1
|
Miro J, Bourgeois CF, Claustres M, Koenig M, Tuffery-Giraud S. Identification of Splicing Factors Involved in DMD Exon Skipping Events Using an In Vitro RNA Binding Assay. Methods Mol Biol 2018; 1687:157-169. [PMID: 29067662 DOI: 10.1007/978-1-4939-7374-3_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Mutation-induced exon skipping in the DMD gene can modulate the severity of the phenotype in patients with Duchenne or Becker Muscular Dystrophy. These alternative splicing events are most likely the result of changes in recruitment of splicing factors at cis-acting elements in the mutated DMD pre-mRNA. The identification of proteins involved can be achieved by an affinity purification procedure. Here, we provide a detailed protocol for the in vitro RNA binding assay that we routinely apply to explore molecular mechanisms underlying splicing defects in the DMD gene. In vitro transcribed RNA probes containing either the wild type or mutated sequence are oxidized and bound to adipic acid dihydrazide-agarose beads. Incubation with a nuclear extract allows the binding of nuclear proteins to the RNA probes. The unbound proteins are washed off and then the specifically RNA-bound proteins are released from the beads by an RNase treatment. After separation by SDS-PAGE, proteins that display differential binding affinities for the wild type and mutant RNA probes are identified by mass spectrometry.
Collapse
Affiliation(s)
- Julie Miro
- Laboratoire de Génétique de Maladies Rares (LGMR), EA7402, Université de Montpellier, Montpellier, 34000, France
| | - Cyril F Bourgeois
- INSERM U1210, CNRS UMR 5239, Laboratory of Biology and Modelling of the Cell, Ecole Normale Supérieure de Lyon, Université de Lyon, 69007, Lyon, France
| | - Mireille Claustres
- Laboratoire de Génétique de Maladies Rares (LGMR), EA7402, Université de Montpellier, Montpellier, 34000, France.,Laboratoire de Génétique Moléculaire, CHU Montpellier, Hôpital Arnaud de Villeneuve, Montpellier, 34000, France
| | - Michel Koenig
- Laboratoire de Génétique de Maladies Rares (LGMR), EA7402, Université de Montpellier, Montpellier, 34000, France.,Laboratoire de Génétique Moléculaire, CHU Montpellier, Hôpital Arnaud de Villeneuve, Montpellier, 34000, France
| | - Sylvie Tuffery-Giraud
- Laboratoire de Génétique de Maladies Rares (LGMR), EA7402, Université de Montpellier, Montpellier, 34000, France.
| |
Collapse
|
2
|
Berthelot V, Mouta-Cardoso G, Hégarat N, Guillonneau F, François JC, Giovannangeli C, Praseuth D, Rusconi F. The human DNA ends proteome uncovers an unexpected entanglement of functional pathways. Nucleic Acids Res 2016; 44:4721-33. [PMID: 26921407 PMCID: PMC4889927 DOI: 10.1093/nar/gkw121] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 02/17/2016] [Indexed: 01/06/2023] Open
Abstract
DNA ends get exposed in cells upon either normal or dysfunctional cellular processes or molecular events. Telomeres need to be protected by the shelterin complex to avoid junctions occurring between chromosomes while failing topoisomerases or clustered DNA damage processing may produce double-strand breaks, thus requiring swift repair to avoid cell death. The rigorous study of the great many proteins involved in the maintenance of DNA integrity is a challenging task because of the innumerous unspecific electrostatic and/or hydrophobic DNA—protein interactions that arise due to the chemical nature of DNA. We devised a technique that discriminates the proteins recruited specifically at DNA ends from those that bind to DNA because of a generic affinity for the double helix. Our study shows that the DNA ends proteome comprises proteins of an unexpectedly wide functional spectrum, ranging from DNA repair to ribosome biogenesis and cytoskeleton, including novel proteins of undocumented function. A global mapping of the identified proteome on published DNA repair protein networks demonstrated the excellent specificity and functional coverage of our purification technique. Finally, the native nucleoproteic complexes that assembled specifically onto DNA ends were shown to be endowed with a highly efficient DNA repair activity.
