この作品は、フォンド ナシオナル デ開発 Científico y Tecnológico (Fondecyt)、チリ、(CW) にプロジェクト 11130263、プロジェクト チリ + NERC エイトによって支えられた (CW) に Colaboración インターナショナル PCI PII20150073 と U-inicia Vicerrectoría デから危惧デチリ (CW) します。
芸術 Químicas y 博士ホルヘ バーブルと参考については、原稿やリオイバニェス デ extensión デ ラ Facultad デ改正ロバート ・ レッシュ サンディエゴ キロガ ロジャー、このプロジェクトの初期の段階で助けタチアナ ナランホ パルマ行きのおかげでください。チリ大学から Farmacéuticas。ビデオを編集するためのマルセロ ・ ペレスとニール · スティーブンスのナレーションを提供するテキストとエロール ・ ワトソンを修正するためにあまりにも感謝します。

1. 準備とゲルの実行
<ol><li>Sambrook とラッセルの14が、SDS の代わりに水を用いたナトリウム Dodecyl 硫酸塩-ポリアクリルアミドゲル電気泳動 (SDS-PAGE) レシピを使用して 12% のポリアクリルアミドゲルの非変性ゲルを準備します。<ol>
<li>解決のゲルの 5 mL の準備、TEMED 0.002 mL、10% 過硫酸アンモニウム、0.05 mL の 1.5 M トリス pH 8.8 1.3 mL アクリルアミド/ビス アクリルアミド (30/0.8 %w/v) 2 mL 1.7 mL の蒸留水を使用します。</li>
		<li>準備スタッキングのゲルの 2 mL は 1.5 mL の水、アクリルアミド/ビス アクリルアミド (30/0.8 %w/v) 0.33 mL、1 M トリス pH 6.8 の 0.25 mL、10% 過硫酸アンモニウム、0.02 mL、TEMED 0.002 mL を使用します。ゲルのサイズは 7.3 cm × 8.2 cm 0.075 × cm (w x d x l)。 注:感度を最高厚さ 0.75 mm の 15 も櫛を使用します。</li>
	</ol>
</li>
	<li>読み込みバッファーと DNA サンプルを 1.5 mL 遠心チューブ (例えば5 μ L の DNA のサンプルを 6 x の読み込みバッファーの使用 1 μ) x 6 の適切な量を追加します。</li>
	<li>垂直電気泳動室にゲルを配置します。<ol>
<li>2 ゲルを実行する 1 x TAE バッファーの 750 mL で部屋を満たします。50 の 1 L を準備する x TAE、トリス基地の 442 g、氷酢酸、57.1 mL と 0.5 M EDTA pH 8 の 100 mL を使用します。1 L の最終巻に蒸留水を追加します。</li>
		<li>ゲルのサンプルをロードします。2 h の 100 V でゲルを実行します。</li>
	</ol>
</li>
	<li>また、Sambrook14のレシピを使用して 1 x TAE agarose のゲルを準備します。<ol>
<li>1 の 300 mL を追加し水平電気泳動室に x TAE。100 V で 45 分のためのゲルを実行します。</li>
	</ol>
</li>
</ol>2. NBT SG (図 1) を汚す私。
<ol><li>
アクリルアミドゲル染色します。
	<ol>
<li>ソリューションの準備: 0.1 w/v NBT と 1.2 SG x 私。 注:エチジウム ブロマイド、GelRed、SG ではなくサイバー ゴールドを使用することが可能だけど、SG の最高のパフォーマンスをしていた。</li>
		<li>1.2 16.75 mL を注ぐ x SYBR 緑のソリューションに適切なサイズの容器。 注:我々 は、コンテナーとしてピペット チップ ボックスの蓋を使用し、これらのボリュームは、このコンテナーを使用してゲルをカバーする計算されます。その寸法は 11.6 cm × 7.6 cm × 2.6 cm (w x d x l)。</li>
		<li>ソリューションをジェルします。3.25 mL 0.1 %w/v NBT 液 0.2 mM NBT を与えるための追加と 1 x (2.0 μ M に相当) SG 私最終濃度。</li>
		<li>プラスチック フィルムで容器を密閉し、完全に任意の周囲の光を遮断するアルミ箔容器をラップします。 注:プラスチック フィルムは、飛散防止のため、染色液にアルミ箔の反応を避けるために使用されます。</li>
		<li>25 分 60 rpm で軌道シェーカーを振る。</li>
		<li>アルミとプラスチック製のカバーを取り外します。最大 90 分のための日光にさらします。興味のバンドが表示されるまでは、5 分ごとに確認してください。</li>
