DNA Interactions with Single-Stranded DNA Binding Proteins and Retroviral Nucleic Acid Chaperones by Force Spectroscopy

Part of the Biological and Medical Physics, Biomedical Engineering book series (BIOMEDICAL)


In this chapter, we compare and contrast the biophysical properties of two ­important classes of nonsequence-specific nucleic acid binding proteins: single-stranded DNA binding proteins (SSBs) from bacteriophages and nucleocapsid proteins (NCs) from retroviruses. The SSBs comprise the primary noncatalytic component of the DNA replication machinery, functioning to bind and protect all available single-stranded DNA (ssDNA) at the DNA replication fork. The NC proteins are necessary components of the RNA reverse transcription complex, playing roles analogous to those of SSBs in DNA replication. The primary function of NC is to facilitate RNA and DNA refolding into low-energy conformations, a property referred to as nucleic acid chaperone activity. This function is necessary for almost every step of retroviral reverse transcription. Application of single molecule DNA force spectroscopy methods has advanced the characterization of bacteriophage SSB and retroviral NC interactions with single-stranded (ss) and double-stranded (ds) DNA molecules beyond what was known from conventional solution studies. By applying single molecule techniques to wild type and mutant NC and SSB proteins from several biological systems, we have been able to illustrate a continuous spectrum of properties that distinguish proteins as effective nucleic acid chaperones or ssDNA stabilizers.


ssDNA Binding Single Molecule Force Spectroscopy dsDNA Binding Bind Site Size Nucleic Acid Chaperone 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



The authors would like to thank Margareta Cruceanu, Kiran Pant, Leila Shokri, and Fei Wang for their original work on these systems. This work was funded by the US National Institutes of Health (GM072462) and National Science Foundation (MCB-0744456).


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© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  1. 1.Department of PhysicsNortheastern UniversityBostonUSA

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