وقد تم تمويل العمل في المختبر من قبل الدكتور برموديز CONACYT (المنحة # 82622) ، ونشكر غابرييلا جوتيريز ، سوسا ، Eliuth رييس - مارتينيز ورودريغيز زيمينا توريس لتسجيل الفيديو الإجراء electroleution.

<ol style=";text-align:right;direction:rtl"><li style=";text-align:right;direction:rtl"> من أجل اختيار شظايا من الحمض النووي التي تهم يمكن تنقيته ، ينبغي حل هذه agarose في المواد الهلامية أو هلام ملون الأكريلاميد مع بروميد إيثيديوم بواسطة الكهربائي باستخدام العازلة 0.5X TBE (تريس بورات ، EDTA) عند 120 فولت لمدة 1 ساعة. وقد استخدم لهذا ، ~ 700 نانوغرام من البلازميد pProEx GdMre11S - (6000 - BP) هضمها من قبل مع وNdeI HindIII على الافراج عن 900 قطعة من الغليان (560 نانوغرام من البلازميد و 84 نانوغرام في جزء منه). </li><li style=";text-align:right;direction:rtl"> ينبغي أن تملأ خزان electroeluter (الشكل 1) مع 0.5X TBE موزعة بالتساوي في كل جانب من الهضبة منتصف رعاية لا صرفها على هضبة متوسطة. </li><li style=";text-align:right;direction:rtl"> يتم قطع الشريط المحدد (أو نطاقات) للخروج من هلام ، وتوضع في حجرة العينة أقرب وقت ممكن إلى القناة الخامسة (شريحة واحدة لكل بئر). وينبغي أن يضاف إلى المخزن تشغيل كل غرفة ، ما يكفي لتغطية شريحة هلام. </li><li style=";text-align:right;direction:rtl"> يجب أن يتم مسح كل قناة V استخدامها مع ماصة باستور للقضاء على أي فقاعة الهواء المحبوس. </li><li style=";text-align:right;direction:rtl"> ثم تضاف برفق 100 من المجاهدين 10 M خلات NH 4 (لتسهيل التصور يتم إضافة كمية صغيرة من اللون الأزرق bromophenol ، وهو ما يكفي فقط لأنه لون) داخل القناة الخامس. </li><li style=";text-align:right;direction:rtl"> يجب إغلاق الغطاء برفق لمنع أي إعادة تعليق من الملح وسادة عالية. </li><li style=";text-align:right;direction:rtl"> وبدأت في Electroelution 100 فولت لمدة 25 دقيقة. </li><li style=";text-align:right;direction:rtl"> عند اكتمال electrolution ، تتم إزالة 400 من المجاهدين V - القناة ، ووضعها في أنبوب microfuge أن تكون عجلت مع 2 مجلدات من الايثانول الباردة والجليكوجين (مستحسن لتحسين استرداد DNA) في 4 درجات مئوية لمدة 1 ساعة أو بين عشية وضحاها. </li><li style=";text-align:right;direction:rtl"> أجهزة الطرد المركزي لمدة 20 دقيقة ، ويغسل إزالة طاف مع الايثانول 70 ٪. </li><li style=";text-align:right;direction:rtl"> أنبوب الجافة وتحديد الحمض النووي في 260 نانومتر OD. </li><li style=";text-align:right;direction:rtl"> وكان الانتعاش الحصول على 75 ٪ (63 نانوغرام تعافى عندما وضعت 84 نانوغرام في قناة V -). </li></ol><img src="/files/ftp_upload/2136/2136fig1.jpg" alt="الشكل 1" /> الشكل 1. Electroeluter الرسم التخطيطي. واشارت الى أنود الكاثود على كل جانب من الحمض النووي ، خزان الواردة في جل شرائح (كما هو موضح مربع أسود) سوف تهاجر نحو الكاثود بسبب شحنتها السالبة. ثم سيتم المحاصرين في وسادة الملح (ممثلة مثلث مقلوب سوداء) الموجود في V - القناة.

