Abstract
Protein-DNA binding assays have been used in a va-riety of applications from fundamental studies re-garding the binding process itself to serve as probes for the detection, quantification and separation of target analytes. Here we describe a novel method of analyzing and identifying intermolecular DNA interactions that allows for the simple separation of interacting nucleoprotein complex components (SSINCC), focusing specifically on DNA-DNA interactions using P1 plasmid active partition system nucleoprotein complexes as a model to demonstrate DNA sequence specificity and tolerance of composite factor complexity. Traditional and recent assays of protein-DNA interaction are summarized and compared with SSINC. Although SSINC is examined here employing P1 partition nucleoprotein complex as an example of DNA-DNA intermolecular association, universal applications of this methodology to nucleo-protein complex studies can be envisioned.
Highlights
The association between proteins and DNA is a fundamental requirement for most vital cellular functions including gene transcription, replication, recombination, repair, segregation, chromosomal stability, cell cycle progression, and epigenetic silencing
We describe a novel method of analyzing and identifying intermolecular DNA interactions that allows for the simple separation of interacting nucleoprotein complex components (SSINCC), focusing on DNA-DNA interactions using P1 plasmid active partition system nucleoprotein complexes as a model to demonstrate DNA sequence specificity and tolerance of composite factor complexity
We describe a novel method of analyzing and identifying intermolecular DNA interactions that allows for the simple separation of interacting nucleoprotein complex components (SSINCC), focusing on DNA-DNA interactions by using P1 plasmid active partition system nucleoprotein complexes as a model to demonstrate DNA sequence specificity and tolerance of
Summary
The association between proteins and DNA is a fundamental requirement for most vital cellular functions including gene transcription, replication, recombination, repair, segregation, chromosomal stability, cell cycle progression, and epigenetic silencing. Protein-DNA binding assays have been used in a variety of fields, such as binding process to serve as probes for the detection, quantification and separation of target analytes [1]. These assays have been used for the study of protein-DNA complex stoichiometry, the detection of DNA damage, and real-time separation of free and bound complexes by electrophoretic mobility. Plasmids serve as tractable model systems to study DNA segregation because they require only a DNA centromere, a centromere-binding protein and a force-generating ATPase. In this study we describe a novel DNA-DNA capture method, and use it to examine the ability of plasmid partition proteins to pair plasmids at their centromeres
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