Collapse
Affiliation(s)
- Vivien Berthelot
- Laboratoire de chimie physique, UMR CNRS 8000, University of Paris-Sud, F-91400 Orsay, France
| | - Gildas Mouta-Cardoso
- Structure et Instabilité des Génomes, INSERM U1154, UMR CNRS/MNHN 7196, F-75005 Paris, France
| | - Nadia Hégarat
- Structure et Instabilité des Génomes, INSERM U1154, UMR CNRS/MNHN 7196, F-75005 Paris, France
| | - François Guillonneau
- Plateforme de spectrométrie de masse 3P5, Institut Cochin, F-75014 Paris, France
| | - Jean-Christophe François
- Inserm and Sorbonne Universities, UPMC, UMR_S 938, Research Center Saint-Antoine, F-75012 Paris, France
| | - Carine Giovannangeli
- Structure et Instabilité des Génomes, INSERM U1154, UMR CNRS/MNHN 7196, F-75005 Paris, France
| | - Danièle Praseuth
- Structure et Instabilité des Génomes, INSERM U1154, UMR CNRS/MNHN 7196, F-75005 Paris, France
| | - Filippo Rusconi
- Laboratoire de chimie physique, UMR CNRS 8000, University of Paris-Sud, F-91400 Orsay, France
| |
Collapse
|
3
|
Ladd AN. New Insights Into the Role of RNA-Binding Proteins in the Regulation of Heart Development. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 324:125-85. [PMID: 27017008 DOI: 10.1016/bs.ircmb.2015.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The regulation of gene expression during development takes place both at the transcriptional and posttranscriptional levels. RNA-binding proteins (RBPs) regulate pre-mRNA processing, mRNA localization, stability, and translation. Many RBPs are expressed in the heart and have been implicated in heart development, function, or disease. This chapter will review the current knowledge about RBPs in the developing heart, focusing on those that regulate posttranscriptional gene expression. The involvement of RBPs at each stage of heart development will be considered in turn, including the establishment of specific cardiac cell types and formation of the primitive heart tube, cardiac morphogenesis, and postnatal maturation and aging. The contributions of RBPs to cardiac birth defects and heart disease will also be considered in these contexts. Finally, the interplay between RBPs and other regulatory factors in the developing heart, such as transcription factors and miRNAs, will be discussed.
Collapse
Affiliation(s)
- A N Ladd
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States of America.
| |
Collapse
|
4
|
Mota É, Sousa F, Queiroz JA, Cruz C. Quantitative analysis of the interaction between l-methionine derivative and oligonucleotides. J Biochem 2014; 157:261-70. [PMID: 25425656 DOI: 10.1093/jb/mvu073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This study explores the use of l-methionine derivative as a potential affinity ligand for nucleic acids purification. The l-methionine derivative is synthesized by activation of the carboxylic acid group with 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide/N-hydroxysuccinimide follow by immobilization on amine sensor surface, previously activated and treated with ethylenediamine. Their affinity towards oligonucleotides has been determined by surface plasmon resonance biosensor. The highest affinity is found for cytosine and thymine, followed by adenine, whereas the lowest affinity is found for guanine. For hetero-oligonucleotides the affinity order is CCCTTT > CCCAAA ≈ AAATTT > GGGTTT, showing that nucleotides with cytosine have the highest affinity, and the presence of guanine reduces the affinity, corroborating with the results obtained with homo-oligonucleotides.
