Este trabajo fue apoyado por un premio CARRERA NSF (MMH), un Barry M. Goldwater de becas (FNB) y un Premio de Investigación de Pregrado ASBMB (CWD). El clon de la sobre-expresión de PBP fue proporcionado amablemente por el Dr. Martin Webb (MRC, Reino Unido).

<ol>
	<li>Johnson, K. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Advances+in+transient-state+kinetics.">Advances in transient-state kinetics.</a> Curr Opin Biotechnol. 9 (1), 87-89 (1998).</li><li>Johnson, K. A. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Kinetic analysis of macromolecules. , (2003).</li><li>Obmolova, G., Ban, C., Hsieh, P., Yang, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Crystal+structures+of+mismatch+repair+protein+MutS+and+its+complex+with+a+substrate+DNA.">Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA.</a> Nature. 407 (6805), 703-710 (2000).</li><li>Lamers, M. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+crystal+structure+of+DNA+mismatch+repair+protein+MutS+binding+to+a+G+x+T+mismatch.">The crystal structure of DNA mismatch repair protein MutS binding to a G x T mismatch.</a> Nature. 407 (6805), 711-717 (2000).</li><li>Warren, J. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structure+of+the+human+MutSalpha+DNA+lesion+recognition+complex.">Structure of the human MutSalpha DNA lesion recognition complex.</a> Mol Cell. 26 (4), 579-592 (2007).</li><li>Kunkel, T. A. &. a. m. p. ;. a. m. p., Erie, D. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> DNA Mismatch Repair. 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M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+effects+of+nucleotides+on+MutS-DNA+binding+kinetics+clarify+the+role+of+MutS+ATPase+activity+in+mismatch+repair.">The effects of nucleotides on MutS-DNA binding kinetics clarify the role of MutS ATPase activity in mismatch repair.</a> J Mol Biol. 366 (4), 1087-1098 (2007).</li><li>Antony, E., Khubchandani, S., Chen, S., Hingorani, M. M., M, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Contribution+of+Msh2+and+Msh6+subunits+to+the+asymmetric+ATPase+and+DNA+mismatch+binding+activities+of+Saccharomyces+cerevisiae+Msh2-Msh6+mismatch+repair+protein.">Contribution of Msh2 and Msh6 subunits to the asymmetric ATPase and DNA mismatch binding activities of Saccharomyces cerevisiae Msh2-Msh6 mismatch repair protein.</a> DNA Repair (Amst). 5 (2), 153-162 (2006).</li><li>Antony, E., Hingorani, M. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mismatch+recognition-coupled+stabilization+of+Msh2-Msh6+in+an+ATP-bound+state+at+the+initiation+of+DNA+repair.">Mismatch recognition-coupled stabilization of Msh2-Msh6 in an ATP-bound state at the initiation of DNA repair.</a> Biochemistry. 42 (25), 7682-7693 (2003).