<ol>
	<li>Sambrook, J., Fritsch, E. F., Maniatis, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Molecular Cloning: A Laboratory Manual. , (1989).</li></ol>

الإعلان عن أي تضارب في المصالح.

ومدة تشغيل تعتمد بشكل كبير على حجم الشظايا ، شظايا عادة لمدة تصل إلى 20 كيلو بايت 50 دقيقة إلى 1 ساعة ويكفي ، في حين أن أجزاء صغيرة مطلوب ضوء الأشعة فوق البنفسجية لمتابعة كل 10 دقائق لمنع شظية من خلال الذهاب الى وسادة الملح وبالتالي الى الغرفة العازلة مصعدي انخفاض الانتعاش. فمن المهم للتأكد من أنه عند تعيين إمدادات الطاقة الخاص في 100 فولت ، وهناك ما لا يقل عن mAmp الحالية من 10. يمكن رصد الفرقة الحمض النووي باستخدام مصباح الأشعة فوق البنفسجية من ناحية وكشف هذا عندما يتخلى عن شريحة هلام. يمكن أيضا أن تكون وسادة الملح مع 3 خلات نا م. هذا الإجراء يسمح radiolabeled تنقية شظايا الحمض النووي أو الحمض النووي الريبي من أحجام مختلفة مع انتعاش جيدة (~ 80 ٪) ، هضمها بواسطة إنزيمات التقييد ، التي تتم معالجتها بواسطة الانزيمات تعديل ، إلخ.

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">	
		
		<div>
		<table border="1">
		<thead>
		<tr>
		<th>Material Name</th>
		<th>Type</th>
		<th>Company</th>
		<th>Catalogue Number</th>
		<th>Comment</th>
		</tr>
		</thead>
		<tbody>
		
<tr>
<td>NdeI</td>
<td>&nbsp;</td>
<td>New England Biolabs</td>
<td>R0111L</td>
<td>&nbsp;</td>
<tr>
<td>HindIII</td>
<td>&nbsp;</td>
<td>New England Biolabs</td>
<td>R0104L</td>
<td>&nbsp;</td>
<tr>
<td>NH4 acetate</td>
<td>&nbsp;</td>
<td>JTBaker</td>
<td>0596</td>
<td>&nbsp;</td>
<tr>
<td>agarose</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
<td>15510-027</td>
<td>&nbsp;</td>
<tr>
<td>Biophotometer</td>
<td>&nbsp;</td>
<td>Eppendorf</td>
<td>6131 000 020</td>
<td>&nbsp;</td>
<tr>
<td>Electroeluter</td>
<td>&nbsp;</td>
<td>IBI</td>
<td>UEA CAT 46000</td>
<td>&nbsp;</td>		</tbody>
		</table>
		</div>

electroeluting dna fragments

وتستخدم شظايا من الحمض النووي لأغراض مختلفة المنقى في البيولوجيا الجزيئية ، ويمكن أن يكونوا مستعدين من خلال إجراءات عدة. معظمها تتطلب الكهربائي السابقة للشظايا من الحمض النووي من أجل فصل عصابة من الفائدة. ثم ، يتم رفعه من هذه الفرقة من agarose هلام أو الأكريلاميد وتنقيتها باستخدام إما : ملزمة وشطف الزجاج أو من جزيئات السيليكا ، والأغشية ثنائي إيثيل أمينو إيثيل السليلوز ، &quot;سحق ونقع الأسلوب&quot; ، electroelution أو في كثير من الأحيان مكلفة تنقية مجموعات تجارية. وبالتالي ، فإن اختيار الأسلوب يعتمد في الغالب على ما يتوفر في المختبر. الإجراء electroelution يسمح احد لتنقية الحمض النووي نظيفة جدا لاستخدامها في عدد كبير من التطبيقات (التسلسل ، radiolabeling ، وتقييد الأنزيمية ، وتعديل الأنزيمية ، الخ الاستنساخ). يتكون هذا الإجراء في وضع الحمض النووي الفرقة التي تحتوي على مادة الأكريلاميد agarose أو شرائح داخل الآبار عينة من electroeluter ، ثم تطبيق الحالية سيجعل جزء الحمض النووي لمغادرة agarose وبالتالي يكون محاصرا في وسادة الملح التي سيتم استردادها في وقت لاحق عن طريق الترسيب الايثانول.