Collapse
Affiliation(s)
- Élia Mota
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - Fani Sousa
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - João A Queiroz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - Carla Cruz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| |
Collapse
|
5
|
Hégarat N, Novopashina D, Fokina AA, Boutorine AS, Venyaminova AG, Praseuth D, François JC. Monitoring DNA triplex formation using multicolor fluorescence and application to insulin-like growth factor I promoter downregulation. FEBS J 2014; 281:1417-1431. [DOI: 10.1111/febs.12714] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 12/30/2013] [Accepted: 01/08/2014] [Indexed: 01/01/2023]
Affiliation(s)
- Nadia Hégarat
- Acides nucléiques: dynamique, ciblage et fonctions biologiques; INSERM U565; Paris France
- Département Régulations, développement et diversité moléculaire; MNHN - CNRS UMR7196; Paris France
| | - Darya Novopashina
- Laboratory of RNA Chemistry; Institute of Chemical Biology and Fundamental Medicine; Siberian Division of Russian Academy of Sciences; Novosibirsk Russia
| | - Alesya A. Fokina
- Laboratory of RNA Chemistry; Institute of Chemical Biology and Fundamental Medicine; Siberian Division of Russian Academy of Sciences; Novosibirsk Russia
| | - Alexandre S. Boutorine
- Acides nucléiques: dynamique, ciblage et fonctions biologiques; INSERM U565; Paris France
- Département Régulations, développement et diversité moléculaire; MNHN - CNRS UMR7196; Paris France
| | - Alya G. Venyaminova
- Laboratory of RNA Chemistry; Institute of Chemical Biology and Fundamental Medicine; Siberian Division of Russian Academy of Sciences; Novosibirsk Russia
| | - Danièle Praseuth
- Acides nucléiques: dynamique, ciblage et fonctions biologiques; INSERM U565; Paris France
- Département Régulations, développement et diversité moléculaire; MNHN - CNRS UMR7196; Paris France
| | - Jean-Christophe François
- Acides nucléiques: dynamique, ciblage et fonctions biologiques; INSERM U565; Paris France
- Département Régulations, développement et diversité moléculaire; MNHN - CNRS UMR7196; Paris France
- Sorbonne Universités; UPMC Univ Paris 06; UMR_S 938; CDR Saint Antoine; Paris France
- Faculté de Médecine and Hôpital Saint Antoine; INSERM; UMR_S 938; CDR Saint Antoine; Paris France
| |
Collapse
|
6
|
Tacheny A, Dieu M, Arnould T, Renard P. Mass spectrometry-based identification of proteins interacting with nucleic acids. J Proteomics 2013; 94:89-109. [PMID: 24060998 DOI: 10.1016/j.jprot.2013.09.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 08/19/2013] [Accepted: 09/13/2013] [Indexed: 01/02/2023]
Abstract
The identification of the regulatory proteins that control DNA transcription as well as RNA stability and translation represents a key step in the comprehension of gene expression regulation. Those proteins can be purified by DNA- or RNA-affinity chromatography, followed by identification by mass spectrometry. Although very simple in the concept, this represents a real technological challenge due to the low abundance of regulatory proteins compared to the highly abundant proteins binding to nucleic acids in a nonsequence-specific manner. Here we review the different strategies that have been set up to reach this purpose, discussing the key parameters that should be considered to increase the chances of success. Typically, two categories of biological questions can be distinguished: the identification of proteins that specifically interact with a precisely defined binding site, mostly addressed by quantitative mass spectrometry, and the identification in a non-comparative manner of the protein complexes recruited by a poorly characterized long regulatory region of nucleic acids. Finally, beside the numerous studies devoted to in vitro-assembled nucleic acid-protein complexes, the scarce data reported on proteomic analyses of in vivo-assembled complexes are described, with a special emphasis on the associated challenges.