		<li>青色光を使用するには、3 光発光ダイオード (LED) と併せて使用を準備し、ゲルの表面 (LED 光源の強度に依存します必要な時間として、継続的に染色チェック) から約 5 mm の Led を配置します。</li>
	</ol>
</li>
	<li>
Agarose のゲル染色します。
	<ol>
<li>準備と 1% の agarose を実行するゲルの 1.4 節で説明した後 (サイズが 1 cm × 6.2 cm × 7 cm; l x 幅 x 奥行)、2.1 は、これらの変更と同じ手順に従ってください。</li>
		<li>1.2 41.9 mL を注ぐ SG x 私ピペット チップ ボックスのふたにソリューションその寸法は 11.6 cm × 7.6 cm × 2.6 cm (w x d x l)。8.1 mL 0.1 %nbt ソリューションを追加します。</li>
		<li>プラスチック フィルムで容器を密閉し、完全に任意の周囲の光を遮断するアルミ箔容器をラップします。</li>
		<li>1 h 60 rpm で軌道シェーカーを振る。</li>
	</ol>
</li>
</ol>3. データ分析。
<ol><li>
NBT SG 私検。
	<ol>
<li>1200 dpi でスキャンすることによって、ゲルの画像を取得します。</li>
		<li>画像解析ソフトウェアをオープン。イメージ エディターを使用してイメージをまっすぐにします。画像密度測定を実行します。</li>
		<li>曲線の下の領域を計算します。DNA 濃度対最大のグラフを準備します。</li>
	</ol>
</li>
</ol>4. DNA の回復。
<ol><li>1 に 1% の agarose のゲルの準備のレシピを使用して x TAE が見つかりました Sambrook14。</li>
	<li>1 の 300 mL を追加し水平電気泳動室に x TAE。100 ng/μ L pDJ10015プラスミッドおよび DNA ラダー図 2に与えられる方式を次の 4 μ L をロードします。100 V で 1 時間のためのゲルを実行します。</li>
	<li>マークし、2 つの 2 mL 遠心チューブの重量を量る。</li>
	<li>真ん中 2 つの同じ部分を持つためにゲルをカットします。それぞれには、はしごと異なる染色法を比較するサンプル プラスミドを含める必要があります。概略図は、図 2にあります。</li>
	<li>ステイン 1 つ NBT SG と半分ステップ 2 のように。<ol>
<li>きれいなメスを使用してプラスミッド バンドをカットします。1 つの管でゲルの部分を保存し、重量を量る。</li>
	</ol>
</li>
	<li>SG とゲルの他の部分を染色私 1 の 50 mL の SG x 私ソリューションと暗闇の中で (60 rpm) 1 h のためのゲルをゆっくりと振る。<ol>
<li>ジェルを transilluminator ときれいなメスを使用してプラスミッド バンドを 2 分カットを公開します。</li>
		<li>他のチューブにゲルの部分を保存し、重量を量る。 注:プロトコルは-20 ° C でチューブを維持しながらここで一時停止できます。</li>
	</ol>
</li>
	<li>商業ゲル抽出キットを使用してプラスミッドの抽出を行います。</li>
</ol>5. プラスミド正規化されます。
<ol><li>1.5 mL 遠心チューブに抽出されたプラスミドの 10 μ L と 60 μ L の水の種類を追加します。ミックス 60 μ 石英キュベットに譲渡または直接、Nanodrop で 2 μ L を使用します。</li>
	<li>230 に 320 の吸収スペクトルを測定 nm。次の数式を使用してサンプルのプラスミド濃度を計算します。 <img alt="Equation 1" src="/files/ftp_upload/56528/56528eq1v3.jpg"> Dは適用される希釈率 (この場合は 70/10) x nm の吸収であり、50 は、dsDNA の μ g/mL への換算係数Ax 。</li>
	<li>9.1 ng/μ L のサンプルを希釈します。</li>
	<li>エシェリヒア属大腸菌(E. 大腸菌) 有能なセル (例えばXL10 ゴールド) を変換次の希釈サンプルの 5 μ L を使用して井上変換手順16 。</li>
	<li>ペトリ皿のコロニーの数をカウントして、希釈します。次の数式17:とコロニー形成単位 (CFU) を計算します。 <img alt="Equation 2" src="/files/ftp_upload/56528/56528eq2v2.jpg"> Dは初期の文化から適用される希釈係数です。</li>
	<li>対になっていない t 検定を実行します。</li>
</ol>