Watch this Scientific Journal Video about Electroeluting DNA Fragments at JoVE.com

Electroeluting DNA Fragments

هذا الإجراء يسمح للتنقية مع شظايا الحمض النووي عالية الغلة.

Electroeluting شظايا الحمض النووي

Purified DNA fragments are used for different purposes in Molecular Biology and they can be prepared by several procedures. Most of them require a ...

Research

JoVE Journal

Biology

27.7K Views.  Research and Advanced Studies Center of National Polytechnic Institute. هذا الإجراء يسمح للتنقية مع شظايا الحمض النووي عالية الغلة.

Video: Electroeluting DNA Fragments

Methylated DNA Immunoprecipitation

The identification of DNA methylation patterns is a common procedure in the study of epigenetics, as methylation is known to have significant effects on gene expression, and is involved with normal development as well as disease 1-4. Thus, the ability to discriminate between methylated DNA and non-methylated DNA is essential for generating methylation profiles for such studies. Methylated DNA immunoprecipitation (MeDIP) is an efficient technique for the extraction of methylated DNA from a sample of interest 5-7. A sample of as little as 200 ng of DNA is sufficient for the antibody, or immunoprecipitation (IP), reaction. DNA is sonicated into fragments ranging in size from 300-1000 bp, and is divided into immunoprecipitated (IP) and input (IN) portions. IP DNA is subsequently heat denatured and then incubated with anti-5'mC, allowing the monoclonal antibody to bind methylated DNA. After this, magnetic beads containing a secondary antibody with affinity for the primary antibody are added, and incubated. These bead-linked antibodies will bind the monoclonal antibody used in the first step. DNA bound to the antibody complex (methylated DNA) is separated from the rest of the DNA by using a magnet to pull the complexes out of solution. Several washes using IP buffer are then performed to remove the unbound, non-methylated DNA. The methylated DNA/antibody complexes are then digested with Proteinase K to digest the antibodies leaving only the methylated DNA intact. The enriched DNA is purified by phenol:chloroform extraction to remove the protein matter and then precipitated and resuspended in water for later use. PCR techniques can be used to validate the efficiency of the MeDIP procedure by analyzing the amplification products of IP and IN DNA for regions known to lack and known to contain methylated sequences. The purified methylated DNA can then be used for locus-specific (PCR) or genome-wide (microarray and sequencing) methylation studies, and is particularly useful when applied in conjunction with other research tools such as gene expression profiling and array comparative genome hybridization (CGH) 8. Further investigation into DNA methylation will lead to the discovery of new epigenetic targets, which in turn, may be useful in developing new therapeutic or prognostic research tools for diseases such as cancer that are characterized by aberrantly methylated DNA 2, 4, 9-11.

This video demonstrates the protocol for methylated DNA immunoprecipitation (MeDIP). MeDIP is a two day procedure that selectively extracts methylated DNA fragments from a genomic DNA sample using antibodies with specificity for 5 -methylcytosine (anti-5 mC).

ميثليته الحمض النووي مناعي

The identification of DNA methylation patterns is a common procedure in the study of epigenetics, as methylation is known to have significant effects on ...

Direct Observation of Enzymes Replicating DNA Using a Single-molecule DNA Stretching Assay

We describe a method for observing real time replication of individual DNA molecules mediated by proteins of the bacteriophage replication system. Linearized &lambda; DNA is modified to have a biotin on the end of one strand, and a digoxigenin moiety on the other end of the same strand. The biotinylated end is attached to a functionalized glass coverslip and the digoxigeninated end to a small bead. The assembly of these DNA-bead tethers on the surface of a flow cell allows a laminar flow to be applied to exert a drag force on the bead. As a result, the DNA is stretched close to and parallel to the surface of the coverslip at a force that is determined by the flow rate (Figure 1). The length of the DNA is measured by monitoring the position of the bead. Length differences between single- and double-stranded DNA are utilized to obtain real-time information on the activity of the replication proteins at the fork. Measuring the position of the bead allows precise determination of the rates and processivities of DNA unwinding and polymerization (Figure 2).