Collapse
Affiliation(s)
- A Tacheny
- Laboratory of Biochemistry and Cell Biology (URBC), NAmur Research Institute for LIfe Sciences (NARILIS), University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
| | | | | | | |
Collapse
|
7
|
Vieregg J, Nelson HM, Stoltz BM, Pierce NA. Selective nucleic acid capture with shielded covalent probes. J Am Chem Soc 2013; 135:9691-9. [PMID: 23745667 PMCID: PMC3703666 DOI: 10.1021/ja4009216] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Indexed: 11/29/2022]
Abstract
Nucleic acid probes are used for diverse applications in vitro, in situ, and in vivo. In any setting, their power is limited by imperfect selectivity (binding of undesired targets) and incomplete affinity (binding is reversible, and not all desired targets bound). These difficulties are fundamental, stemming from reliance on base pairing to provide both selectivity and affinity. Shielded covalent (SC) probes eliminate the longstanding trade-off between selectivity and durable target capture, achieving selectivity via programmable base pairing and molecular conformation change, and durable target capture via activatable covalent cross-linking. In pure and mixed samples, SC probes covalently capture complementary DNA or RNA oligo targets and reject two-nucleotide mismatched targets with near-quantitative yields at room temperature, achieving discrimination ratios of 2-3 orders of magnitude. Semiquantitative studies with full-length mRNA targets demonstrate selective covalent capture comparable to that for RNA oligo targets. Single-nucleotide DNA or RNA mismatches, including nearly isoenergetic RNA wobble pairs, can be efficiently rejected with discrimination ratios of 1-2 orders of magnitude. Covalent capture yields appear consistent with the thermodynamics of probe/target hybridization, facilitating rational probe design. If desired, cross-links can be reversed to release the target after capture. In contrast to existing probe chemistries, SC probes achieve the high sequence selectivity of a structured probe, yet durably retain their targets even under denaturing conditions. This previously incompatible combination of properties suggests diverse applications based on selective and stable binding of nucleic acid targets under conditions where base-pairing is disrupted (e.g., by stringent washes in vitro or in situ, or by enzymes in vivo).
Collapse
Affiliation(s)
- Jeffrey
R. Vieregg
- Department
of Bioengineering, Department of Chemistry, Department of Computing and Mathematical Sciences, California Institute of Technology,
Pasadena, California 91125, United States
| | - Hosea M. Nelson
- Department
of Bioengineering, Department of Chemistry, Department of Computing and Mathematical Sciences, California Institute of Technology,
Pasadena, California 91125, United States
| | - Brian M. Stoltz
- Department
of Bioengineering, Department of Chemistry, Department of Computing and Mathematical Sciences, California Institute of Technology,
Pasadena, California 91125, United States
| | - Niles A. Pierce
- Department
of Bioengineering, Department of Chemistry, Department of Computing and Mathematical Sciences, California Institute of Technology,
Pasadena, California 91125, United States
| |
Collapse
|
8
|
Puch CBMD, Barbier E, Sauvaigo S, Gasparutto D, Breton J. Tools and strategies for DNA damage interactome analysis. Mutat Res 2012; 752:72-83. [PMID: 23220222 DOI: 10.1016/j.mrrev.2012.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 11/01/2012] [Accepted: 11/22/2012] [Indexed: 11/26/2022]
Abstract
DNA is the target of multiple endogenous and exogenous agents generating chemical lesions on the double helix. Cellular DNA damage response pathways rely on a myriad of proteins interacting with DNA alterations. The cartography of this interactome currently includes well known actors of chromatin remodelling, DNA repair or proteins hijacked from their natural functions such as transcription factors. In order to go further into the characterisation of these protein networks, proteomics-based methods began to be used in the early 2000s. The strategies are diverse and include mainly (i) damaged DNA molecules used as targets on protein microarrays, (ii) damaged DNA probes used to trap within complex cellular extracts proteins that are then separated and identified by proteomics, (iii) identification of chromatin- bound proteins after a genotoxic stress, or (iv) identification of proteins associated with other proteins already known to be part of DNA damage interactome. All these approaches have already been performed to find new proteins recognizing oxidised bases, abasic sites, strand breaks or crosslinks generated by anticancer drugs such as nitrogen mustards and platinating agents. Identified interactions are generally confirmed using complementary methods such as electromobility shift assays or surface plasmon resonance. These strategies allowed, for example, demonstration of interactions between cisplatin-DNA crosslinks and PARP-1 or the protein complex PTW/PP. The next challenging step will be to understand the biological repercussions of these newly identified interactions which may help to unravel new mechanisms involved in genetic toxicology, discover new cellular responses to anticancer drugs or identify new biomarkers and therapeutic targets.