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著者が明らかに何もありません。

感受性と小説 DNA 染色法は NBT が減少し、私はこの記事で紹介した SG の使用に基づいています。このプロトコルの重要なステップは、NBT SG でゲルのインキュベーション時間私ソリューションおよび NBT の濃度。Agarose のゲルのより大きい厚さのために agarose のゲルの染色時間はアクリルアミドゲルよりも長くなります。このメソッド、NBT が接触して析出物も SDS 存在下で働きません。ゲルは、...

生物化学および分子生物学の発展に伴い、DNA を含む研究は DNA を分析する優れたテクニックが必要。DNA 染色する最初の方法は銀染色、非常に敏感であるが、欠けている選択性および回収はできません。その後、DNA を蛍光染色の開発許可サンプル回復の可能性のある DNA の選択的定量です。DNA の定量化に使用される最初の蛍光染料の一つは、変異2エチジウム ブロマイド1、だった。しかし、今は、安全 GelRed、SYBR グリーンなどの機密性の高い蛍光染料類の改善私 (SG 私)3;しかし、すべてこれらの蛍光染料の紫外線 (UV) transilluminator または蛍光を使用する必要があります。
4メチレン ブルーとクリスタル バイオレット5,6,7,8,9, など目に見えて、DNA を染色する方法がありますが、これらのすべてに苦しむに対する感度を下げると選択性。テトラゾリウム塩有機化合物減少に影響を受け、この場合彼らは不溶性を形成し、色塩沈殿10,11。最近では、DNA の正テトラゾリウム リング12のためにバインドするいくつかの二価テトラゾリウム塩を示されています。
最近文書13を汚し、ポリアクリルアミドゲルの DNA の定量化手法を表示する方法を提案、ニトロ ブルー テトラゾリウム (NBT) と GelRed、臭化エチジウムなど蛍光色素と呼ばれる二価テトラゾリウム塩の還元SYBR グリーン私とサイバー金。青色のライトや日光の存在下で勤務し、品質向上と回収を許可この反応と比較して SG の使用に私 UV transilluminator。本稿の目的は、テトラゾリウムを用いた染色技術の詳細なプロトコルを提供する塩です。