</li><li>Finkelstein, J., Antony, E., Hingorani, M. M., O'Donnell, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Overproduction+and+analysis+of+eukaryotic+multiprotein+complexes+in+Escherichia+coli+using+a+dual-vector+strategy.">Overproduction and analysis of eukaryotic multiprotein complexes in Escherichia coli using a dual-vector strategy.</a> Anal Biochem. 319 (1), 78-87 (2003).</li><li>Zhai, J., Hingorani, M. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=S.+cerevisiae+Msh2-Msh6+DNA+binding+kinetics+reveal+a+mechanism+of+targeting+sites+for+DNA+mismatch+repair.">S. cerevisiae Msh2-Msh6 DNA binding kinetics reveal a mechanism of targeting sites for DNA mismatch repair.</a> Proc Natl Acad Sci U S A. 107 (2), 680-685 (2010).</li><li>Brune, M., Hunter, J. L., Corrie, J. E., Webb, M. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Direct,+real-time+measurement+of+rapid+inorganic+phosphate+release+using+a+novel+fluorescent+probe+and+its+application+to+actomyosin+subfragment+1+ATPase.">Direct, real-time measurement of rapid inorganic phosphate release using a novel fluorescent probe and its application to actomyosin subfragment 1 ATPase.</a> Biochemistry. 33 (27), 8262-8271 (1994).</li><li>Brune, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mechanism+of+inorganic+phosphate+interaction+with+phosphate+binding+protein+from+Escherichia+coli.">Mechanism of inorganic phosphate interaction with phosphate binding protein from Escherichia coli.</a> Biochemistry. 37 (29), 10370-10380 (1998).</li><li>Antony, E., Hingorani, M. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Asymmetric+ATP+binding+and+hydrolysis+activity+of+the+Thermus+aquaticus+MutS+dimer+is+key+to+modulation+of+its+interactions+with+mismatched+DNA.">Asymmetric ATP binding and hydrolysis activity of the Thermus aquaticus MutS dimer is key to modulation of its interactions with mismatched DNA.</a> Biochemistry. 43 (41), 13115-13128 (2004).</li><li>Gradia, S., Acharya, S., Fishel, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+human+mismatch+recognition+complex+hMSH2-hMSH6+functions+as+a+novel+molecular+switch.">The human mismatch recognition complex hMSH2-hMSH6 functions as a novel molecular switch.</a> Cell. 91 (7), 995-1005 (1997).</li><li>Mazur, D. J., Mendillo, M. L., Kolodner, R. 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El ejemplo de una proteína de unión al ADN desajuste se describe aquí se muestra la eficacia y utilidad de los métodos cinéticos transitoria para el estudio de los mecanismos de las moléculas biológicas. Mediciones de flujo detenido en la escala de tiempo de rotación único previsto una evidencia inequívoca de la unión rápida y específica de la proteína MSH2, MSH6 a un par de bases coincidentes y la formación de un complejo de ADN de larga duración proteína X en la reacción 9. Por otra parte,...

