저자는 감사의 말씀을 프랭크 박사 지앙 박사 데이비드 린 박사 버나드 Yurke 박사 우다이 Chippada을 DNA 겔 기술을 개발에 대한 자신의 기여에 대한; 박사 노넬 Hadzimichalis, SMIT 샤 킴벌리 피터 맨, 자신의 의견이 원고의 편집 로버트 Arter; 척수에 뉴저지위원회 연구 (그랜트 # 07A-019-SCR1, NAL)와 뉴저지 신경 과학 연구소 (MLP)을 포함하여 자금 출처; 및 조직 공학 출판사, 부품이 권한은 그림 3을 다시 인쇄 할 수있는 권한에 대한 그림 2와 그림 4와 생체 재료를 다시 인쇄 할 수.

<ol>
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저자가 공개하는 게 없다.

DNA 겔의 능력은 연화 시키거나 세포 접착 그들에게 세포 기능의 동적 강성 조직의 역할을 연구하는 이상적인 모델을 만든다 전후 완고. 세가지 설계는 기계적 및 생물학적 연구에 사용되었다. 그러나, 모든 세 개의 디자인 가교 길이는 DNA 겔 탄성 (표 2)에 영향을주지 않는 나타내는 각종 비율로 가교 유사한 탄력성이있다. 대조적으로, 아크릴 아마이드 농도는 탄성에 영향을 미친다. ?...

