浄化および DesB ジオキシゲナーゼ活性と抑制の勉強用酸素電極による速度論的解析

Oxygen-sensitive proteins, including those enzymes which utilize oxygen as a substrate, can have reduced stability when purified using traditional aerobic ...

Expression and Purification of Nuclease-Free Oxygen Scavenger Protocatechuate 3,4-Dioxygenase

Single molecule (SM) microscopy is used in the study of dynamic molecular interactions of fluorophore labeled biomolecules in real time. However, fluorophores are prone to loss of signal via photobleaching by dissolved oxygen (O2). To prevent photobleaching and extend the fluorophore lifetime, oxygen scavenging systems (OSS) are employed to reduce O2. Commercially available OSS may be contaminated by nucleases that damage or degrade nucleic acids, confounding interpretation of experimental results. Here we detail a protocol for the expression and purification of highly active Pseudomonas putida protocatechuate-3,4-dioxygenase (PCD) with no detectable nuclease contamination. PCD can efficiently remove reactive O2 species by conversion of the substrate protocatechuic acid (PCA) to 3-carboxy-cis,cis-muconic acid. This method can be used in any aqueous system where O2 plays a detrimental role in data acquisition. This method is effective in producing highly active, nuclease free PCD in comparison with commercially available PCD.

Protocatechuate 3,4-dioxygenase (PCD) can enzymatically remove free diatomic oxygen from an aqueous system using its substrate protocatechuic acid (PCA). This protocol describes the expression, purification, and activity analysis of this oxygen scavenging enzyme.

ヌクレアーゼフリー酸素スカベンジャープロトカテク酸プロトカテクエート3,4-ジオキシゲナーゼの発現と精製

Single molecule (SM) microscopy is used in the study of dynamic molecular interactions of fluorophore labeled biomolecules in real time. However, ...

A Customizable Approach for the Enzymatic Production and Purification of Diterpenoid Natural Products

Diterpenoids form a diverse class of small molecule natural products that are widely distributed across the kingdoms of life and have critical biological functions in developmental processes, interorganismal interactions, and environmental adaptation. Due to these various bioactivities, many diterpenoids are also of economic importance as pharmaceuticals, food additives, biofuels, and other bioproducts. Advanced genomics and biochemical approaches have enabled a rapid increase in the knowledge of diterpenoid-metabolic genes, enzymes, and pathways. However, the structural complexity of diterpenoids and the narrow taxonomic distribution of individual compounds in often only a single species remain constraining factors for their efficient production. Availability of a broader range of metabolic enzymes now provide resources for producing diterpenoids in sufficient titers and purity to facilitate a deeper investigation of this important metabolite group. Drawing on established tools for microbial and plant-based enzyme co-expression, we present an easily operated and customizable protocol for the enzymatic production of diterpenoids in either Escherichia coli or Nicotiana benthamiana, and the purification of desired products via silica chromatography and semi-preparative HPLC. Using the group of maize (Zea mays) dolabralexin diterpenoids as an example, we highlight how modular combinations of diterpene synthase (diTPS) and cytochrome P450 monooxygenase (P450) enzymes can be used to generate different diterpenoid scaffolds. Purified compounds can be used in various downstream applications, such as metabolite structural analyses, enzyme structure-function studies, and in vitro and in planta bioactivity experiments.

Here we present easy to use protocols for producing and purifying diterpenoid metabolites through the combinatorial expression of biosynthetic enzymes in Escherichia coli or Nicotiana benthamiana, followed by chromatographic product purification. The resulting metabolites are suitable for various studies including molecular structure characterization, enzyme functional studies, and bioactivity assays.

ジテルペノイド天然物の酵素生産と精製のためのカスタマイズ可能なアプローチ

Diterpenoids form a diverse class of small molecule natural products that are widely distributed across the kingdoms of life and have critical biological ...

Single Cell Analysis Of Transcriptionally Active Alleles By Single Molecule FISH

Gene transcription is an essential process in cell biology, and allows cells to interpret and respond to internal and external cues. Traditional bulk population methods (Northern blot, PCR, and RNAseq) that measure mRNA levels lack the ability to provide information on cell-to-cell variation in responses. Precise single cell and allelic visualization and quantification is possible via single molecule RNA fluorescence in situ hybridization (smFISH). RNA-FISH is performed by hybridizing target RNAs with labeled oligonucleotide probes. These can be imaged in medium/high throughput modalities, and, through image analysis pipelines, provide quantitative data on both mature and nascent RNAs, all at the single cell level. The fixation, permeabilization, hybridization and imaging steps have been optimized in the lab over many years using the model system described herein, which results in successful and robust single cell analysis of smFISH labeling. The main goal with sample preparation and processing is to produce high quality images characterized by a high signal-to-noise ratio to reduce false positives and provide data that are more accurate. Here, we present a protocol describing the pipeline from sample preparation to data analysis in conjunction with suggestions and optimization steps to tailor to specific samples.&#160;

Single molecule RNA fluorescence in situ hybridization (smFISH) is a method to accurately quantify levels and localization of specific RNAs at the single cell level. Here, we report our validated lab protocols for wet-bench processing, imaging and image analysis for single cell quantification of specific RNAs.

単一分子FISHによる転写活性アレスの単一細胞解析

Gene transcription is an essential process in cell biology, and allows cells to interpret and respond to internal and external cues. Traditional bulk ...