<table border="1"><tr><td> ADN nombre </td><td> Secuencia </td></tr><tr><td> 37 G </td><td> 5&#39;-TTC TCC AGC ATT TAT AGA G TA CCA TAC TGA ACA TTC T -3 &#39; </td></tr><tr><td> 37 T (2-Ap) </td><td> 5&#39;-ATG TGA ATC ATG AGT GTA T Ap T TGC ATC TGA AGG AAA T -3 &#39; </td></tr><tr><td> 37 T </td><td> 5&#39;-ATG TGA ATC ATG AGT GTA T A T TGC ATC TGA AGG AAA -3 T &#39; </td></tr></table>

application of stopped-flow kinetics methods to investigate the mechanism of action of a dna repair protein

Análisis de la cinética transitoria es indispensable para entender el funcionamiento de las macromoléculas biológicas, ya que este método proporciona información mecanicista, incluidas las concentraciones del sitio activo y constantes intrínsecas que rigen la función tasa de macromoléculas. En el caso de las enzimas, por ejemplo, las mediciones de estado transitorio o constante pre-identificar y caracterizar los eventos individuales en el camino de reacción, mientras que las mediciones en estado estacionario sólo el rendimiento eficiencia global catalítica y la especificidad. Eventos individuales como las interacciones proteína-proteína o proteína-ligando y la limitación de la velocidad a menudo se producen cambios conformacionales en la escala de tiempo de milisegundos, y se puede medir directamente por flujo detenido y productos químicos apagar los métodos de flujo. Dada una señal óptica, tales como la fluorescencia, se detuvo el flujo sirve como una herramienta poderosa y accesible para el seguimiento de la reacción de la unión del sustrato para liberar el producto y el volumen de negocios 1,2 catalítico. En este sentido, el informe de aplicación de la cinética de flujo detenido para investigar el mecanismo de acción de MSH2, MSH6, una proteína de reparación del ADN eucariota que reconoce pares de bases y los desajustes de inserción / deleción bucles en el ADN y la reparación de las señales de desequilibrio (MMR) 3-5. De este modo, MSH2, MSH6 aumenta la precisión de la replicación del ADN por tres órdenes de magnitud (frecuencia de errores disminuye a partir de ~ 10 -6 a 10 -9 bases), y por lo tanto ayuda a preservar la integridad genómica. No es de extrañar, defectos humanos MSH2, MSH6 función está asociada con el cáncer de colon hereditario no polipósico y otros cánceres esporádicos 6-8. A fin de comprender el mecanismo de acción de esta proteína ADN metabólica fundamental, que están investigando la dinámica de MSH2, MSH6 interacción con el ADN no coinciden, así como la actividad de la ATPasa de que los combustibles de sus acciones en la MMR. De unión al ADN se mide por la rápida mezcla MSH2, MSH6 con el ADN que contiene un 2-aminopurine (2-Ap) fluoróforo al lado de un G: T desajustes y el control de la consiguiente aumento de la fluorescencia de 2-aminopurine en tiempo real. ADN disociación se mide mediante la mezcla de pre-formado MSH2, MSH6 G: T (2-Ap) complejo de falta de coincidencia con el ADN trampa sin etiquetar y disminuir el control de la fluorescencia en el tiempo 9. Pre-ATPasa constante cinética de estado se mide por la variación en la fluorescencia de 7-dietilamino-3-((((2-maleimidyl) etil) amino) carbonil) cumarina)-etiquetados proteínas de unión a fosfato (MDCC-PBP) de fosfato de unión ( Pi), publicado por MSH2, MSH6 después de la hidrólisis de ATP 9,10. Los datos revelan una rápida unión de MSH2, MSH6 a un G: no coincide el T y la formación de una larga vida MSH2, MSH6 G: T complejo, que a su vez se traduce en la supresión de la hidrólisis de ATP y la estabilización de la proteína en forma de ATP obligado . La cinética de la reacción proporcionan un claro apoyo a la hipótesis de que la ATP con destino MSH2, MSH6 señales de reparación del ADN en el enlace de un par de bases no coinciden en la doble hélice. F. Noé Biro y Zhai Jie contribuido a este trabajo por igual.

Watch this Scientific Journal Video about Application of Stopped-flow Kinetics Methods to Investigate the Mechanism of Action of a DNA Repair Protein at JoVE.com

Application of Stopped-flow Kinetics Methods to Investigate the Mechanism of Action of a DNA Repair Protein | Biology | Video

Application of Stopped-flow Kinetics Methods to Investigate the Mechanism of Action of a DNA Repair Protein

MSH2, MSH6 es responsable de iniciar la reparación de errores de replicación del ADN. Aquí se presenta un enfoque cinética transitoria hacia la comprensión de cómo funciona esta proteína crítica. El informe pone de manifiesto de flujo detenido experimentos para medir la unión de ADN, acoplado y la cinética de la ATPasa subyacente MSH2, MSH6 mecanismo de acción de reparación del ADN.

Aplicación de métodos de flujo detenido Cinética para investigar el mecanismo de acción de una proteína de reparación del ADN

Transient kinetic analysis is indispensable for understanding the workings of biological macromolecules, since this approach yields mechanistic ...

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18.0K vistas.  Wesleyan University. MSH2, MSH6 es responsable de iniciar la reparación de errores de replicación del ADN. Aquí se presenta un enfoque cinética transitoria hacia la comprensión de cómo funciona esta proteína crítica. El informe pone de manifiesto de flujo detenido experimentos para medir la unión de ADN, acoplado y la cinética de la ATPasa subyacente MSH2, MSH6 mecanismo de acción de reparación del ADN.

Video: Application of Stopped-flow Kinetics Methods to Investigate the Mechanism of Action of a DNA Repair Protein