정적 및 동적 기질은 세포의 기능에 조직 탄성 또는 강성의 영향을 연구하기 위해 개발 된 생체 물질의 두 가지 범주이다. 정적 기판은 세포가 도금 및 / 또는 일단 제작 된 후 물리적 속성을 변경할 수 없습니다. 폴리 아크릴 아미드 (PA) 겔은 제어 공학 조사 5,17 위해 합성했다 제 이차원 정적 기판이었다. PA 젤은 다용도, 저렴, 쉽게 준비하고, 탄성 계수의 넓은 범위로 제조 될 수있다. 이 기술의 장점은 PA가 일반적으로 적용 기판 젤하게하지만, 정적 기판은 생체 내에서 세포 외 기질 (ECM) 및 주변 세포 환경의 동적 특성을 나타내는 것은 아닙니다. 예를 들면, ECM은 상해, 현상, 또는 질병의 결과로서 강성 변화를 겪는다. 동적 기판 따라서 제어 공학 연구에서 조직을 흉내 낸 기판 모델로 선호 <sup&gt; 22,24,25. 수많은 합성은 자연적인, 이차원, 삼차원, 정적 및 동적 생체 재료는 티슈 1,3,6,16,23,26 강성을 모방하기 위해 개발되어왔다. 몇몇 기판들은 동적 기계적 특성을 변경 2,4,7,8,12,15,16 열, UV, 전류, 이온, 및 pH 변화를 필요로하지만, 이들 자극은 하이드로 겔의 생체 응용을 제한 할 수있다. DNA 가교 폴리 아크릴 아미드 하이드로 겔 (DNA 젤)은 동적 이차원 탄성 기판이다. DNA의 가교는 미디어에 단일 가닥 DNA (ssDNA를)의 첨가에 의한 DNA 젤 강성, 시간, 공간, 가역적 변조 허용하거나 9-11,13,14,18,21 버퍼. 자극이 탄성 변조 적용되는 상기 동적 젤과는 달리, DNA 젤은 탄성의 변화에​​ 대한 적용 ssDNA의의 확산에 의존하고 있습니다. 따라서 세포가 성장 상부 겔 표면은, 속도 오 때문에 변조 된 첫 번째 영역은F 탄성 변조 겔 두께에 의존한다. DNA 젤 그러나 비스 아크릴 아미드 가교는 DNA (그림 1)으로 구성 가교로 대체됩니다, 그들은 폴리 아크릴 아미드 백본을 가지고 그 자신의 PA 젤 대응과 유사하다. 두 ssDNAs (SA1 및 SA2)가 겔의 가교 결합 된 DNA를 만드는 가교제 스트랜드 (L2)와 함께 혼성화. SA1과 SA2는 모두 PA 네트워크에 효과적으로 통합하기위한 5 &#39;끝에 Acrydite 수정을 포함하는 별개의 시퀀스를 가지고있다. 젤, SA1과 SA2의 준비를위한 개별적으로 PA 백본으로 중합하고, 그 후, 중합 SA1과 SA2 함께 혼합된다. L2, 가교제는, SA1 및 SA2 혼합물에 첨가된다. L2의 염기 서열을 모두 SA1과 SA2에 상보적인 서열이며, L2는 DNA의 가교 결합을 형성하기 위해 플러스 SA1 SA2와 혼성화. 초기, DNA 젤 탄력성 L2 농도 및 가교 (표 1 모두에 의해 결정된다 </strong&gt; 및 2). SA1과 SA2가 (100 % 젤로 지정) L2에 의해 백퍼센트 가교 때문에 L2, SA1, SA2와 동등한 화학 양 론적 양을 포함하는 DNA 젤은 뻣뻣한 젤입니다. 따라서 낮은 DNA 가교의 비율과, L2에서 결과의 낮은 농도, 부드러운 DNA 젤. (50 % 젤로 지정) 50 % 가교 낮은 젤은 9-11를 구성하고있다. <img alt="그림 1" src="/files/ftp_upload/51323/51323fig1highres.jpg" /> 도 1 DNA 겔 가교 uncrosslinking 개략적 9-11,13,14,18,21 1 단계 :. SA1 (적색)과 SA2 (청색)은 개별적으로 폴리 아크릴 아미드 백본 (흑)로 중합된다. 중합 후, SA1과 SA2 중합 솔루션은 함께 혼합. 단계 2 : L2 (녹색)을 첨가하고, 겔의 가교 결합을 형성하기 위해 플러스 SA1 SA2와 혼성화된다. 3 단계 : R2는 t으로 하이브 리다그는 L2의 발붙일. 4 단계 : R2의 발붙일 하이브리드는 SA1과 SA2에서 L2의 압축 풀기를 추진한다. PA 젤과는 달리, DNA 젤은 완고하고 합성 한 후 부드럽게. 이러한 이유로, DNA 겔상에서 성장한 세포를 동적 강성도 변화를 실시 할 수있다. 세포 접착 성 겔 완고, L2는 가교 결합의 비율을 증가시키기 위해 낮은 퍼센트 겔 배양 배지에 첨가 될 수있다. 세포 접착 성 젤을 부드럽게하기 위해, L2는 가교 10,13,21의 비율을 감소 제거 할 수 있습니다. L2는 L2가 SA1과 SA2 (표 1)에서 uncrosslink 할 수 있도록 3 &#39;끝에 추가 발붙일 순서가 있습니다. L2를 제거하여 R2라고 반전 가닥의 혼성화에 의해 달성된다. R2는 L2의 전체 길이에 상보과 L2의 발붙일와 제 혼성화. 발붙일 하이브리드는 가교을 제거하고 겔 강성을 감소 SA1과 SA2에서 L2의 압축 풀기를 추진한다. 이 보고서에서와지시 보강 및 DNA 젤 연화의 제조에 제공되는 단계별 비디오. 100 % 및 80 % 겔 제제가 기재되어 있지만,이 프로토콜은 다른 초기 및 최종 가교 백분율 DNA 겔을 만들 맞추어 질 수있다. 일반적으로, 100 % 및 80 % 겔은, 제조되는 유리 커버 슬립 상에 고정화 된, 작용 및 세포 시드. L2는 80 %의 겔 매체에 첨가하고 R2가 100 % 겔, 도금 후 48 시간의 매체에 첨가된다. 미디어 R2의 첨가는 가교 결합 된 80 % 100 % 겔을 부드럽게하는 반면 매체 L2의 첨가는 가교 결합 된 100 % ~ 80 % 겔을 경화된다. 보강 된 겔은 80 → 100 % 젤로 지정되어 연화 겔은 텍스트의 80 → 100 % 젤 지정되어 있습니다. 제어 또는 정적 젤, ssDNA를 들어 TS 구성된 또는 100 %와 80 %의 젤의 또 다른 세트에 전달된다. 탄성 변조 다음 두 최소 일 후, 세포를 처리 및 분석 할 수있다. <table border="0" cellpadding="0" cellspacing="0" fo:kEEP-together.within 페이지 = &quot;항상&quot;&gt; <tbody align="center"><tr><td rowspan="2"></td><td rowspan="2"> DNA의 가교 </td><td rowspan="2"> 기지 # </td><td> 시퀀스 (발붙일) </td><td rowspan="2"> 수정 </td><td rowspan="2"> 녹는 온도 (T m의 ° C) </td><td rowspan="2"> 댓글 </td></tr><tr><td> 5 &#39;→ 3&#39; </td></tr><tr><td rowspan="4"> 디자인 한 </td><td> SA1 </td><td> 10 </td><td> GCA CCT TTG C </td><td> 5 &#39;Acrydite </td><td> 34.9 </td><td></td></tr><tr><td> SA2 </td><td> 10 </td><td> GTC AGA ATG </td><td> 5 &#39;Acrydite </td><td> 23.6 </td><td></td></tr><tr><td> L2 </td><td> 30 </td><td> TCA TTC TGA C GC AAA GGT GC G CTA CAC TTG </td><td></td><td> 56 </td><td>10 염기쌍으로 발 시퀀스가​​ 포함되어 있습니다. </td></tr><tr><td> R2 </td><td> 30 </td><td> CAA GTG의 TAG CGC ACC TTT GCG TCA GAA TGA </td><td></td><td></td><td> R2는 L2에 상보 </td></tr><tr><td rowspan="4"> 디자인이 </td><td> SA1 </td><td> 14 </td><td> CGT GGC ATA GGA CT </td><td> 5 &#39;Acrydite </td><td> 46.​​9 </td><td></td></tr><tr><td> SA2 </td><td> 14 </td><td> GTT TCC CAA TCA GA </td><td> 5 &#39;Acrydite </td><td> 40.2 </td><td></td></tr><tr><td> L2 </td><td> 40 </td><td> TCT GAT TGG GAA AC GTC CTA TGC CAC G GT TAC CTT CAT C </td><td></td><td> 65.9 </td><td> 12 bp의 순서 발붙일 곳이 포함되어 있습니다. </td></tr><tr><td> R2 </td><td> 40 </td><td> GAT GAA GGT AAC CGT GGC ATA GGA CTG TTT CCC AAT CAG </td><td></td><td> 65.9 </td><td> R2는 L2에 상보 </td></tr><tr><td rowspan="3"> 사이트 디자인N 세 </td><td> SA1 </td><td> 20 </td><td> ACG GAG GTG TAT GCA ATG TC </td><td> 5 &#39;Acrydite </td><td> 55 </td><td></td></tr><tr><td> SA2 </td><td> 20 </td><td> CAT GCT의 TAG GGA CGA CTG GA </td><td> 5 &#39;Acrydite </td><td> 56.6 </td><td></td></tr><tr><td> L2 </td><td> 40 </td><td> TCC AGT CGT CCC TAA GCA TG G ACA TTG CAT ACA CCT CCG T </td><td></td><td> 68.8 </td><td> 발붙일는 포함되어 있지 않습니다. </td></tr><tr><td rowspan="2"> 제어 </td><td rowspan="2"> 제어 </td><td rowspan="2"> 20 ~ 40 </td><td> AAA AAA (등) 또는 </td><td rowspan="2"></td><td rowspan="2"></td><td rowspan="2"></td></tr><tr><td> TTT TTT (등) </td></tr></tbody></table> 셀룰러 및 기계 연구 라 여러 가지 사용했다. ssDNA를 9-11,13,14,18,21 표 1 염기 서열ifferent 가교 디자인은 정적 및 동적 기계적 특성의 범위 DNA 젤을 생성합니다. 가교 디자인 변조 파라미터는 기본 시퀀스와 시퀀스 길이 또는 가교 길이이다. 굵게 및 기울임 꼴 글꼴은 SA1과 L2 사이에 각각 SA2와 L2 사이의 염기쌍을 보여줍니다. <table border="0" cellpadding="0" cellspacing="0" fo:keep-together.within-page="always"><tbody align="center"><tr><td rowspan="2"></td><td colspan="8"> 디자인 </td></tr><tr><td colspan="3"> 1 </td><td colspan="3"> 이 </td><td colspan="2"> 3 </td></tr><tr><td> 아크릴 아미드 농도 (%) </td><td colspan="3"> 10 </td><td colspan="3"> 10 </td><td> 10 </td><td> 4 </td></tr><tr><td> SA1 플러스 L2에 하이브리드 SA2 (% 가교) </td><td> 50 </td><td> 80 </td><td> 100 </td><td> 50 </td><td> 80 </td><td> 100 </td><td> 100 </td><td> 100 </td></tr><tr><td> &lt;강한&gt; 탄성 (kPa의, ± SEM을 의미) </td><td> 6.6 ± 0.6 </td><td> 17.1 ± 0.8 </td><td> 29.8 ± 2.5 </td><td> 5.85 ± 0.62 </td><td> 12.67 ± 1.33 </td><td> 22.88 ± 2.77 </td><td> 25.2 ± 0.5 </td><td> 10.4 ± 0.6 </td></tr></tbody></table> 표 2 DNA 젤 9-11,13,14,18,21. 아크릴 아마이드 농도 비율 가교 결합 및 가교 길이의 영률 (E)의 DNA 젤에서 변조 될 수있다. 디자인 1, 2, 3은 각각 20, 28, 및 40 bp의 길이가 가교. 모든 설계를위한 100 % 젤은 젤 탄력에 영향을주지 않습니다 가교 길이를 나타내는 유사한 계수가있다. 하지만, 아크릴 아마이드 농도 변화는 DNA 겔 탄성을 변경.