Collapse
Affiliation(s)
| | - Ewa Barbier
- Laboratoire Lésions des Acides Nucléiques, SCIB, UMR-E3 CEA/UJF-Grenoble 1, INAC, 17 rue des Martyrs, Grenoble, F-38054, France
| | - Sylvie Sauvaigo
- Laboratoire Lésions des Acides Nucléiques, SCIB, UMR-E3 CEA/UJF-Grenoble 1, INAC, 17 rue des Martyrs, Grenoble, F-38054, France
| | - Didier Gasparutto
- Laboratoire Lésions des Acides Nucléiques, SCIB, UMR-E3 CEA/UJF-Grenoble 1, INAC, 17 rue des Martyrs, Grenoble, F-38054, France
| | - Jean Breton
- Laboratoire Lésions des Acides Nucléiques, SCIB, UMR-E3 CEA/UJF-Grenoble 1, INAC, 17 rue des Martyrs, Grenoble, F-38054, France; UFR de Pharmacie, Université Joseph Fourier-Grenoble 1, Domaine de la Merci, La Tronche, F-38706, France.
| |
Collapse
|
9
|
Nakamura RL, Landt SG, Mai E, Nejim J, Chen L, Frankel AD. A cell-based method for screening RNA-protein interactions: identification of constitutive transport element-interacting proteins. PLoS One 2012; 7:e48194. [PMID: 23133567 PMCID: PMC3485056 DOI: 10.1371/journal.pone.0048194] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 09/24/2012] [Indexed: 12/21/2022] Open
Abstract
We have developed a mammalian cell-based screening platform to identify proteins that assemble into RNA-protein complexes. Based on Tat-mediated activation of the HIV LTR, proteins that interact with an RNA target elicit expression of a GFP reporter and are captured by fluorescence activated cell sorting. This "Tat-hybrid" screening platform was used to identify proteins that interact with the Mason Pfizer monkey virus (MPMV) constitutive transport element (CTE), a structured RNA hairpin that mediates the transport of unspliced viral mRNAs from the nucleus to the cytoplasm. Several hnRNP-like proteins, including hnRNP A1, were identified and shown to interact with the CTE with selectivity in the reporter system comparable to Tap, a known CTE-binding protein. In vitro gel shift and pull-down assays showed that hnRNP A1 is able to form a complex with the CTE and Tap and that the RGG domain of hnRNP A1 mediates binding to Tap. These results suggest that hnRNP-like proteins may be part of larger export-competent RNA-protein complexes and that the RGG domains of these proteins play an important role in directing these binding events. The results also demonstrate the utility of the screening platform for identifying and characterizing new components of RNA-protein complexes.
Collapse
Affiliation(s)
- Robert L. Nakamura
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Stephen G. Landt
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Emily Mai
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Jemiel Nejim
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Lily Chen
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Alan D. Frankel
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
| |
Collapse
|
10
|
Sousa F, Cruz C, Queiroz JA. Amino acids-nucleotides biomolecular recognition: from biological occurrence to affinity chromatography. J Mol Recognit 2011; 23:505-18. [PMID: 21038352 DOI: 10.1002/jmr.1053] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In this review, the protein-DNA interactions are discussed considering different perspectives, and the biological occurrence of this interaction is explained at atomic level. The evaluation of the amino acid-nucleotide recognition has been investigated analysing datasets for predicting the association preferences and the geometry that favours the interaction. Based on this knowledge, an affinity chromatographic method was developed also exploiting this biological favoured contact. In fact, the implementation of this technique brings the possibility to apply the concept of molecular interactions to the development of new purification methodologies. In addition, the integration of the information recovered by all the different perspectives can bring new insights about some biological mechanisms, though not totally clarified.
Collapse
Affiliation(s)
- F Sousa
- CICS-Centro de Investigação em Ciências da Saúde, University of Beira Interior, 6201-001 Covilhã, Portugal.