We describe a method for observing real time replication of individual DNA molecules mediated by proteins of the bacteriophage replication system.

الملاحظة المباشرة من الحمض النووي الانزيمات تكرار استخدام الحمض النووي جزيء واحدة تمتد الفحص

We describe a method for observing real time replication of individual DNA molecules mediated by proteins of the bacteriophage replication system. ...

DNA-based Fish Species Identification Protocol

We have developed a fast, simple, and accurate DNA-based screening method to identify the fish species present in fresh and processed seafood samples. This versatile method employs PCR amplification of genomic DNA extracted from fish samples, followed by restriction fragment length polymorphism (RFLP) analysis to generate fragment patterns that can be resolved on the Agilent 2100 Bioanalyzer and matched to the correct species using RFLP pattern matching software.
The fish identification method uses a simple, reliable, spin column- based protocol to isolate DNA from fish samples. The samples are treated with proteinase K to release the nucleic acids into solution. DNA is then isolated by suspending the sample in binding buffer and loading onto a micro- spin cup containing a silica- based fiber matrix. The nucleic acids in the sample bind to the fiber matrix. The immobilized nucleic acids are washed to remove contaminants, and total DNA is recovered in a final volume of 100 &mu;l. The isolated DNA is ready for PCR amplification with the provided primers that bind to sequences found in all fish genomes. The PCR products are then digested with three different restriction enzymes and resolved on the Agilent 2100 Bioanalyzer. The fragment lengths produced in the digestion reactions can be used to determine the species of fish from which the DNA sample was prepared, using the RFLP pattern matching software containing a database of experimentally- derived RFLP patterns from commercially relevant fish species.

This publication describes how to use the Agilent Fish Species Identification System to identify the species of a fish by extracting DNA and performing PCR and RFLP analysis.

الحمض النووي القائم على تحديد الأنواع السمكية البروتوكول

We have developed a fast, simple, and accurate DNA-based screening method to identify the fish species present in fresh and processed seafood samples. ...

DNA Stable-Isotope Probing (DNA-SIP)

DNA stable-isotope probing (DNA-SIP) is a powerful technique for identifying active microorganisms that assimilate particular carbon substrates and nutrients into cellular biomass. As such, this cultivation-independent technique has been an important methodology for assigning metabolic function to the diverse communities inhabiting a wide range of terrestrial and aquatic environments. Following the incubation of an environmental sample with stable-isotope labelled compounds, extracted nucleic acid is subjected to density gradient ultracentrifugation and subsequent gradient fractionation to separate nucleic acids of differing densities. Purification of DNA from cesium chloride retrieves labelled and unlabelled DNA for subsequent molecular characterization (e.g. fingerprinting, microarrays, clone libraries, metagenomics). This JoVE video protocol provides visual step-by-step explanations of the protocol for density gradient ultracentrifugation, gradient fractionation and recovery of labelled DNA. The protocol also includes sample SIP data and highlights important tips and cautions that must be considered to ensure a successful DNA-SIP analysis.

DNA Stable-Isotope Probing DNA-SIP

DNA stable-isotope probing is a cultivation-independent method to identify and characterize active communities of microorganisms that are capable of utilizing specific substrates. Assimilation of substrate enriched in heavy isotope leads to incorporation of labelled atoms into microbial biomass. Density gradient ultracentrifugation retrieves labelled DNA for downstream molecular analyses.

DNA - النظائر المستقرة جس (DNA - SIP)

DNA stable-isotope probing (DNA-SIP) is a powerful technique for identifying active microorganisms that assimilate particular carbon substrates and ...