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr>
			<td>ssDNA</td>
			<td>Integrated DNA Technologies (Coralville, Iowa) idtdna.com</td>
			<td></td>
			<td>Do not vortex ssDNA. Gentle invert the vial and/or pipette solution to mix.</td>
		</tr>
		<tr>
			<td>PBS with calcium and magnesium</td>
			<td></td>
			<td></td>
			<td>Any brand.</td>
		</tr>
		<tr>
			<td>100X Tris-EDTA buffer (TE buffer)</td>
			<td>Sigma-Aldrich (St. Loius, MO) sigmaldrich.com</td>
			<td>T9285</td>
			<td></td>
		</tr>
		<tr>
			<td>10X Tris-Borate-EDTA buffer (TBE buffer)</td>
			<td>Sigma-Aldrich (St. Loius, MO)</td>
			<td>93290</td>
			<td>TBE is a reproductive toxin.</td>
		</tr>
		<tr>
			<td>40% Acrylamide solution</td>
			<td>Fisher Scientific (Pittsburg, PA)</td>
			<td>BP14021</td>
			<td>Acrylamide is a toxin.</td>
		</tr>
		<tr>
			<td>Ammonium persulfate (APS)</td>
			<td>Sigma-Aldrich (St. Loius, MO)</td>
			<td>A3678</td>
			<td>Prepare a 2% solution in TE buffer. APS is a toxin and irratant.</td>
		</tr>
		<tr>
			<td>Tetramethylethylenediamine (TEMED)</td>
			<td>Sigma-Aldrich (St. Loius, MO)</td>
			<td>T9281</td>
			<td>Prepare a 20% solution in TE buffer. TEMED is flammable, a corrosive, and a toxin.</td>
		</tr>
		<tr>
			<td rowspan="2">12-mm diameter round coverglass</td>
			<td rowspan="2">Fisher Scientific (Pittsburg, PA) fishersci.com</td>
			<td rowspan="2">12-545-82</td>
			<td rowspan="2"></td>
		</tr>
		<tr>
			<td>Norland optical adhesive 72</td>
			<td>Norland Products (Cranbury, NJ) norlandprod.com</td>
			<td>NOA72</td>
			<td></td>
		</tr>
		<tr>
			<td rowspan="2">24-well tissue culture plate</td>
			<td rowspan="2"></td>
			<td rowspan="2"></td>
			<td rowspan="2">Any brand.</td>
		</tr>
		<tr>
			<td rowspan="2">Microcentrifuge tubes</td>
			<td rowspan="2"></td>
			<td rowspan="2"></td>
			<td rowspan="2">Any brand.</td>
		</tr>
		<tr>
			<td>Sulfo-SANPAH</td>
			<td>ProteoChem or Thermo Fisher, (Rockland, IL) proteochem.com or thermofisher.com</td>
			<td>C111 or 22589</td>
			<td>Prepare a 0.315 mg/ml solution in water immediately before use. Dissolve at 37&#176;C and filter sterilze. It is normal to observe undisolved sulfo-SANPAH in the filter. Sulfo-SANPAH is light sensitive and, therefore, the solution should be protect from light until UV exposure.</td>
		</tr>
		<tr>
			<td>Poly-D-Lysine (PDL)</td>
			<td>Sigma-Aldrich (St. Loius, MO)</td>
			<td>P6407</td>
			<td>Prepare a 0.2 mg/ml solution in water and filter sterilize.</td>
		</tr>
		<tr>
			<td>Collagen Type I</td>
			<td>Affymetrix (Santa Clara, CA) affymetrix.com</td>
			<td>13813</td>
			<td>Prepare a 0.2 mg/ml solution in 0.2 N acetic acid. Solution needs to remain cold at all times to avoid polymerization. Acetic acid is a flammable, toxic, and corrosive.</td>
		</tr>
		<tr>
			<td>22 X 60 cover glass</td>
			<td>Fisher Scientific (Pittsburg, PA)</td>
			<td>12-544-G</td>
			<td></td>
		</tr>
		<tr>
			<td>Positive-displacement pipette</td>
			<td>Gilson, Inc (Middletown, WI) gilson.com</td>
			<td>F148504</td>
			<td></td>
		</tr>
		<tr>
			<td>Heat block</td>
			<td>Fisher Scientific (Pittsburg, PA)</td>
			<td>11-718</td>
			<td></td>
		</tr>
		<tr>
			<td>UV light source</td>
			<td></td>
			<td></td>
			<td>Place gels as close as possible to the UV light. UV light can cause skin or eye injury.</td>
		</tr>
		<tr>
			<td>Thermometer</td>
			<td></td>
			<td></td>
			<td>Any brand.</td>
		</tr>
		<tr>
			<td>Nitrogen gas</td>
			<td>GTS-Welco (Flemington, NJ) www.praxairmidatlantic.com/</td>
			<td>NI 5.0UH-R</td>
			<td></td>
		</tr>
	</tbody>
</table>