Genetic Studies of Human DNA Repair Proteins Using Yeast as a Model System 

Understanding the roles of human DNA repair proteins in genetic pathways is a formidable challenge to many researchers. Genetic studies in mammalian systems have been limited due to the lack of readily available tools including defined mutant genetic cell lines, regulatory expression systems, and appropriate selectable markers. To circumvent these difficulties, model genetic systems in lower eukaryotes have become an attractive choice for the study of functionally conserved DNA repair proteins and pathways. We have developed a model yeast system to study the poorly defined genetic functions of the Werner syndrome helicase-nuclease (WRN) in nucleic acid metabolism. Cellular phenotypes associated with defined genetic mutant backgrounds can be investigated to clarify the cellular and molecular functions of WRN through its catalytic activities and protein interactions. The human WRN gene and associated variants, cloned into DNA plasmids for expression in yeast, can be placed under the control of a regulatory plasmid element. The expression construct can then be transformed into the appropriate yeast mutant background, and genetic function assayed by a variety of methodologies. Using this approach, we determined that WRN, like its related RecQ family members BLM and Sgs1, operates in a Top3-dependent pathway that is likely to be important for genomic stability. This is described in our recent publication [1] at <a href="http://www.impactaging.com">www.impactaging.com</a>. Detailed methods of specific assays for genetic complementation studies in yeast are provided in this paper.

Genetic Studies of Human DNA Repair Proteins Using Yeast as a Model System

Genetic studies in yeast can be employed to investigate the molecular and cellular functions of human genes in cellular DNA metabolism. Methods are described for the genetic characterization of the human WRN gene product defective in the premature aging disorder Werner syndrome in functionally conserved pathways using yeast as a tractable model system.

Los estudios genéticos de proteínas humanas de reparación del ADN utilizando la levadura como un sistema modelo

Understanding the roles of human DNA repair proteins in genetic pathways is a formidable challenge to many researchers.  Genetic studies in mammalian ...

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Imaging Mismatch Repair and Cellular Responses to DNA Damage in Bacillus subtilis

Both prokaryotes and eukaryotes respond to DNA damage through a complex set of physiological changes. Alterations in gene expression, the redistribution of existing proteins, and the assembly of new protein complexes can be stimulated by a variety of DNA lesions and mismatched DNA base pairs. Fluorescence microscopy has been used as a powerful experimental tool for visualizing and quantifying these and other responses to DNA lesions and to monitor DNA replication status within the complex subcellular architecture of a living cell. Translational fusions between fluorescent reporter proteins and components of the DNA replication and repair machinery have been used to determine the cues that target DNA repair proteins to their cognate lesions in vivo and to understand how these proteins are organized within bacterial cells. In addition, transcriptional and translational fusions linked to DNA damage inducible promoters have revealed which cells within a population have activated genotoxic stress responses. In this review, we provide a detailed protocol for using fluorescence microscopy to image the assembly of DNA repair and DNA replication complexes in single bacterial cells. In particular, this work focuses on imaging mismatch repair proteins, homologous recombination, DNA replication and an SOS-inducible protein in Bacillus subtilis. All of the procedures described here are easily amenable for imaging protein complexes in a variety of bacterial species.

Imaging Mismatch Repair and Cellular Responses to DNA Damage in Bacillus subtilis

A detailed protocol is described for imaging the real time formation of DNA repair complexes in Bacillus subtilis cells.

Imágenes de reparación del ADN y la respuesta celular al daño del ADN en Bacillus subtilis</em

Both prokaryotes and eukaryotes respond to DNA damage through a complex set of physiological changes. Alterations in gene expression, the redistribution ...

The Importance of Correct Protein Concentration for Kinetics and Affinity Determination in Structure-function Analysis 

In this study, we explore the interaction between the bovine cysteine protease inhibitor cystatin B and a catalytically inactive form of papain (Fig. 1), a plant cysteine protease, by real-time label-free analysis using Biacore X100. Several cystatin B variants with point mutations in areas of interaction with papain, are produced. For each cystatin B variant we determine its specific binding concentration using calibration-free concentration analysis (CFCA) and compare the values obtained with total protein concentration as determined by A280. After that, the kinetics of each cystatin B variant binding to papain is measured using single-cycle kinetics (SCK). We show that one of the four cystatin B variants we examine is only partially active for binding. This partial activity, revealed by CFCA, translates to a significant difference in the association rate constant (ka) and affinity (KD), compared to the values calculated using total protein concentration. Using CFCA in combination with kinetic analysis in a structure-function study contributes to obtaining reliable results, and helps to make the right interpretation of the interaction mechanism.