<table border="0" cellpadding="0" cellspacing="0" width="785">
	<tbody>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">Nitro blue tetrazolium</td>
			<td style="width:227px;">Gold Biotechnology</td>
			<td style="width:307px;">298-83-9</td>
			<td style="width:64px;">reagent used in the staining</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">SYBR Green I 10000X</td>
			<td style="width:227px;">Thermo-Fisher</td>
			<td style="width:307px;">S7563</td>
			<td>reagent used in the staining</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">Gel extraction kit</td>
			<td style="width:227px;">QIAGEN</td>
			<td style="width:307px;">28704</td>
			<td>used to extract plasmid from the gel in integrity assay</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">DNA ladder</td>
			<td style="width:227px;">Thermo-Fisher</td>
			<td style="width:307px;">SM 1331</td>
			<td>used to make calibration curves and as reference to cut band in integrity assay</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">Agar Agar</td>
			<td style="width:227px;">Merck</td>
			<td style="width:307px;"></td>
			<td>used to make LB-ampicillin culture plates&#160;</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">sodium chloride</td>
			<td style="width:227px;">Merck</td>
			<td style="width:307px;">1064045000</td>
			<td>used to make LB-ampicillin culture plates&#160;</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">yeast extract</td>
			<td style="width:227px;">Becton, Dickinson and Company</td>
			<td style="width:307px;">212750</td>
			<td>used to make LB-ampicillin culture plates&#160;</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">peptone</td>
			<td style="width:227px;">Merck</td>
			<td style="width:307px;">72161000</td>
			<td>used to make LB-ampicillin culture plates&#160;</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">TEMED</td>
			<td style="width:227px;">AMRESCO</td>
			<td style="width:307px;">761</td>
			<td>used to make polyacrylamide gels</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">ammonium persulfate</td>
			<td style="width:227px;">Calbiochem</td>
			<td style="width:307px;">2310</td>
			<td>used to make polyacrylamide gels</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">acrylamide</td>
			<td style="width:227px;">invitrogen</td>
			<td style="width:307px;">15512-023</td>
			<td>used to make polyacrylamide gels</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">bisacrylamide</td>
			<td style="width:227px;">SIGMA</td>
			<td style="width:307px;">146072</td>
			<td>used to make polyacrylamide gels</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">Tris-base</td>
			<td style="width:227px;">Merck</td>
			<td style="width:307px;">1083821000</td>
			<td>used to make TAE buffer and non-denaturing polyacrylamide gel tris-HCl buffer</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">EDTA</td>
			<td style="width:227px;">J.T. Baker</td>
			<td style="width:307px;">8993-01</td>
			<td>used to make TAE buffer</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">Acetic acid</td>
			<td style="width:227px;">Merck</td>
			<td style="width:307px;">1,000,632,500</td>
			<td>used to make TAE buffer</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">agarose</td>
			<td style="width:227px;">Merck</td>
			<td style="width:307px;">16802</td>
			<td>used to make TAE buffer</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">spectrophotometer</td>
			<td style="width:227px;">Tecan</td>
			<td style="width:307px;">infinite 200 pro</td>
			<td>used to quantify DNA plasmid</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">water purificatiom unit</td>
			<td style="width:227px;">Merck</td>
			<td style="width:307px;">Elix 100</td>
			<td>use to make water type 1 (ASTM) used in spectrophotometry and DNA dilutions\</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">distilled water</td>
			<td style="width:227px;"></td>
			<td style="width:307px;">-</td>
			<td>used in gels, culture medium, stainings and general solutions</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">HCl</td>
			<td style="width:227px;">J.T. Baker</td>
			<td>9535-03</td>
			<td>used to make non-denaturing polyacrylamide gel tris-HCl buffer</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">6X DNA loading dye</td>
			<td style="width:227px;">Thermo-Fisher</td>
			<td style="width:307px;">R0610</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">5 mm Blue LED</td>
			<td style="width:227px;">Jinyuan electronics</td>
			<td style="width:307px;">SP-021</td>
			<td>light source used in integrity assay</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">protoboard</td>
			<td style="width:227px;">KANDH</td>
			<td style="width:307px;">KH102</td>
			<td>light source support and circuit&#160;</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">9 V battery</td>
			<td style="width:227px;">Duracell</td>
			<td style="width:307px;">-</td>
			<td>used to power the LED&#39;s</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:187px;">horizontal electrophoresis chamber</td>
			<td style="width:227px;">Biorad</td>
			<td style="width:307px;">1704486EDU</td>
			<td>used to make and run agarose gel in integrity assay</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">vertical electrophoresis kit</td>
			<td style="width:227px;">Biorad</td>
			<td style="width:307px;">1658002EDU</td>
			<td>used to run polyacrylamide gels in calibration curves</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">power supply</td>
			<td style="width:227px;">Biorad</td>
			<td style="width:307px;">1645050&#160;</td>
			<td>used to power the electrophoresis</td>
		</tr>
	</tbody>
</table>

dna staining method based on formazan precipitation induced by blue light exposure

DNA 染色法、生物医学研究のため非常に重要です。色の沈殿物の形成によって肉眼に目に DNA の可視化を可能にする簡単な方法を考案しました。それは、アクリルアミドを浸漬、または agarose DNA ゲル 1 x (2.0 μ M に相当) の溶液に SYBR グリーン私 (SG 私) と紫色を作り出す 0.20 mM ニトロ ブルー テトラゾリウム塩日光に露出されたときの沈殿または具体的に青色のライト。また、提案手法を用いた染色 agarose のゲルにアンピシリン耐性プラスミドを用いた DNA 回復試験を行った。コロニーの大きい数はより伝統的な手法で得られた SG を使用して染色私は紫外光照射。説明メソッドは高速、特定、および、transilluminator なし「肉眼で見える」生体分子の可視化をできるように DNA 検出のための非毒性を安価でフィールドでの使用に適した。これらの理由から、私たちの新しい DNA 染色法の研究と業界の両方に潜在的な利点があります。

紫塩沈殿物 (質量13によって確認される) DNA があるが表示されます。実験では, DNA の梯子は較正曲線 (図 3) に読み込まれました。アクリルアミドと agarose のゲルのプロトコルが動作しますが、低強度があり agarose の長い時間がかかります。しかし、agarose のゲルの使用により、市販のキットを使用してサンプルの回復、それは抽?...