preparation of dna-crosslinked polyacrylamide hydrogels

제어 공학은 세포 형태와 기능을 연출 물리적 신호의 중요한 역할을 해결하는 새로운 과학 분야이다. 조직 경화 질병, 개발 및 부상으로 변조하기 때문에 예를 들어, 세포 기능에 조직 탄성 효과는 제어 공학 연구의 중요한 영역이다. 세포가 일단 도금 강성을 변경할 수없는 고정 조직 모방 재료, 또는 재료는 주로 세포의 기능에 대한 조직의 강성의 영향을 조사하기 위해 사용된다. 정적 스터디에서 수집 된 정보는 가치가 있지만, 이러한 연구는 생체 내에서 세포 미세 환경의 동적 특성을 나타내는 것은 아닙니다. 더 세포 기능에 동적 강성의 영향을 해결하기 위해, 우리는 DNA 가교 폴리 아크릴 아미드 하이드로 겔 시스템 (DNA 젤)을 개발 하였다. 다른 동적 기판과 달리, DNA 겔이 감소 또는 자극없이 제조 후 강성도를 증가시키는 능력을 가지고있다. DNA 젤은 DNA의 crossl 구성폴리 아크릴 아미드 백본으로 중합 잉크. 추가 및 단일 가닥 DNA의 전달을 통해 가교를 제거하는 것은 시간, 공간, 겔 탄성 가역 제어 할 수 있습니다. 우리는 DNA 젤 탄성 동적 변조 섬유 아세포와 신경 세포의 행동에 영향을 미치는 것을 이전 보고서에 표시했다. 이 보고서와 비디오에서 우리는 준비 DNA 젤에서 DNA 겔 가교 메커니즘과 단계별 지침을 설명하는 회로도를 제공한다.

우리의 연구에 앞서, 세포 ECM 상호 호환 생체 물질은 정적 또는 동적 비가역 단방향 기판 상에 관찰되었다. 이 기판은 정확하게 세포 미세 환경의 동적 특성을 반영하지 않습니다. 우리의 작업은 연화에 세포 ECM 상호 작용을 공부하고 동적 생체 재료를 보강하기위한 더 많은 생리 학적 모델을 제공함으로써 기존의 기술 패러다임을 이동합니다. 이전 연구에서, 우리는 이러한 젤에 다양한 세포 모?...