The Importance of Correct Protein Concentration for Kinetics and Affinity Determination in Structure-function Analysis

We apply label-free protein interaction analysis using Biacore X100 for structure-function analysis of the binding of several cystatin B mutants to papain through kinetic characterization. Calibration-free concentration analysis (CFCA) measures the concentration of protein with retained binding activity without the need for a standard curve. We show that confirmation of concentrations using CFCA increases the reliability of the kinetic analysis and that kinetic constants can reliably be determined even if the activity of a recombinant protein is reduced.

La importancia de la concentración de la proteína correcta para la cinética y la determinación de afinidad en el análisis de la estructura-función

In this study, we explore the interaction between the bovine cysteine protease inhibitor cystatin B and a catalytically inactive form of papain (Fig. 1), ...

Application of an In vitro DNA Protection Assay to Visualize Stress Mediation Properties of the Dps Protein

Oxidative stress is an unavoidable byproduct of aerobic life. Molecular oxygen is essential for terrestrial metabolism, but it also takes part in many damaging reactions within living organisms. The combination of aerobic metabolism and iron, which is another vital compound for life, is enough to produce radicals through Fenton chemistry and degrade cellular components. DNA degradation is arguably the most damaging process involving intracellular radicals, as DNA repair is far from trivial. The assay presented in this article offers a quantitative technique to measure and visualize the effect of molecules and enzymes on radical-mediated DNA damage.
The DNA protection assay is a simple, quick, and robust tool for the in vitro characterization of the protective properties of proteins or chemicals. It involves exposing DNA to a damaging oxidative reaction and adding varying concentrations of the compound of interest. The reduction or increase of DNA damage as a function of compound concentration is then visualized using gel electrophoresis. In this article we demonstrate the technique of the DNA protection assay by measuring the protective properties of the DNA-binding protein from starved cells (Dps). Dps is a mini-ferritin that is utilized by more than 300 bacterial species to powerfully combat environmental stressors. Here we present the Dps purification protocol and the optimized assay conditions for evaluating DNA protection by Dps.

Application of an In vitro DNA Protection Assay to Visualize Stress Mediation Properties of the Dps Protein

The DNA-binding protein from starved cells (Dps) plays a crucial role in combating bacterial stress. This article discusses the purification of E. coli Dps and the protocol for an in vitro assay demonstrating Dps-mediated protection of DNA from degradation by reactive oxygen species.

La aplicación de un<em&gt; In vitro</em&gt; DNA ensayo de protección de visualizar Estrés Mediación propiedades de la proteína Dps

Oxidative stress is an unavoidable byproduct of  aerobic life.  Molecular oxygen is  essential for terrestrial metabolism, but it also takes part in many ...

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.

Imágenes en tiempo real de Soltero Engineered ARN transcritos en células vivas utilizando Ratiometric bimoleculares Balizas

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 Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

REPLACE is a unique strategy developed to more effectively target protein-protein interactions (PPIs). It aims to expand available drug target space by providing improved methodology for the identification of inhibitors for such binding sites and which represent the majority of potential drug targets. The main goal of this paper is to provide a methodological overview of the use and application of the REPLACE strategy which involves computational and synthetic chemistry approaches. REPLACE is exemplified through its application to the development of non-ATP competitive cyclin dependent kinases (CDK) inhibitors as anti-tumor therapeutics. CDKs are frequently deregulated in cancer and hence are considered as important targets for drug development. Inhibition of CDK2/cyclin A in S phase has been reported to promote selective apoptosis of cancer cells in a p53 independent manner through the E2F1 pathway. Targeting the protein-protein interaction at the cyclin binding groove (CBG) is an approach which will allow the specific inhibition of cell cycle over transcriptional CDKs. The CBG is recognized by a consensus sequence derived from CDK substrates and tumor suppressor proteins termed the cyclin binding motif (CBM). The CBM has previously been optimized to an octapeptide from p21Waf (HAKRRIF) and then further truncated to a pentapeptide retaining sufficient activity (RRLIF). Peptides in general are not cell permeable, are metabolically unstable and therefore the REPLACE (REplacement with Partial Ligand Alternatives through Computational Enrichment) strategy has been applied in order to generate more drug-like inhibitors. The strategy begins with the design of Fragment ligated inhibitory peptides (FLIPs) that selectively inhibit cell cycle CDK/cyclin complexes. FLIPs were generated by iteratively replacing residues of HAKRRLIF/RRLIF with fragment like small molecules (capping groups), starting from the N-terminus (Ncaps), followed by replacement on the C-terminus. These compounds are starting points for the generation of non-ATP competitive CDK inhibitors as anti-tumor therapeutics.