Generation of RNA/DNA Hybrids in Genomic DNA by Transformation using RNA-containing Oligonucleotides

Synthetic short nucleic acid polymers, oligonucleotides (oligos), are the most functional and widespread tools of molecular biology. Oligos can be produced to contain any desired DNA or RNA sequence and can be prepared to include a wide variety of base and sugar modifications. Moreover, oligos can be designed to mimic specific nucleic acid alterations and thus, can serve as important tools to investigate effects of DNA damage and mechanisms of repair. We found that Thermo Scientific Dharmacon RNA-containing oligos with a length between 50 and 80 nucleotides can be particularly suitable to study, in vivo, functions and consequences of chromosomal RNA/DNA hybrids and of ribonucleotides embedded into DNA. RNA/DNA hybrids can readily form during DNA replication, repair and transcription, however, very little is known about the stability of RNA/DNA hybrids in cells and to which extent these hybrids can affect the genetic integrity of cells. RNA-containing oligos, therefore, represent a perfect vector to introduce ribonucleotides into chromosomal DNA and generate RNA/DNA hybrids of chosen length and base composition. Here we present the protocol for the incorporation of ribonucleotides into the genome of the eukaryotic model system yeast /Saccharomyces cerevisiae/. Yet, our lab has utilized Thermo Scientific Dharmacon RNA-containing oligos to generate RNA/DNA hybrids at the chromosomal level in different cell systems, from bacteria to human cells.

This work shows how to form an RNA/DNA hybrid at the chromosomal level and reveal transfer of genetic information from RNA to genomic DNA in yeast cells.

جيل من الحمض النووي الريبي / الحمض النووي DNA في الجينوم الهجائن التي تحول باستخدام الحمض النووي الريبي التي تحتوي على [أليغنوكليوتيد]

Synthetic short nucleic acid polymers, oligonucleotides (oligos), are the most functional and widespread tools of molecular biology. Oligos can be ...

Visualization of DNA Replication in the Vertebrate Model System DT40 using the DNA Fiber Technique

Maintenance of replication fork stability is of utmost importance for dividing cells to preserve viability and prevent disease. The processes involved not only ensure faithful genome duplication in the face of endogenous and exogenous DNA damage but also prevent genomic instability, a recognized causative factor in tumor development.
Here, we describe a simple and cost-effective fluorescence microscopy-based method to visualize DNA replication in the avian B-cell line DT40. This cell line provides a powerful tool to investigate protein function in vivo by reverse genetics in vertebrate cells1. DNA fiber fluorography in DT40 cells lacking a specific gene allows one to elucidate the function of this gene product in DNA replication and genome stability. Traditional methods to analyze replication fork dynamics in vertebrate cells rely on measuring the overall rate of DNA synthesis in a population of pulse-labeled cells. This is a quantitative approach and does not allow for qualitative analysis of parameters that influence DNA synthesis. In contrast, the rate of movement of active forks can be followed directly when using the DNA fiber technique2-4. In this approach, nascent DNA is labeled in vivo by incorporation of halogenated nucleotides (Fig 1A). Subsequently, individual fibers are stretched onto a microscope slide, and the labeled DNA replication tracts are stained with specific antibodies and visualized by fluorescence microscopy (Fig 1B). Initiation of replication as well as fork directionality is determined by the consecutive use of two differently modified analogues. Furthermore, the dual-labeling approach allows for quantitative analysis of parameters that influence DNA synthesis during the S-phase, i.e. replication structures such as ongoing and stalled forks, replication origin density as well as fork terminations. Finally, the experimental procedure can be accomplished within a day, and requires only general laboratory equipment and a fluorescence microscope.

DT40, a model vertebrate genetic system, provides a powerful tool to analyze protein function. Here we describe a simple method that allows qualitative analysis of parameters that influence DNA synthesis during the S-phase in DT40 cells at the single molecule level.

تصور تكرار الحمض النووي في DT40 النظام النموذجي الفقارية باستخدام تقنيات الحمض النووي الألياف

Maintenance of replication fork stability is of utmost importance for dividing cells to preserve viability and prevent disease. The processes involved not ...