| | | | | |
Collapse
|
11
|
Michlewski G, Cáceres JF. RNase-assisted RNA chromatography. RNA (NEW YORK, N.Y.) 2010; 16:1673-1678. [PMID: 20571124 PMCID: PMC2905764 DOI: 10.1261/rna.2136010] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2010] [Accepted: 05/11/2010] [Indexed: 05/29/2023]
Abstract
RNA chromatography combined with mass spectrometry represents a widely used experimental approach to identify RNA-binding proteins that recognize specific RNA targets. An important drawback of most of these protocols is the high background due to direct or indirect nonspecific binding of cellular proteins to the beads. In many cases this can hamper the detection of individual proteins due to their low levels and/or comigration with contaminating proteins. Increasing the salt concentration during washing steps can reduce background, but at the cost of using less physiological salt concentrations and the likely loss of important RNA-binding proteins that are less stringently bound to a given RNA, as well as the disassembly of protein or ribonucleoprotein complexes. Here, we describe an improved RNA chromatography method that relies on the use of a cocktail of RNases in the elution step. This results in the release of proteins specifically associated with the RNA ligand and almost complete elimination of background noise, allowing a more sensitive and thorough detection of RNA-binding proteins recognizing a specific RNA transcript.
Collapse
Affiliation(s)
- Gracjan Michlewski
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh EH4 2XU, United Kingdom.
| | | |
Collapse
|
12
|
Sidorova NY, Hung S, Rau DC. Stabilizing labile DNA-protein complexes in polyacrylamide gels. Electrophoresis 2010; 31:648-53. [PMID: 20108261 DOI: 10.1002/elps.200900573] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The electrophoretic mobility-shift assay (EMSA) is one of the most popular tools in molecular biology for measuring DNA-protein interactions. EMSA, as standardly practiced today, works well for complexes with association binding constants K(a)>10(9) M(-1) under normal conditions of salt and pH. Many DNA-protein complexes are not stable enough so that they dissociate while moving through the gel matrix giving smeared bands that are difficult to quantitate reliably. In this work we demonstrate that the addition of the osmolyte triethylene glycol to polyacrylamide gels dramatically stabilizes labile restriction endonuclease EcoRI complexes with nonspecific DNA sequences enabling quantitation of binding using EMSA. The significant improvement of the technique resulting from the addition of osmolytes to the gel matrix greatly extends the range of binding constants of protein-DNA complexes that can be investigated using this widely used assay. Extension of this approach to other techniques used for separating bound and free components such as gel chromatography and CE is straightforward.
Collapse
Affiliation(s)
- Nina Y Sidorova
- Laboratory of Physical and Structural Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
| | | | | |
Collapse
|
13
|
Yuan Y, Shi X, Li X, Lu W, Cai Y, Gu L, Liu L, Li M, Kong X, Xing M. Prediction of interactiveness of proteins and nucleic acids based on feature selections. Mol Divers 2009; 14:627-33. [PMID: 19816781 DOI: 10.1007/s11030-009-9198-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Accepted: 09/07/2009] [Indexed: 11/29/2022]
Abstract
It is important to identify which proteins can interact with nucleic acids for the purpose of protein annotation, since interactions between nucleic acids and proteins involve in numerous cellular processes such as replication, transcription, splicing, and DNA repair. This research tries to identify proteins that can interact with DNA, RNA, and rRNA, respectively. mRMR (Minimum redundancy and maximum relevance), with its elegant mathematical formulation, has been applied widely in processing biological data and feature analysis since its introduction in 2005. mRMR plus incremental feature selection (IFS) is known to be very efficient in feature selection and analysis, and able to improve both effectiveness and efficiency of a prediction model. IFS is applied to decide how many features should be selected from feature list provided by mRMR. In the end, the selected features of mRMR and IFS are further refined by a conventional feature selection method--forward feature wrapper (FFW), by reordering the features. Each protein is coded by 132 features including amino acid compositions and physicochemical properties. After the feature selection, k-Nearest Neighbor algorithm, the adopted prediction model, is trained and tested. As a result, the optimized prediction accuracies for the DNA, RNA, and rRNA are 82.0, 83.4, and 92.3%, respectively. Furthermore, the most important features that contribute to the prediction are identified and analyzed biologically. The predictor, developed for this research, is available for public access at http://chemdata.shu.edu.cn/protein_na_mrmr/.
Collapse
Affiliation(s)
- YouLang Yuan
- Chemical Data mining Laboratory, Department of Chemistry, College of Sciences, Shanghai University, 99 Shang-Da Road, Shanghai, 200444, People's Republic of China
| | | | | | | | | | | | | | | | | | | |
Collapse
|