Watch this Scientific Journal Video about Preparation of DNA-crosslinked Polyacrylamide Hydrogels at JoVE.com

Preparation of DNA-crosslinked Polyacrylamide Hydrogels

본 연구실은 더 세포 기능에 티슈 강성 변조의 효과를 이해하는 DNA 가교 폴리 아크릴 아미드 하이드로 겔, 하이드로 겔 동적 시스템을 개발했다. 여기서, 우리는 이러한 하이드로 겔을 제조하기위한 회로도, 설명, 및 프로토콜을 제공한다.

DNA-가교 폴리 아크릴 아미드 하이드로 겔의 제조

Mechanobiology is an emerging scientific area that addresses the critical role of physical cues in directing cell morphology and function. For example, ...

preparation-of-dna-crosslinked-polyacrylamide-hydrogels

Research

JoVE Journal

Biology

14.4K 조회수.  JFK Medical Center.  본 연구실은 더 세포 기능에 티슈 강성 변조의 효과를 이해하는 DNA 가교 폴리 아크릴 아미드 하이드로 겔, 하이드로 겔 동적 시스템을 개발했다. 여기서, 우리는 이러한 하이드로 겔을 제조하기위한 회로도, 설명, 및 프로토콜을 제공한다. 

비디오: Preparation of DNA-crosslinked Polyacrylamide Hydrogels

Fast and Sensitive Colloidal Coomassie G-250 Staining for Proteins in Polyacrylamide Gels

Coomassie Brilliant Blue (CBB) is a dye commonly used for the visualization of proteins separated by SDS-PAGE, offering a simple staining procedure and high quantitation. Furthermore, it is completely compatible with mass spectrometric protein identification. But despite these advantages, CBB is regarded to be less sensitive than silver or fluorescence stainings and therefore rarely used for the detection of proteins in analytical gel-based proteomic approaches.
Several improvements of the original Coomassie protocol1 have been made to increase the sensitivity of CBB. Two major modifications were introduced to enhance the detection of low-abundant proteins by converting the dye molecules into colloidal particles: In 1988, Neuhoff and colleagues applied 20% methanol and higher concentrations of ammonium sulfate into the CBB G-250 based staining solution2, and in 2004 Candiano et al. established Blue Silver using CBB G-250 with phosphoric acid in the presence of ammonium sulfate and methanol3. Nevertheless, all these modifications just allow a detection of approximately 10 ng protein. A widely fameless protocol for colloidal Coomassie staining was published by Kang et al. in 2002 where they modified Neuhoff's colloidal CBB staining protocol regarding the complexing substances. Instead of ammonium sulfate they used aluminum sulfate and methanol was replaced by the less toxic ethanol4. The novel aluminum-based staining in Kang's study showed superior sensitivity that detects as low as 1 ng/band (phosphorylase b) with little sensitivity variation depending on proteins.
Here, we demonstrate application of Kang's protocol for fast and sensitive colloidal Coomassie staining of proteins in analytical purposes. We will illustrate the quick and easy protocol using two-dimensional gels routinely performed in our working group.

This video shall popularize a colloidal Coomassie G-250 staining protocol according to Kang et al. for the detection of average 4 ng protein in gels. The staining is completed within 2 hours and without any effort. We routinely use Kang's protocol for analytical purposes in gel-based proteomics.

Polyacrylamide의 젤의 단백질에 대한 신속하고 민감한 콜로이드 쿠매시 G - 250 스테 이닝

Coomassie Brilliant Blue (CBB) is a dye commonly used for the visualization of proteins separated by SDS-PAGE, offering a simple staining procedure and ...

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생물학

Denaturing Urea Polyacrylamide Gel Electrophoresis (Urea PAGE)

Urea PAGE or denaturing urea polyacrylamide gel electrophoresis employs 6-8 M urea, which denatures secondary DNA or RNA structures and is used for their separation in a polyacrylamide gel matrix based on the molecular weight. Fragments between 2 to 500 bases, with length differences as small as a single nucleotide, can be separated using this method1. The migration of the sample is dependent on the chosen acrylamide concentration. A higher percentage of polyacrylamide resolves lower molecular weight fragments. The combination of urea and temperatures of 45-55 &deg;C during the gel run allows for the separation of unstructured DNA or RNA molecules.
In general this method is required to analyze or purify single stranded DNA or RNA fragments, such as synthesized or labeled oligonucleotides or products from enzymatic cleavage reactions.
In this video article we show how to prepare and run the denaturing urea polyacrylamide gels. Technical tips are included, in addition to the original protocol 1,2.

Denaturing Urea Polyacrylamide Gel Electrophoresis Urea PAGE

Denaturing urea polyacrylamide gel electrophoresis is used to separate single-stranded DNA or RNA up to a limit of 500 nucleotides. Urea in combination with heat denatures samples and unstructured single strands migrate within the gel matrix according to their molecular weight.

Denaturing 요소의 Polyacrylamide 젤 전기 영동 (우레아 페이지)

Urea PAGE or denaturing urea polyacrylamide gel electrophoresis employs 6-8 M urea, which denatures secondary DNA or RNA structures and is used for their ...