Agarose Gel Electrophoresis for the Separation of DNA Fragments

Agarose gel electrophoresis is the most effective way of separating DNA fragments of varying sizes ranging from 100 bp to 25 kb1. Agarose is isolated from the seaweed genera Gelidium and Gracilaria, and consists of repeated agarobiose (L- and D-galactose) subunits2. During gelation, agarose polymers associate non-covalently and form a network of bundles whose pore sizes determine a gel&#39;s molecular sieving properties. The use of agarose gel electrophoresis revolutionized the separation of DNA. Prior to the adoption of agarose gels, DNA was primarily separated using sucrose density gradient centrifugation, which only provided an approximation of size. To separate DNA using agarose gel electrophoresis, the DNA is loaded into pre-cast wells in the gel and a current applied. The phosphate backbone of the DNA (and RNA) molecule is negatively charged, therefore when placed in an electric field, DNA fragments will migrate to the positively charged anode. Because DNA has a uniform mass/charge ratio, DNA molecules are separated by size within an agarose gel in a pattern such that the distance traveled is inversely proportional to the log of its molecular weight3. The leading model for DNA movement through an agarose gel is &#34;biased reptation&#34;, whereby the leading edge moves forward and pulls the rest of the molecule along4. The rate of migration of a DNA molecule through a gel is determined by the following: 1) size of DNA molecule; 2) agarose concentration; 3) DNA conformation5; 4) voltage applied, 5) presence of ethidium bromide, 6) type of agarose and 7) electrophoresis buffer. After separation, the DNA molecules can be visualized under uv light after staining with an appropriate dye. By following this protocol, students should be able to: 
 
1. Understand the mechanism by which DNA fragments are separated within a gel matrix 
2. Understand how conformation of the DNA molecule will determine its mobility through a gel matrix 
3. Identify an agarose solution of appropriate concentration for their needs 
4. Prepare an agarose gel for electrophoresis of DNA samples 
5. Set up the gel electrophoresis apparatus and power supply 
6. Select an appropriate voltage for the separation of DNA fragments 
7. Understand the mechanism by which ethidium bromide allows for the visualization of DNA bands 
8. Determine the sizes of separated DNA fragments 
&#160;

A basic protocol for the separation of DNA fragments using agarose gel electrophoresis is described.

الاغاروز الكهربائي للهلام لفصل أجزاء الحمض النووي

Agarose gel electrophoresis is the most effective way of separating DNA fragments of varying sizes ranging from 100 bp to 25 kb1. Agarose is isolated from ...

Iterative Optimization of DNA Duplexes for Crystallization of SeqA-DNA Complexes

Escherichia coli SeqA is a negative regulator of DNA replication that prevents premature reinitiation events by sequestering hemimethylated GATC clusters within the origin of replication1. Beyond the origin, SeqA is found at the replication forks, where it organizes newly replicated DNA into higher ordered structures2. SeqA associates only weakly with single GATC sequences, but it forms high affinity complexes with DNA duplexes containing multiple GATC sites. The minimal functional and structural unit of SeqA is a dimer, thereby explaining the requirement of at least two GATC sequences to form a high-affinity complex with hemimethylated DNA3. Additionally, the SeqA architecture, with the oligomerization and DNA-binding domains separated by a flexible linker, allows binding to GATC repeats separated by up to three helical turns. Therefore, understanding the function of SeqA at a molecular level requires the structural analysis of SeqA bound to multiple GATC sequences. In protein-DNA crystallization, DNA can have none to an exceptional effect on the packing interactions depending on the relative sizes and architecture of the protein and the DNA. If the protein is larger than the DNA or footprints most of the DNA, the crystal packing is primarily mediated by protein-protein interactions. Conversely, when the protein is the same size or smaller than the DNA or it only covers a fraction of the DNA, DNA-DNA and DNA-protein interactions dominate crystal packing. Therefore, crystallization of protein-DNA complexes requires the systematic screening of DNA length4 and DNA ends (blunt or overhang)5-7. In this report, we describe how to design, optimize, purify and crystallize hemimethylated DNA duplexes containing tandem GATC repeats in complex with a dimeric variant of SeqA (SeqA&Delta;(41-59)-A25R) to obtain crystals suitable for structure determination.

