Biology 210
GENETICS
13 February,1998

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Chapter 6a The Molecular Organisation of Bacterial Chromosomes
-or-
Bacterial Chromatin from a DNA-centric perspective

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A Brief Outline

I. The Problem: DNA Compaction

Three aspects of DNA compaction in bacteria:
A. Flexibility
B. DNA supercoiling
  • Toroidal supercoils from proteins ("restrained" supercoils)

  • Plectonemic supercoils ("unrestrained")

C.Intrinsic DNA curvature
II. What IS "curved DNA"? III. On the Biological Significance of curved DNA

note: This is based on a lecture that was originally given as a "keynote" talk on the first day of a week-long EMBO Workshop on Nucleoid-Associated Proteins: Structure, Function & Genetics, in Camerino, Italy, in May, 1997. This was actually meant to be the first part of an introduction or overview of DNA/protein interactions in bacterial chromatin.  I discussed the "DNA" part, and Professor Andrew Travers (from the MRC in Cambridge) talked about bacterial chromatin-associated proteins and their binding to DNA. The references and questions are from a "Workshop on DNA Structure & Function" I gave in Oslo, Norway, during the 1996/1997 academic year.


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I. The Problem Stated: DNA Compaction

<-----length of bacteria------>
Lac operon (Figure 11_3 from Hartl & Jones, 1998).



Three aspects of DNA compaction in bacteria:
  A. Flexibility

There are two different ways of looking at DNA flexibility:

       1. Persistence length of DNA - this is relatively non-specific, and just has to do with the overall "rigidity" of DNA.  On average, DNA has a persistance length of about 44 nm, which is quite a bit longer than proteins.  One way of thinking about this is that proteins tend to fold up into little spheres (I like to say "blobs"), and DNA is a bit more rigid.

Description of persistence length. This is taken from Cantor and Schimmel, Biophysical Chemistry, page 1012 (W.H.Freeman & Co., San Fransisco, 1980).

 

The point of all this is that, on average DNA has a persistence length of about 130 bp, and this is quite a bit longer than proteins.   The measured values for persistence length have been found to depend several environmental factors, such as temperature and concentration of salt.  So the value of the persistence length for DNA is usually in the range of 120 to 150 bp, depending on the conditions of the experiment.  My own personal opinion is that inside bacterial cells, the persistence length is probably around 140 bp.
 
 DNA (ave.)         polyglycine          poly-L-valine
<---------->            <->                <----->
a = 44 nm           a = 0.6 nm            a = 22 nm
(about 130 bp)
 

However, the DNA persistence length varies with sequence, and can be quite large for certain sequences:

        (A5N10)n
<------------------------>
        a = 80 nm
      (about 235 bp)
 

where (A5N10)n is the following sequence:

5' GGCCCAAAAAGGCCGGGCCCAAAAAGGCCGGGCCCAAAAAGGCCGGGCCC...3'
 

   Thus,  a few specific DNA sequences can be quite rigid, with a persistence length that is almost twice as long as that for an average DNA molecule.  For other  DNA sequences, the persistence length can be much lower than the average - these sequences are said to be very "flexible" - for example, regions such as ...TATATA... can substantially reduce the rigidity of the helix.  Why is the persistence so much longer for certain DNA sequences?  Part of the answer from this will come when we talk about curved DNA (below).
 


         2. Anisotropic flexibility, or "bendability" of DNA - this is very much sequence-specific, and is different from the static rigidity described above.  This is a measure of a particular sequence to be deformed by a protein (or some other external force).  Some sequences are BOTH isotropically flexible and "bendable" - for example, the TATA motifs.  There are other sequences that can be easily be bent by a protein in a particular direction.  Perhaps one of the best examples of this is the binding site for the Integration Host Factor (IHF) - there are certain base pairs that are highly distorted upon binding of this protein, as can be seen in this picture, based on the crystal structure:

Figure 2 from P.A. Rice, S. Yan, K. Mizuuchi,  and H.A. Nash, Cell, 87:1295-1306, (1996).  Notice the yellow proline at the tip of each arm intercalates between the DNA bases.

IHF binding to DNA

It is quite impressive that this protein induces a bend of 180 degrees into a DNA helix.  On the other hand, when you consider that the DNA must be compacted more than a thousand fold in the cell, it is probably not that suprising that almost ANY protein that binds to DNA will bend it.

I recently read a review article of DNA/protein crystal structures; our of more than 100 different structures characterised, nearly all of them distorted or bent the DNA helix (some more so than others, obviously!).
 






B. DNA supercoiling

Introduction and Historical background