We describe implementation of the REPLACE strategy for targeting protein-protein interactions. REPLACE is an iterative strategy involving synthetic and computational approaches for the conversion of optimized peptidic inhibitors into drug like molecules.

El desarrollo de inhibidores de interacciones proteína-proteína a través REEMPLAZAR: Aplicación al Diseño y Desarrollo para no ATP inhibidores de CDK Competitiva

REPLACE is a unique strategy developed to more effectively target protein-protein interactions (PPIs). It aims to expand available drug target space by ...

Chromatin Immunoprecipitation Assay for the Identification of Arabidopsis Protein-DNA Interactions In Vivo

Intricate gene regulatory networks orchestrate biological processes and developmental transitions in plants. Selective transcriptional activation and silencing of genes mediate the response of plants to environmental signals and developmental cues. Therefore, insights into the mechanisms that control plant gene expression are essential to gain a deep understanding of how biological processes are regulated in plants. The chromatin immunoprecipitation (ChIP) technique described here is a procedure to identify the DNA-binding sites of proteins in genes or genomic regions of the model species Arabidopsis thaliana. The interactions with DNA of proteins of interest such as transcription factors, chromatin proteins or posttranslationally modified versions of histones can be efficiently analyzed with the ChIP protocol. This method is based on the fixation of protein-DNA interactions in vivo, random fragmentation of chromatin, immunoprecipitation of protein-DNA complexes with specific antibodies, and quantification of the DNA associated with the protein of interest by PCR techniques. The use of this methodology in Arabidopsis has contributed significantly to unveil transcriptional regulatory mechanisms that control a variety of plant biological processes. This approach allowed the identification of the binding sites of the Arabidopsis chromatin protein EBS to regulatory regions of the master gene of flowering FT. The impact of this protein in the accumulation of particular histone marks in the genomic region of FT was also revealed through ChIP analysis.

Chromatin Immunoprecipitation Assay for the Identification of Arabidopsis Protein-DNA Interactions In Vivo

Chromatin immunoprecipitation is a powerful technique for the identification of DNA binding sites of Arabidopsis proteins in vivo. This procedure includes chromatin cross-linking and fragmentation, immunoprecipitation with selective antibodies against the protein of interest, and qPCR analysis of bound DNA. We describe a simple ChIP assay optimized for Arabidopsis plants.

Ensayo de inmunoprecipitación de la cromatina para la Identificación de Arabidopsis proteína-DNA<em&gt; En Vivo</em

Intricate gene regulatory networks orchestrate biological processes and developmental transitions in plants. Selective transcriptional activation and ...

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

Retroviruses exhibit signature integration preferences on both the local and global scales. Here, we present a detailed protocol for (1) generation of diverse libraries of retroviral integration sites using ligation-mediated PCR (LM-PCR) amplification and next-generation sequencing (NGS), (2) mapping the genomic location of each virus-host junction using BEDTools, and (3) analyzing the data for statistical relevance. Genomic DNA extracted from infected cells is fragmented by digestion with restriction enzymes or by sonication. After suitable DNA end-repair, double-stranded linkers are ligated onto the DNA ends, and semi-nested PCR is conducted using primers complementary to both the long terminal repeat (LTR) end of the virus and the ligated linker DNA. The PCR primers carry sequences required for DNA clustering during NGS, negating the requirement for separate adapter ligation. Quality control (QC) is conducted to assess DNA fragment size distribution and adapter DNA incorporation prior to NGS. Sequence output files are filtered for LTR-containing reads, and the sequences defining the LTR and the linker are cropped away. Trimmed host cell sequences are mapped to a reference genome using BLAT and are filtered for minimally 97% identity to a unique point in the reference genome. Unique integration sites are scrutinized for adjacent nucleotide (nt) sequence and distribution relative to various genomic features. Using this protocol, integration site libraries of high complexity can be constructed from genomic DNA in three days. The entire protocol that encompasses exogenous viral infection of susceptible tissue culture cells to integration site analysis can therefore be conducted in approximately one to two weeks. Recent applications of this technology pertain to longitudinal analysis of integration sites from HIV-infected patients.