Crystal structure of protein&#x2013;DNA complexes can provide insight into protein function, mechanism, as well as, the nature of the specific interaction. Here, we report how to optimize the length, sequence and ends of duplex DNA for co-crystallization with Escherichia coli SeqA, a negative regulator of replication initiation.

تكرارية الأمثل من دوبلكسات DNA لبلورة-DNA من SeqA مجمعات

Escherichia coli SeqA is a negative regulator of DNA replication that prevents premature reinitiation events by sequestering hemimethylated GATC clusters ...

Preparation of DNA-crosslinked Polyacrylamide Hydrogels

Mechanobiology is an emerging scientific area that addresses the critical role of physical cues in directing cell morphology and function. For example, the effect of tissue elasticity on cell function is a major area of mechanobiology research because tissue stiffness modulates with disease, development, and injury. Static tissue-mimicking materials, or materials that cannot alter stiffness once cells are plated, are predominately used to investigate the effects of tissue stiffness on cell functions. While information gathered from static studies is valuable, these studies are not indicative of the dynamic nature of the cellular microenvironment in vivo. To better address the effects of dynamic stiffness on cell function, we developed a DNA-crosslinked polyacrylamide hydrogel system (DNA gels). Unlike other dynamic substrates, DNA gels have the ability to decrease or increase in stiffness after fabrication without stimuli. DNA gels consist of DNA crosslinks that are polymerized into a polyacrylamide backbone. Adding and removing crosslinks via delivery of single-stranded DNA allows temporal, spatial, and reversible control of gel elasticity. We have shown in previous reports that dynamic modulation of DNA gel elasticity influences fibroblast and neuron behavior. In this report and video, we provide a schematic that describes the DNA gel crosslinking mechanisms and step-by-step instructions on the preparation DNA gels.

Our laboratory has developed DNA-crosslinked polyacrylamide hydrogels, a dynamic hydrogel system, to better understand the effects of modulating tissue stiffness on cell function. Here, we provide schematics, descriptions, and protocols to prepare these hydrogels.

إعداد crosslinked-DNA بولي أكريلاميد الهلاميات المائية

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

Real-time Imaging of Single Engineered RNA Transcripts in Living Cells Using Ratiometric Bimolecular Beacons

The growing realization that both the temporal and spatial regulation of gene expression can have important consequences on cell function has led to the development of diverse techniques to visualize individual RNA transcripts in single living cells. One promising technique that has recently been described utilizes an oligonucleotide-based optical probe, ratiometric bimolecular beacon (RBMB), to detect RNA transcripts that were engineered to contain at least four tandem repeats of the RBMB target sequence in the 3&#8217;-untranslated region. RBMBs are specifically designed to emit a bright fluorescent signal upon hybridization to complementary RNA, but otherwise remain quenched. The use of a synthetic probe in this approach allows photostable, red-shifted, and highly emissive organic dyes to be used for imaging. Binding of multiple RBMBs to the engineered RNA transcripts results in discrete fluorescence spots when viewed under a wide-field fluorescent microscope. Consequently, the movement of individual RNA transcripts can be readily visualized in real-time by taking a time series of fluorescent images. Here we describe the preparation and purification of RBMBs, delivery into cells by microporation and live-cell imaging of single RNA transcripts.

Ratiometric bimolecular beacons (RBMBs) can be used to image single engineered RNA transcripts in living cells. Here, we describe the preparation and purification of RBMBs, delivery of RBMBs into cells by microporation and fluorescent imaging of single RNA transcripts in real-time.

التصوير في الوقت الحقيقي من واحدة المهندسة رنا النصوص في الخلايا الحية عن طريق Ratiometric ثنائي الجزيء منارات

The growing realization that both the temporal and spatial regulation of gene expression can have important consequences on cell function has led to the ...