Watch this Scientific Journal Video about DNA Staining Method Based on Formazan Precipitation Induced by Blue Light Exposure at JoVE.com

DNA Staining Method Based on Formazan Precipitation Induced by Blue Light Exposure

このメソッドにより、選択的染色とゲルの DNA の定量化 SYBR グリーンでゲルを浸す私/ニトロ ブルー テトラゾリウム ソリューションと、日光や青い光源にそれを公開します。これは表示の沈殿物を生成する、フィールドでの使用に最適の機器はほぼ不要します。

DNA 染色青い光曝露による塩の沈殿物に基づく法

DNA staining methods are very important for biomedical research. We designed a simple method that allows DNA visualization to the naked eye by the ...

dna-staining-method-based-on-formazan-precipitation-induced-blue

Research

JoVE Journal

Biochemistry

9.4K ビュー.  Universidad de Chile. このメソッドにより、選択的染色とゲルの DNA の定量化 SYBR グリーンでゲルを浸す私/ニトロ ブルー テトラゾリウム ソリューションと、日光や青い光源にそれを公開します。これは表示の沈殿物を生成する、フィールドでの使用に最適の機器はほぼ不要します。

ビデオ: DNA Staining Method Based on Formazan Precipitation Induced by Blue Light Exposure

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

Most proteins act in association with others; hence, it is crucial to characterize these functional units in order to fully understand biological processes. Affinity purification coupled to mass spectrometry (AP-MS) has become the method of choice for identifying protein-protein interactions. However, conventional AP-MS studies provide information on protein interactions, but the organizational information is lost. To address this issue, we developed a strategy to unravel the distinct functional assemblies a protein might be involved in, by resolving affinity-purified protein complexes prior to their characterization by mass spectrometry. Protein complexes isolated through affinity purification of a bait protein using an epitope tag and competitive elution are separated through blue native electrophoresis. Comparison of protein migration profiles through correlation profiling using quantitative mass spectrometry allows assignment of interacting proteins to distinct molecular entities. This method is able to resolve protein complexes of close molecular weights that might not be resolved by traditional chromatographic techniques such as gel filtration. With little more work than conventional AP-geLC-MS/MS, we demonstrate this strategy may in many cases be adequate for obtaining protein complex topological information concomitantly to identifying protein interactions.

Here we present protocols for affinity purification of protein complexes and their separation by blue native PAGE, followed by protein correlation profiling using label free quantitative mass spectrometry. This method is useful to resolve interactomes into distinct protein complexes.

ブルーネイティブPAGEおよびタンパク質相関プロファイリングによってアフィニティー精製タンパク質複合体の解決

Most proteins act in association with others; hence, it is crucial to characterize these functional units in order to fully understand biological ...

生化学

Real-time Tracking of DNA Fragment Separation by Smartphone

Slab gel electrophoresis (SGE) is the most common method for the separation of DNA fragments; thus, it is broadly applied to the field of biology and others. However, the traditional SGE protocol is quite tedious, and the experiment takes a long time. Moreover, the chemical consumption in SGE experiments is very high. This work proposes a simple method for the separation of DNA fragments based on an SGE chip. The chip is made by an engraving machine. Two plastic sheets are used for the excitation and emission wavelengths of the optical signal. The fluorescence signal of the DNA bands is collected by smartphone. To validate this method, 50, 100, and 1,000 bp DNA ladders were separated. The results demonstrate that a DNA ladder smaller than 5,000 bp can be resolved within 12 min and with high resolution when using this method, indicating that it is an ideal substitute for the traditional SGE method.

Traditional slab gel electrophoresis (SGE) experiments require a complicated apparatus and high chemical consumption. This work presents a protocol that describes a low-cost method to separate DNA fragments within a short timeframe.

スマートフォンによるDNA断片分離のリアルタイム追跡

Slab gel electrophoresis (SGE) is the most common method for the separation of DNA fragments; thus, it is broadly applied to the field of biology and ...