Cellular Encapsulation in 3D Hydrogels for Tissue Engineering 

The 3D encapsulation of cells within hydrogels represents an increasingly important and popular technique for culturing cells and towards the development of constructs for tissue engineering. This environment better mimics what cells observe in vivo, compared to standard tissue culture, due to the tissue-like properties and 3D environment. Synthetic polymeric hydrogels are water-swollen networks that can be designed to be stable or to degrade through hydrolysis or proteolysis as new tissue is deposited by encapsulated cells. A wide variety of polymers have been explored for these applications, such as poly(ethylene glycol) and hyaluronic acid. Most commonly, the polymer is functionalized with reactive groups such as methacrylates or acrylates capable of undergoing crosslinking through various mechanisms. In the past decade, much progress has been made in engineering these microenvironments - e.g., via the physical or pendant covalent incorporation of biochemical cues - to improve viability and direct cellular phenotype, including the differentiation of encapsulated stem cells (Burdick et al.).
The following methods for the 3D encapsulation of cells have been optimized in our and other laboratories to maximize cytocompatibility and minimize the number of hydrogel processing steps. In the following protocols (see Figure 1 for an illustration of the procedure), it is assumed that functionalized polymers capable of undergoing crosslinking are already in hand; excellent reviews of polymer chemistry as applied to the field of tissue engineering may be found elsewhere (Burdick et al.) and these methods are compatible with a range of polymer types. Further, the Michael-type addition (see Lutolf et al.) and light-initiated free radical (see Elisseeff et al.) mechanisms focused on here constitute only a small portion of the reported crosslinking techniques. Mixed mode crosslinking, in which a portion of reactive groups is first consumed by addition crosslinking and followed by a radical mechanism, is another commonly used and powerful paradigm for directing the phenotype of encapsulated cells (Khetan et al., Salinas et al.).

Cellular Encapsulation in 3D Hydrogels for Tissue Engineering

We present protocols for the 3-dimensional (3D) encapsulation of cells within synthetic hydrogels. The encapsulation procedure is outlined for two commonly used methods of crosslinking (michael-type addition and light-initiated free radical mechanisms), as well as a number of techniques for assessing encapsulated cell behavior.

조직 공학을위한 3D Hydrogels에서 셀룰러 봉지

The 3D encapsulation of cells within hydrogels represents an increasingly important and popular technique for culturing cells and towards the development ...

Blue Native Polyacrylamide Gel Electrophoresis (BN-PAGE) for Analysis of Multiprotein Complexes from Cellular Lysates

Multiprotein complexes (MPCs) play a crucial role in cell signalling, since most proteins can be found in functional or regulatory complexes with other proteins (Sali, Glaeser et al. 2003). Thus, the study of protein-protein interaction networks requires the detailed characterization of MPCs to gain an integrative understanding of protein function and regulation. For identification and analysis, MPCs must be separated under native conditions. In this video, we describe the analysis of MPCs by blue native polyacrylamide gel electrophoresis (BN-PAGE). BN-PAGE is a technique that allows separation of MPCs in a native conformation with a higher resolution than offered by gel filtration or sucrose density ultracentrifugation, and is therefore useful to determine MPC size, composition, and relative abundance (Sch&auml;gger and von Jagow 1991); (Sch&auml;gger, Cramer et al. 1994). By this method, proteins are separated according to their hydrodynamic size and shape in a polyacrylamide matrix. Here, we demonstrate the analysis of MPCs of total cellular lysates, pointing out that lysate dialysis is the crucial step to make BN-PAGE applicable to these biological samples. Using a combination of first dimension BN- and second dimension SDS-PAGE, we show that MPCs separated by BN-PAGE can be further subdivided into their individual constituents by SDS-PAGE. Visualization of the MPC components upon gel separation is performed by standard immunoblotting. As an example for MPC analysis by BN-PAGE, we chose the well-characterized eukaryotic 19S, 20S, and 26S proteasomes.

Blue Native Polyacrylamide Gel Electrophoresis BN-PAGE for Analysis of Multiprotein Complexes from Cellular Lysates

In this video, we describe the characterization of multiprotein complexes (MPCs) by blue native polyacrylamide gel electrophoresis (BN-PAGE). In a first dimension, dialyzed cellular lysates are separated by BN-PAGE to identify individual MPCs. In a second dimension SDS-PAGE, MPCs of interest are further subdivided to analyze their constituents by immunoblotting.

셀룰러 Lysates에서 Multiprotein의 단지의 분석을 위해 블루 기본 Polyacrylamide 젤 전기 영동 (BN - PAGE)

Multiprotein complexes (MPCs) play a crucial role in cell signalling, since most proteins can be found in functional or regulatory complexes with other ...

Mechanical Stimulation of Chondrocyte-agarose Hydrogels

Articular cartilage suffers from a limited repair capacity when damaged by mechanical insult or degraded by disease, such as osteoarthritis. To remedy this deficiency, several medical interventions have been developed. One such method is to resurface the damaged area with tissue-engineered cartilage; however, the engineered tissue typically lacks the biochemical properties and durability of native cartilage, questioning its long-term survivability. This limits the application of cartilage tissue engineering to the repair of small focal defects, relying on the surrounding tissue to protect the implanted material. To improve the properties of the developed tissue, mechanical stimulation is a popular method utilized to enhance the synthesis of cartilaginous extracellular matrix as well as the resultant mechanical properties of the engineered tissue. Mechanical stimulation applies forces to the tissue constructs analogous to those experienced in vivo. This is based on the premise that the mechanical environment, in part, regulates the development and maintenance of native tissue1,2. The most commonly applied form of mechanical stimulation in cartilage tissue engineering is dynamic compression at physiologic strains of approximately 5-20% at a frequency of 1 Hz1,3. Several studies have investigated the effects of dynamic compression and have shown it to have a positive effect on chondrocyte metabolism and biosynthesis, ultimately affecting the functional properties of the developed tissue4-8. In this paper, we illustrate the method to mechanically stimulate chondrocyte-agarose hydrogel constructs under dynamic compression and analyze changes in biosynthesis through biochemical and radioisotope assays. This method can also be readily modified to assess any potentially induced changes in cellular response as a result of mechanical stimuli.

