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CbpA is DNA binding protein found in E. coli and binds non-specifically to curved DNA (Cosgriff et al., 2010), when the bacterium is in a static phase of growth.

The use of "curved DNA" confuses me. Is the term "curved DNA" essentially the same as "Circular DNA"?

Cosgriff, S. et al. Dimerization and DNA-dependent aggregation of the Escherichia coli nucleoid protein and chaperone CbpA. Mol. Microbiol. 77, 1289–1300 (2010).

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  • $\begingroup$ It might be useful to link the source where you read the term, it could provide additional context that would be helpful for answering the question. $\endgroup$
    – Mad Scientist
    Commented Mar 16, 2012 at 12:15
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    $\begingroup$ I've provided a link to the reference and unipot $\endgroup$
    – harpalss
    Commented Mar 16, 2012 at 12:30

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I never heard of the term until today but a quick search implies that certain DNA sequences are more pliable than others. Most notable is the Widom sequence which binds to Histones. It is also noted that DNA isn't a free floating polymer but that there is also some directionality in its bend. It seems that the concept is bested explored in this review: Curved DNA.

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it is not necessarily circular - the transcription factors usually require a curvature that is much greater than what a plasmid will have, and the requirement can show up on eukaryotic proteins as well. DNA binding proteins will cause a local loop or curvature that fit the transcription factor.

The classic picture is for the Gal and Lac repressor proteins which bind 2 strands simultaneously, causing a loop in the DNA.

Reference: see fig 1 in: http://genesdev.cshlp.org/content/3/5/606.full.pdf+html

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I'm hardly an authority on this topic, but I distinctly recall an amazing report the mid-1990s of the co-crystal structure the yeast TATA binding protein in complex with DNA. The structure shows that TBP bends the DNA axis by approximately 80 degrees, presumably in order to expose bases and improve recognition. The structure is available at RCSB: http://www.rcsb.org/pdb/explore.do?structureId=1ytb . (Make sure you check out the Jmol view.)

Thermodynamically speaking, bending DNA would require energy. Therefore, DNA that was pre-bent (e.g., due to auxiliary binding proteins or composition bias) would improve binding.

So, I suspect that in the context DNA binding proteins, "curved" refers to the static curvature of unbound DNA or to the bending of DNA upon binding in order to facilitate recognition.

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