DNA Polymerase Activity Assay Using Near-infrared Fluorescent Labeled DNA Visualized by Acrylamide Gel Electrophoresis

For any enzyme, robust, quantitative methods are required for characterization of both native and engineered enzymes. For DNA polymerases, DNA synthesis can be characterized using an in vitro DNA synthesis assay followed by polyacrylamide gel electrophoresis. The goal of this assay is to quantify synthesis of both natural DNA and modified DNA (M-DNA). These approaches are particularly useful for resolving oligonucleotides with single nucleotide resolution, enabling observation of individual steps during enzymatic oligonucleotide synthesis. These methods have been applied to the evaluation of an array of biochemical and biophysical properties such as the measurement of steady-state rate constants of individual steps of DNA synthesis, the error rate of DNA synthesis, and DNA binding affinity. By using modified components including, but not limited to, modified nucleoside triphosphates (NTP), M-DNA, and/or mutant DNA polymerases, the relative utility of substrate-DNA polymerase pairs can be effectively evaluated. Here, we detail the assay itself, including the changes that must be made to accommodate nontraditional primer DNA labeling strategies such as near-infrared fluorescently labeled DNA. Additionally, we have detailed crucial technical steps for acrylamide gel pouring and running, which can often be technically challenging.

This protocol describes the characterization of DNA polymerase synthesis of modified DNA through observation of changes to near-infrared fluorescently labeled DNA using gel electrophoresis and gel imaging. Acrylamide gels are used for high resolution imaging of the separation of short nucleic acids, which migrate at different rates depending on size.

アクリルアミドゲル電気泳動法で可視化した近赤外蛍光標識 DNA を用いた DNA ポリメラーゼ活性測定法

For any enzyme, robust, quantitative methods are required for characterization of both native and engineered enzymes. For DNA polymerases, DNA synthesis ...

A Simple Method for High Throughput Chemical Screening in Caenorhabditis Elegans

Caenorhabditis elegans is a useful organism for testing chemical effects on physiology. Whole organism small molecule screens offer significant advantages for identifying biologically active chemical structures that can modify complex phenotypes such as lifespan. Described here is a simple protocol for producing hundreds of 96-well culture plates with fairly consistent numbers of C. elegans in each well. Next, we specified how to use these cultures to screen thousands of chemicals for effects on the lifespan of the nematode C. elegans. This protocol makes use of temperature sensitive sterile strains, agar plate conditions, and simple animal handling to facilitate the rapid and high throughput production of synchronized animal cultures for screening.

A Simple Method for High Throughput Chemical Screening in Caenorhabditis Elegans

Here we describe a simple protocol for rapidly producing hundreds of nematode growth media agar, 96-well culture plates with consistent numbers of Caenorhhabditis elegans per well. These cultures are useful for the phenotypic screening of whole organisms. We focus here on using these cultures to screen chemicals for pro-longevity effects.

カエノラブディティス ・ エレガンスにおけるハイスループット化合物スクリーニングのための簡単な方法

Caenorhabditis elegans is a useful organism for testing chemical effects on physiology. Whole organism small molecule screens offer significant advantages ...

Electrochemical Detection of Deuterium Kinetic Isotope Effect on Extracellular Electron Transport in Shewanella oneidensis MR-1

Direct electrochemical detection of c-type cytochrome complexes embedded in the bacterial outer membrane (outer membrane c-type cytochrome complexes; OM c-Cyts) has recently emerged as a novel whole-cell analytical method to characterize the bacterial electron transport from the respiratory chain to the cell exterior, referred to as the extracellular electron transport (EET). While the pathway and kinetics of the electron flow during the EET reaction have been investigated, a whole-cell electrochemical method to examine the impact of cation transport associated with EET has not yet been established. In the present study, an example of a biochemical technique to examine the deuterium kinetic isotope effect (KIE) on EET through OM c-Cyts using a model microbe, Shewanella oneidensis MR-1, is described. The KIE on the EET process can be obtained if the EET through OM c-Cyts acts as the rate-limiting step in the microbial current production. To that end, before the addition of D2O, the supernatant solution was replaced with fresh media containing a sufficient amount of the electron donor to support the rate of upstream metabolic reactions, and to remove the planktonic cells from a uniform monolayer biofilm on the working electrode. Alternative methods to confirm the rate-limiting step in microbial current production as EET through OM c-Cyts are also described. Our technique of a whole-cell electrochemical assay for investigating proton transport kinetics can be applied to other electroactive microbial strains.

