David Ussery
Tuesday, 17 April, 2001
This lecture is about DNA structural analysis for the Escherichia coli genomes. In a real sense, it is a continuation of last Friday's talk. In the first part ("DNA is like Coca-cola"), I will talk about DNA Structures, and their possible biological meanings. Then, in the second half, I will talk about DNA structures and promoters (in E. coli of course as an example), and discuss structural organisation of promoters in bacterial genomes in general.
As with the last lecture, I have made separate file, containing specific LEARNING OBJECTIVES for this lecture, as well as a "self-test quiz", which I recommend having a look at, BEFORE the lecture, if possible.
| Coke | DNA | Solubility |
| water | water |
|
| Sugar (sucrose) | Sugar (dexoyribose) |
High |
| Phosphate
(PO4- acid) |
phosphate |
|
| caffeine | bases
(A,T,C,G) |
low |
Compare the structures of Caffeine: 
with Adenine: 
Here's the structure of caffeine, flipped:
Caffeine is a "base analogue" of Adenine, and in fact can sometimes be incorporated into a growing DNA chain, instead of Adenine. Caffeine is a weak mutagen, for this reason.
The
important property contributing
to DNA helix stability is the stacking of the base-pairs on top of one
another, due to hydrophobic forces. (Remember, the bases "hate"
water, and are not very soluble.) Free bases will stack on top of
each other and form a helix in solution! This type of process is
called "self-assembly", where you just throw something in solution, and
it fits together on its own, with no extra work needed.
| Dinucleotide base pairs |
Stacking energies (Kcal/mol bp) |
twist angle | |
A-DNA family - this is most common for double stranded RNA, RNA/DNA hybrids,
as well as for certain DNA sequences, such as long stretches of purines.
B-DNA family - DNA exists in the "B-DNA form", most of the time inside the cells of
living organisms. This is the classical "Watson-Crick" structure.
Z-DNA family - this is much more rare than the other two families, although certains
sequences (such as runs of GC repeats (GCGCGC)) can form Z-DNA easily.
| Organism | Kingdom | Size | A-DNA Rn or Yn where n>4 bp |  | Z-DNA (YR)6 or (RY)6 | | length dist. plot |
| E. coli K-12 | Monera (Bacteria) | 4,639,221 bp (complete) | |||||
| P. abyssi | Monera (Archaea) | 1,765,111 bp (complete) | |||||
| S. pombe chr. | Fungi (yeast) | 5,325,148 bp (~12 Mbp total) | |||||
| L. major chr. 3 | Protista (protozoa) | 384,499 bp (~40 Mbp total) | |||||
| A. thaliana chr. 1 (bottom half) | Plantae (thale cress) | 14,668,8831 bp (~100 Mbp total) | |||||
| H. sapiens chr. 22 | Animalae (humans) | 34,601,435 bp (~3000 Mbp total) | |||||
| Expected values | n bp |
Background - What is a "DNA Structural Atlas"?
Three Views of Escherichia coli:The DNA Structural Atlas
The Genome Atlas (combined view)
Part 2 of the lecture - DNA structures and promoters
MORE ABOUT DNA:
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last updated 19 April, 2001 by Dave Ussery