We describe a protocol for amplifying retroviral integration sites from the genomic DNA of infected cells, sequencing the amplified virus-host junctions, and then mapping these sequences to a reference genome. We also describe techniques to quantify the distribution of integration sites relative to various genomic annotations using BEDTools.

Amplificación, secuenciación de próxima generación, y Genómica Mapeo de ADN retrovirales sitios de integración

Retroviruses exhibit signature integration preferences on both the local and global scales. Here, we present a detailed protocol for (1) generation of ...

Visualization of Surface-tethered Large DNA Molecules with a Fluorescent Protein DNA Binding Peptide

Large DNA molecules tethered on the functionalized glass surface have been utilized in polymer physics and biochemistry particularly for investigating interactions between DNA and its binding proteins. Here, we report a method that uses fluorescent microscopy for visualizing large DNA molecules tethered on the surface. First, glass coverslips are biotinylated and passivated by coating with biotinylated polyethylene glycol, which specifically binds biotinylated DNA via avidin protein linkers and significantly reduces undesirable binding from non-specific interactions of proteins or DNA molecules on the surface. Second, the DNA molecules are biotinylated by two different methods depending on their terminals. The blunt ended DNA is tagged with biotinylated dUTP at its 3' hydroxyl terminus, by terminal transferase, while the sticky ended DNA is hybridized with biotinylated complimentary oligonucleotides by DNA ligase. Finally, a microfluidic shear flow makes single DNA molecules stretch to their full contour lengths after being stained with fluorescent protein-DNA binding peptide (FP-DBP).

We present an approach for visualizing fluorescent protein DNA binding peptide (FP-DBP)-stained large DNA molecules tethered on the polyethylene glycol (PEG) and avidin-coated glass surface and stretched with microfluidic shear flows.

La visualización de atado-gran superficie moléculas de ADN con un ADN Fluorescent Protein unión del péptido

Large DNA molecules tethered on the functionalized glass surface have been utilized in polymer physics and biochemistry particularly for investigating ...

Advanced Confocal Microscopy Techniques to Study Protein-protein Interactions and Kinetics at DNA Lesions

Local microirradiation with lasers represents a useful tool for studies of DNA-repair-related processes in live cells. Here, we describe a methodological approach to analyzing protein kinetics at DNA lesions over time or protein-protein interactions on locally microirradiated chromatin. We also show how to recognize individual phases of the cell cycle using the Fucci cellular system to study cell-cycle-dependent protein kinetics at DNA lesions. A methodological description of the use of two UV lasers (355 nm and 405 nm) to induce different types of DNA damage is also presented. Only the cells microirradiated by the 405-nm diode laser proceeded through mitosis normally and were devoid of cyclobutane pyrimidine dimers (CPDs). We also show how microirradiated cells can be fixed at a given time point to perform immunodetection of the endogenous proteins of interest. For the DNA repair studies, we additionally describe the use of biophysical methods including FRAP (Fluorescence Recovery After Photobleaching) and FLIM (Fluorescence Lifetime Imaging Microscopy) in cells with spontaneously occurring DNA damage foci. We also show an application of FLIM-FRET (Fluorescence Resonance Energy Transfer) in experimental studies of protein-protein interactions.

Laser microirradiation is a useful tool for studies of DNA repair in living cells. A methodological approach for the use of UVA lasers to induce various DNA lesions is shown. We have optimized a method for local microirradiation that maintains the normal cell cycle; thus, irradiated cells proceed through mitosis.

Avanzadas técnicas de Microscopía Confocal para estudiar las interacciones proteína-proteína y cinética en las lesiones del ADN

Local microirradiation with lasers represents a useful tool for studies of DNA-repair-related processes in live cells. Here, we describe a methodological ...