Introduction to Bioinformatics
David Ussery
Tuesday, 11 November, 2001 (Part 2)
This lecture is about DNA structural analysis for the Escherichia coli genomes. In a real sense, it is a continuation of the previous talk from earlier today. 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)
<--length
of bacteria-->
Transcriptional Regulation by different sigma-factors.
E.coli RNA Polymerase subunits Gene Mass
KDaFunction -35 Sequence separ. -10 Sequence #molecules
per cell# genes
regulatedrpoA 40 alpha subunit - - - ~4000 - rpoB 155 beta subnit - - - ~2000 - rpoC 160 beta' subunit - - - ~2000 - rpoD 70 sigma70
GeneralTTGACA 16-18 bp TATAAT 600 3851 rpoN 54 sigma54
NitrogenCTGGNA 6 bp TTGCA ~50 177 rpoS 38 sigma38
Stationary? - ? 200 (log)
600
(stat.)68 rpoH 32 sigma32
Heat shockCCCTTGAA 13-15 bp CCCGATNT ~50 75 fliA 28 sigma28
FlagellarCTAAA 15 bp GCCGATAA ~20 13 rpoE 24 sigma24
High temp.
heat shock? - ? < 5 4 ? fecI 19 sigma19
iron transp.? - ? < 5 2 ?
- There are about 1500 - 2000 copies of RNAP holoenzyme per cell (that is, a, b/b')
- For bacteria growing in "log phase":
- ~600 copies of RpoD (s70)
- ~200 copies of RpoS (s38)
- [RpoS] increases to ~600 copies per cell in stationary phase or osmotic shock.
Logo plots for E. coli Sigma factors.
Structural profiles for E. coli Sigma70 and Sigma38 promoters
Table of structural profiles for 17 different sequenced genomes
Today (Tuesday, 17 April, 2001)
[PubMed]
Friday (6 April, 2001)
Link to a list of recent papers and talks on DNA structures.
Davies, Kevin, "CRACKING THE GENOME: Inside the Race to Unlock Human DNA - Craig Ventor, Francis Collins, James Watson, and the Story of the Greatest Scientific Discovery of Our Time", (The Free Press, New York, 2001). Amazon Barnes&Noble
Watson, James D. "A PASSION FOR DNA: Genes, Genomes, and Society", (Oxford University Press, Oxford, 2000). Amazon Barnes&Noble
Sinden, Richard R., "DNA: STRUCTURE and FUNCTION", (Academic Press, New York, 1994). Amazon Barnes&Noble
Calladine,C.R., Drew,H.R., "Understanding DNA: The Molecule and How It Works", (2nd edition, Academic Press, San Diego, 1997). Amazon Barnes&Noble
A List of more than a thousand books about DNA
Link to the E. coli GenomeAtlas page
Last modified Wednesday, 15 August, 2001 by David Ussery