Electrochemical Detection of Deuterium Kinetic Isotope Effect on Extracellular Electron Transport in Shewanella oneidensis MR-1

Here we present a protocol of whole-cell electrochemical experiments to study the contribution of proton transport to the rate of extracellular electron transport via the outer-membrane cytochromes complex in Shewanella oneidensis MR-1.

電気化学検出の重水素速度論的同位体効果シェワネラ oneidensis氏 1 の細胞外電子輸送

Direct electrochemical detection of c-type cytochrome complexes embedded in the bacterial outer membrane (outer membrane c-type cytochrome complexes; OM ...

Analysis of Thylakoid Membrane Protein Complexes by Blue Native Gel Electrophoresis

Photosynthetic electron transfer chain (ETC) converts solar energy to chemical energy in the form of NADPH and ATP. Four large protein complexes embedded in the thylakoid membrane harvest solar energy to drive electrons from water to NADP+ via two photosystems, and use the created proton gradient for production of ATP. Photosystem PSII, PSI, cytochrome b6f (Cyt b6f) and ATPase are all multiprotein complexes with distinct orientation and dynamics in the thylakoid membrane. Valuable information about the composition and interactions of the protein complexes in the thylakoid membrane can be obtained by solubilizing the complexes from the membrane integrity by mild detergents followed by native gel electrophoretic separation of the complexes. Blue native polyacrylamide gel electrophoresis (BN-PAGE) is an analytical method used for the separation of protein complexes in their native and functional form. The method can be used for protein complex purification for more detailed structural analysis, but it also provides a tool to dissect the dynamic interactions between the protein complexes. The method was developed for the analysis of mitochondrial respiratory protein complexes, but has since been optimized and improved for the dissection of the thylakoid protein complexes. Here, we provide a detailed up-to-date protocol for analysis of labile photosynthetic protein complexes and their interactions in Arabidopsis thaliana.

A protocol for the elucidation of plant thylakoid protein complex organization and composition with blue native polyacrylamide gel electrophoresis (BN-PAGE) and 2D-SDS-PAGE is described. The protocol is optimized for Arabidopsis thaliana, but can be used for other plant species with minor modifications.

ブルー ネイティブ電気泳動によってチラコイド膜タンパク質複合体の解析

Photosynthetic electron transfer chain (ETC) converts solar energy to chemical energy in the form of NADPH and ATP. Four large protein complexes embedded ...

Analysis of &#946;-Amyloid-induced Abnormalities on Fibrin Clot Structure by Spectroscopy and Scanning Electron Microscopy

This article presents methods for generating in vitro fibrin clots and analyzing the effect of beta-amyloid (A&#946;) protein on clot formation and structure by spectrometry and scanning electron microscopy (SEM). A&#946;, which forms neurotoxic amyloid aggregates in Alzheimer&#39;s disease (AD), has been shown to interact with fibrinogen. This A&#946;-fibrinogen interaction makes the fibrin clot structurally abnormal and resistant to fibrinolysis. A&#946;-induced abnormalities in fibrin clotting may also contribute to cerebrovascular aspects of the AD pathology such as microinfarcts, inflammation, as well as, cerebral amyloid angiopathy (CAA). Given the potentially critical role of neurovascular deficits in AD pathology, developing compounds which can inhibit or lessen the A&#946;-fibrinogen interaction has promising therapeutic value. In vitro methods by which fibrin clot formation can be easily and systematically assessed are potentially useful tools for developing therapeutic compounds. Presented here is an optimized protocol for in vitro generation of the fibrin clot, as well as analysis of the effect of A&#946; and A&#946;-fibrinogen interaction inhibitors. The clot turbidity assay is rapid, highly reproducible and can be used to test multiple conditions simultaneously, allowing for the screening of large numbers of A&#946;-fibrinogen inhibitors. Hit compounds from this screening can be further evaluated for their ability to ameliorate A&#946;-induced structural abnormalities of the fibrin clot architecture using SEM. The effectiveness of these optimized protocols is demonstrated here using TDI-2760, a recently identified A&#946;-fibrinogen interaction inhibitor.

Presented here are two methods that can be used individually or in combination to analyze the effect of beta-amyloid on fibrin clot structure. Included is a protocol for creating an in vitro fibrin clot, followed by clot turbidity and scanning electron microscopy methods.

