30431 Introduktion til Bioinformatik
4 September, 1998
 
DNA is like Coca-Cola
 coke_logo.gif 

 
 

"...A structure this pretty just had to exist."
 
 
 DNA helix
 
 
DNA is like Coke. 
Coke bottle 
DNA is like Coca-Cola
Coke DNA Solubility
water water
-
Sugar (sucrose)  Sugar (dexoyribose)
VERY 
High
Phosphate  
(PO4- acid)		 phosphate
moderate
caffeine bases  
(A,T,C,G)
extremely
low
 
Compare the structures of Caffeine: Caffeine

with Adenine: 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 VERY MOST 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.
 

DNAmovDNAmovDNAmovDNAmovDNAmovDNAmov

 

Properties of individual dinucleotide base pairs
Dinucleotide 
base pairs		 Stacking energies 
(Kcal/mol bp)		 twist angle
bp/turn
(GC).(GC)
-14.59
40.0
9.0
(AC).(GT)
-10.51
34.4
10.5
(TC).(GA)
-9.81
36.9
9.8
(CG).(CG)
-9.61
29.8
12.1
(GG).(CC)
-8.26
33.7
10.7
(AT).(AT)
-6.57
32.1
11.4
(TG).(CA)
-6.57
34.5
10.4
(AG).(CT)
-6.78
27.9
13.0
(AA).(TT)
-5.37
35.6
10.1
(TA).(TA)
3.82
36.0
10.0
The base stacking energies are from: Ornstein,R.L., Rein,R., Breen,D.L., and MacElroy,R.D., Biopolymers, 17:2341-2360, (1978).  The helical twist angles (and their implied bp/turn) are from Kabsch,Sander, and Trifonov, Nucleic Acids Research, 10:1097-1104, (1982).
 
 

 

 
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