The biosynthesis of cartilaginous extracellular matrix by chondrocytes can be affected by application of mechanical stimuli. This method describes the technique of applying dynamic compressive strains to chondrocytes encapsulated in 3D constructs and the evaluation of induced changes in chondrocyte metabolism.

Chondrocyte - 아가로 오스 Hydrogels의 기계적 자극

Articular cartilage suffers from a limited repair capacity when damaged by mechanical insult or degraded by disease, such as osteoarthritis. To remedy ...

FRET Imaging in Three-dimensional Hydrogels

Imaging of F&#246;rster resonance energy transfer (FRET)&#160;is a powerful tool for examining cell biology in real-time. Studies utilizing FRET commonly employ two-dimensional (2D) culture, which does not mimic the three-dimensional (3D) cellular microenvironment. A method to perform quenched emission FRET imaging using conventional widefield epifluorescence microscopy of cells within a 3D hydrogel environment is presented. Here an analysis method for ratiometric FRET probes that yields linear ratios over the probe activation range is described. Measurement of intracellular cyclic adenosine monophosphate (cAMP) levels is demonstrated in chondrocytes under forskolin stimulation using a probe for EPAC1 activation (ICUE1) and the ability to detect differences in cAMP signaling dependent on hydrogel material type, herein a photocrosslinking hydrogel (PC-gel, polyethylene glycol dimethacrylate) and a thermoresponsive hydrogel (TR-gel). Compared with 2D FRET methods, this method requires little additional work. Laboratories already utilizing FRET imaging in 2D can easily adopt this method to perform cellular studies in a 3D microenvironment. It can further be applied to high throughput drug screening in engineered 3D microtissues. Additionally, it is compatible with other forms of FRET imaging, such as anisotropy measurement and fluorescence lifetime imaging (FLIM), and with advanced microscopy platforms using confocal, pulsed, or modulated illumination.

F&#246;rster resonance energy transfer (FRET) imaging is a powerful tool for real-time cell biology studies. Here a method for FRET imaging cells in physiologic three-dimensional (3D) hydrogel microenvironments using conventional epifluorescence microscopy is presented. An analysis for ratiometric FRET probes that yields linear ratios over the activation range is described.

3 차원 히드로 겔의 이미지를 FRET

Imaging of F&#246;rster resonance energy transfer (FRET)&#160;is a powerful tool for examining cell biology in real-time. Studies utilizing FRET commonly ...

Proteolytically Degraded Alginate Hydrogels and Hydrophobic Microbioreactors for Porcine Oocyte Encapsulation

In reproductive biology, the biotechnology revolution that began with artificial insemination and embryo transfer technology led to the development of assisted reproduction techniques such as oocyte in vitro maturation (IVM), in vitro fertilization (IVF) and cloning of domestic animals by nuclear transfer from somatic cell. IVM is the method particularly of significance. It is the platform technology for the supply of mature, good quality oocytes for applications such as reduction of the generation interval in commercially important or endangered species, research concerning in vitro human reproduction, and production of transgenic animals for cell therapies. The term oocyte quality includes its competence to complete maturation, be fertilized, thereby resulting in healthy offspring. This means that oocytes of good quality are paramount for successful fertilization including IVF procedures. This poses many difficulties to develop a reliable culture method that would support growth not only of human oocytes but also of other large mammalian species. The first step in IVM is the in vitro culture of oocytes. This work describes two protocols for the 3D culture of porcine oocytes. In the first, 3D model cumulus-oocyte complexes (COCs) are encapsulated in a fibrin-alginate bead interpenetrating network, in which a mixture of fibrin and alginate are gelled simultaneously. In the second one, COCs are suspended in a drop of medium and encapsulated with fluorinated ethylene propylene (FEP; a copolymer of hexafluoropropylene and tetrafluoroethylene) powder particles to form microbioreactors defined as Liquid Marbles (LM). Both 3D systems maintain the gaseous in vitro culture environment. They also maintain COCs 3D organization by preventing their flattening and consequent disruption of gap junctions, thereby preserving the functional relationship between the oocyte, and surrounding follicular cells.

Presented here are two protocols for the encapsulation of porcine oocytes in 3D culture conditions. In the first, cumulus-oocyte complexes (COCs) are encapsulated in fibrin-alginate beads. In the second, they are enclosed with fluorinated ethylene propylene powder particles (microbioreactors). Both systems ensure optimal conditions to maintain their 3D organization.

포르신 오시테 캡슐화를 위한 프로틸분해 된 알기네이트 하이드로겔 및 소수성 미생물 반응기

In reproductive biology, the biotechnology revolution that began with artificial insemination and embryo transfer technology led to the development of ...