Β アミロイド誘起分光と電子顕微鏡によるフィブリン血栓構造異常の解析

This article presents methods for generating in vitro fibrin clots and analyzing the effect of beta-amyloid (A&#946;) protein on clot formation and ...

DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling

DNA primase synthesizes short RNA primers that initiate DNA synthesis of Okazaki fragments on the lagging strand by DNA polymerase during DNA replication. The binding of prokaryotic DnaG-like primases to DNA occurs at a specific trinucleotide recognition sequence. It is a pivotal step in the formation of Okazaki fragments. Conventional biochemical tools that are used to determine the DNA recognition sequence of DNA primase provide only limited information. Using a high-throughput microarray-based binding assay and consecutive biochemical analyses, it has been shown that 1) the specific binding context (flanking sequences of the recognition site) influences the binding strength of the DNA primase to its template DNA, and 2) stronger binding of primase to the DNA yields longer RNA primers, indicating higher processivity of the enzyme. This method combines PBM and primase activity assay and is designated as high-throughput primase profiling (HTPP), and it allows characterization of specific sequence recognition by DNA primase in unprecedented time and scalability.&#160;

Protein binding microarray (PBM) experiments combined with biochemical assays link the binding and catalytic properties of DNA primase, an enzyme that synthesizes RNA primers on template DNA. This method, designated as high-throughput primase profiling (HTPP), can be used to reveal DNA-binding patterns of a variety of enzymes.

ハイスループットプリマゼプロファイリングを用いたDNAプリマゼによるDNA配列認識

DNA primase synthesizes short RNA primers that initiate DNA synthesis of Okazaki fragments on the lagging strand by DNA polymerase during DNA replication. ...

Visualizing Surface T-Cell Receptor Dynamics Four-Dimensionally Using Lattice Light-Sheet Microscopy

The signaling and function of a cell are dictated by the dynamic structures and interactions of its surface receptors. To truly understand the structure-function relationship of these receptors in situ, we need to visualize and track them on the live cell surface with enough spatiotemporal resolution. Here we show how to use recently developed Lattice Light-Sheet Microscopy (LLSM) to image T-cell receptors (TCRs) four-dimensionally (4D, space and time) at the live cell membrane. T cells are one of the main effector cells of the adaptive immune system, and here we used T cells as an example to show that the signaling and function of these cells are driven by the dynamics and interactions of the TCRs. LLSM allows for 4D imaging with unprecedented spatiotemporal resolution. This microscopy technique therefore can be generally applied to a wide array of surface or intracellular molecules of different cells in biology.

The goal of this protocol is to show how to use Lattice Light-Sheet Microscopy to four-dimensionally visualize surface receptor dynamics in live cells. Here T cell receptors on CD4+ primary T cells are shown.

格子光シート顕微鏡による表面T細胞受容体ダイナミクスの可視化4次元的な研究

The signaling and function of a cell are dictated by the dynamic structures and interactions of its surface receptors. To truly understand the ...

Measuring Interactions between Fluorescent Probes and Lignin in Plant Sections by sFLIM Based on Native Autofluorescence

In lignocellulosic biomass (LB), the activity of enzymes is limited by the appearance of non-specific interactions with lignin during the hydrolysis process, which maintains enzymes far from their substrate. Characterization of these complex interactions is thus a challenge in complex substrates such as LB. The method here measures molecular interactions between fluorophore-tagged molecules and native autofluorescent lignin, to be revealed by F&#246;rster resonance energy transfer (FRET). Contrary to FRET measurements in living cells using two exogenous fluorophores, FRET measurements in plants using lignin is not trivial due to its complex autofluorescence. We have developed an original acquisition and analysis pipeline with correlated observation of two complementary properties of fluorescence: fluorescence emission and lifetime. sFLIM (spectral and fluorescent lifetime imaging microscopy) provides the quantification of these interactions with high sensitivity, revealing different interaction levels between biomolecules and lignin.

This protocol describes an original setup combining spectral and fluorescence lifetime measurements to evaluate F&#246;rster resonance energy transfer (FRET) between rhodamine-based fluorescent probes and lignin polymer directly in thick plant sections.

ネイティブ自己蛍光に基づくsFLIMによる植物切片における蛍光プローブとリグニン間の相互作用の測定

In lignocellulosic biomass (LB), the activity of enzymes is limited by the appearance of non-specific interactions with lignin during the hydrolysis ...