Thermodynamics of Cooperative DNA Recognition at a Replication Origin and Transcription Regulatory Site

Dellarole, Mariano; Sánchez, Ignacio E.

doi:10.1021/bi1014908

Cited by 10 publications

(10 citation statements)

References 71 publications

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“…9,10 In budding yeast, replicators and origins are together defined as ARSs (autonomously replicating sequences), upon which multiple initiation proteins are assembled stepwise. This is the only eukaryote in which ORC specifically recognizes a 17 bp T-rich consensus sequence called ACS (ARS consensus sequence).…”

Section: Resultsmentioning

confidence: 99%

New insights into replication origin characteristics in metazoans

Cayrou¹,

Coulombe²,

Puy³

et al. 2012

Cell Cycle

168

143

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We recently reported the identification and characterization of DNA replication origins (Oris) in metazoan cell lines. Here, we describe additional bioinformatic analyses showing that the previously identified GC-rich sequence elements form origin G-rich repeated elements (OGREs) that are present in 67% to 90% of the DNA replication origins from Drosophila to human cells, respectively. Our analyses also show that initiation of DNA synthesis takes place precisely at 160 bp (Drosophila) and 280 bp (mouse) from the OGRE. We also found that in most CpG islands, an OGRE is positioned in opposite orientation on each of the two DNA strands and detected two sites of initiation of DNA synthesis upstream or downstream of each OGRE. Conversely, Oris not associated with CpG islands have a single initiation site. OGRE density along chromosomes correlated with previously published replication timing data. Ori sequences centered on the OGRE are also predicted to have high intrinsic nucleosome occupancy. Finally, OGREs predict G-quadruplex structures at Oris that might be structural elements controlling the choice or activation of replication origins.

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Section: Resultsmentioning

confidence: 99%

New insights into replication origin characteristics in metazoans

Cayrou¹,

Coulombe²,

Puy³

et al. 2012

Cell Cycle

168

143

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show abstract

“…The amplitude of such titration isotherms contains information on the molar enthalpy changes ΔH of molecular complex formation, which in turn may be interpreted in the context of structural thermodynamics. For systems with multi-site binding, ITC can provide information on stoichiometry and cooperativity of molecular complexes [7–14]. …”

Section: Introductionmentioning

confidence: 99%

“…Beyond merely organizing separate complementary experiments into a hierarchical, multi-stage interpretation, global analysis takes full advantage of all possible constraints of the model and the full statistics of the data by simultaneously and directly fitting all experimental data with one explicit global model. Natural applications of gITC analysis are multi-site binding processes of homo- and hetero-oligomerizing macromolecules [9–11,13,14,15 ( this volume ),23,33–37], displacement experiments [22,38,39], and protonation-linked and other linked binding analyses varying temperature to determine heat capacity changes or buffer composition to determine salt or other co-factor linkage [24,26,28]. …”

Section: Introductionmentioning

confidence: 99%

“…SEDPHAT is a computational platform for global analysis of data from various biophysical techniques, including gITC, which has been widely adopted in ITC applications [11–14,15 ( this volume ),17,19,24,33–62]. Distinguishing aspects of SEDPHAT in comparison with other gITC platforms include the absence of data-specific or model-specific programming by the user, allowing for seamless combination of titration experiments in a graphical user interface, and offering many different pre-programmed multi-site models for two- and three-component systems [9].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

SEDPHAT – A platform for global ITC analysis and global multi-method analysis of molecular interactions

Zhao

Piszczek

Schuck

2015

Methods

309

290

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Isothermal titration calorimetry experiments can provide significantly more detailed information about molecular interactions when combined in global analysis. For example, global analysis can improve the precision of binding affinity and enthalpy, and of possible linkage parameters, even for simple bimolecular interactions, and greatly facilitate the study of multi-site and multi-component systems with competition or cooperativity. A pre-requisite for global analysis is the departure from the traditional binding model, including an ‘n’-value describing unphysical, non-integral numbers of sites. Instead, concentration correction factors can be introduced to account for either errors in the concentration determination or for the presence of inactive fractions of material. SEDPHAT is a computer program that embeds these ideas and provides a graphical user interface for the seamless combination of biophysical experiments to be globally modeled with a large number of different binding models. It offers statistical tools for the rigorous determination of parameter errors, correlations, as well as advanced statistical functions for global ITC (gITC) and global multi-method analysis (GMMA). SEDPHAT will also take full advantage of error bars of individual titration data points determined with the unbiased integration software NITPIC. The present communication reviews principles and strategies of global analysis for ITC and its extension to GMMA in SEDPHAT. We will also introduce a new graphical tool for aiding experimental design by surveying the concentration space and generating simulated data sets, which can be subsequently statistically examined for their information content. This procedure can replace the ‘c’-value as an experimental design parameter, which ceases to be helpful for multi-site systems and in the context of gITC.

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“…Protein/peptide interactions with metals and ions Protein/peptide interactions with nucleic acids Lipid/membrane interactions …”

Section: Introductionmentioning

confidence: 99%

Applications of isothermal titration calorimetry in pure and applied research—survey of the literature from 2010

Ghai

Falconer

Collins

2011

J of Molecular Recognition

167

108

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Isothermal titration calorimetry (ITC) is a biophysical technique for measuring the formation and dissociation of molecular complexes and has become an invaluable tool in many branches of science from cell biology to food chemistry. By measuring the heat absorbed or released during bond formation, ITC provides accurate, rapid, and label-free measurement of the thermodynamics of molecular interactions. In this review, we survey the recent literature reporting the use of ITC and have highlighted a number of interesting studies that provide a flavour of the diverse systems to which ITC can be applied. These include measurements of protein-protein and protein-membrane interactions required for macromolecular assembly, analysis of enzyme kinetics, experimental validation of molecular dynamics simulations, and even in manufacturing applications such as food science. Some highlights include studies of the biological complex formed by Staphylococcus aureus enterotoxin C3 and the murine T-cell receptor, the mechanism of membrane association of the Parkinson's disease-associated protein α-synuclein, and the role of non-specific tannin-protein interactions in the quality of different beverages. Recent developments in automation are overcoming limitations on throughput imposed by previous manual procedures and promise to greatly extend usefulness of ITC in the future. We also attempt to impart some practical advice for getting the most out of ITC data for those researchers less familiar with the method.

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Thermodynamics of Cooperative DNA Recognition at a Replication Origin and Transcription Regulatory Site

Cited by 10 publications

References 71 publications

New insights into replication origin characteristics in metazoans

New insights into replication origin characteristics in metazoans

SEDPHAT – A platform for global ITC analysis and global multi-method analysis of molecular interactions

Applications of isothermal titration calorimetry in pure and applied research—survey of the literature from 2010

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