Detection of Glycosaminoglycans by Polyacrylamide Gel Electrophoresis and Silver Staining

Sulfated glycosaminoglycans (GAGs) such as heparan sulfate (HS) and chondroitin sulfate (CS) are ubiquitous in living organisms and play a critical role in a variety of basic biological structures and processes. As polymers, GAGs exist as a polydisperse mixture containing polysaccharide chains that can range from 4000 Da to well over 40,000 Da. Within these chains exists domains of sulfation, conferring a pattern of negative charge that facilitates interaction with positively charged residues of cognate protein ligands. Sulfated domains of GAGs must be of sufficient length to allow for these electrostatic interactions. To understand the function of GAGs in biological tissues, the investigator must be able to isolate, purify, and measure the size of GAGs. This report describes a practical and versatile polyacrylamide gel electrophoresis-based technique that can be leveraged to resolve relatively small differences in size between GAGs isolated from a variety of biological tissue types.

This report describes techniques to isolate and purify sulfated glycosaminoglycans (GAGs) from biological samples and a polyacrylamide gel electrophoresis approach to approximate their size. GAGs contribute to tissue structure and influence signaling processes via electrostatic interaction with proteins. GAG polymer length contributes to their binding affinity for cognate ligands.

폴리아크릴아미드 젤 전기포및 은 염색에 의한 글리코아미노글리칸 검출

Sulfated glycosaminoglycans (GAGs) such as heparan sulfate (HS) and chondroitin sulfate (CS) are ubiquitous in living organisms and play a critical role ...

An Improved Chemotaxis Assay for the Rapid Identification of Rhizobacterial Chemoattractants in Root Exudates

Chemotaxis identification is very important for the research and application of rhizosphere growth-promoting bacteria. We established a straightforward method to quickly identify the chemoattractants that could induce the chemotactic movement of rhizosphere growth-promoting bacteria on sterile glass slides via simple steps. Bacteria solution (OD600 = 0.5) and sterile chemoattractant aqueous solution were added dropwise on the glass slide at an interval of 1 cm. An inoculating loop was used to connect the chemoattractant aqueous solution to the bacterial solution. The slide was kept at room temperature for 20 min on the clean bench. Finally, the chemoattractant aqueous solution was collected for bacterial counting and microscopic observation. In this study, through multiple comparisons of experimental results, the method overcame multiple shortcomings of traditional bacterial chemotaxis methods. The method reduced the error of plate counting and shortened the experimental cycle. For the identification of chemoattractant substances, this new method can save 2-3 days compared to the traditional method. Additionally, this method allows any researcher to systematically complete a bacterial chemotaxis experiment within 1-2 days. The protocol can be considered a valuable resource for understanding plant-microbe interactions.

Here, we present an improved chemotaxis assay protocol. The goal of this protocol is to reduce the steps and costs of traditional bacterial chemotaxis methods and to serve as a valuable resource for understanding plant-microbe interactions.

루트 엑수데이트에서 뿌리 균 화학 물질의 신속 한 식별에 대 한 향상 된 화학 분석

Chemotaxis identification is very important for the research and application of rhizosphere growth-promoting bacteria. We established a straightforward ...

다양한 하이드로겔 매트릭스에 CFPS 반응 임베딩

Methods for Embedding Cell-Free Protein Synthesis Reactions in Macro-Scale Hydrogels

Synthetic gene networks provide a platform for scientists and engineers to design and build novel systems with functionality encoded at a genetic level. While the dominant paradigm for the deployment of gene networks is within a cellular chassis, synthetic gene networks may also be deployed in cell-free environments. Promising applications of cell-free gene networks include biosensors, as these devices have been demonstrated against biotic (Ebola, Zika, and SARS-CoV-2 viruses) and abiotic (heavy metals, sulfides, pesticides, and other organic contaminants) targets. Cell-free systems are typically deployed in liquid form within a reaction vessel. Being able to embed such reactions in a physical matrix, however, may facilitate their broader application in a wider set of environments. To this end, methods for embedding cell-free protein synthesis (CFPS) reactions in a variety of hydrogel matrices have been developed. One of the key properties of hydrogels conducive to this work is the high-water reconstitution capacity of hydrogel materials. Additionally, hydrogels possess physical and chemical characteristics that are functionally beneficial. Hydrogels can be freeze-dried for storage and rehydrated for use later. Two step-by-step protocols for the inclusion and assay of CFPS reactions in hydrogels are presented. First, a CFPS system can be incorporated into a hydrogel via rehydration with a cell lysate. The system within the hydrogel can then be induced or expressed constitutively for complete protein expression through the hydrogel. Second, cell lysate can be introduced to a hydrogel at the point of polymerization, and the entire system can be freeze-dried and rehydrated at a later point with an aqueous solution containing the inducer for the expression system encoded within the hydrogel. These methods have the potential to allow for cell-free gene networks that confer sensory capabilities to hydrogel materials, with the potential for deployment beyond the laboratory.

저자 스포트라이트: 하이드로겔에 cell-free 단백질 합성 반응을 포함하기 위한 새로운 접근법 

Here, we present two protocols for embedding cell-free protein synthesis reactions in macro-scale hydrogel matrices without the need for an external liquid phase.

거시적 규모의 하이드로겔에 cell-free 단백질 합성 반응을 임베딩하는 방법

Synthetic gene networks provide a platform for scientists and engineers to design and build novel systems with functionality encoded at a genetic level. ...