Re: Why does DNA have an helicoidal shape ?

Hello!!

What an interesting  question, and one often disussed in biophysics.  If I 
had to weigh in on a certain side it would be that of your father, after 
all, mathematics will explain most (but certainly not all) things in 
biophysics.  Regarding the weights of the bases, this has very little 
effect on the helical structure of DNA since the bases are similar in 
mass.  How those bases interact, number of torsion angles, their electron 
clouds, and many other considerations are of importance though.  I will 
address this question with the assumption that you know the structure of 
standard B-DNA (derived by Watson and Crick) which will be my reference 
point. 

Lets look at what type of interactions are taking place:

1) Base Stacking
	This occurs between the aromatic bases of the nucleic acids with 
the hydrophobic faces orienting themselves along the helical axis creating 
a hydrophobic interior to the helix.  This is evident by intercalation of 
hydrophobic molecules such as ethidium bromide into the helix interior.  
Base stacking plays a predominant role in the melting and annealing of DNA.

2) Hydrogen Bonds
	Hydrogen bonds play an important role in the structure of DNA.  
For every C-G base pair there are three H-bonds and for every T-A base 
pair there are two, assuming Watson-Crick pairing.  This is important in 
holding the two strands together as well since there are usually a 
significant number of H-bonds along the length of the helix contributing 
to its stability.  

3) Electrostatic Interactions
	Remember, on each base there is a phosphate oriented towards the 
outside of the helix.  Each base pair has two phosphate groups at a 
distance of approximately 1.7Angstroms (same side of the chain).  The high 
electronegativity of the phosphates is usually screened by cations in the 
solution.  They are essentially screened from one another by the solvent.  
Some cations bind tighter (Mg++) then others (K+ for example) lighter to 
the minor groove of B-DNA though the phosphates almost always remain 
partially negatively charged.  This is evident by single stranded DNA 
(phosphates farther apart) is favored in low-salt conditions while double 
stranded DNA(phosphates closer) is favored in high-salt conditions.  The 
latter brings about another factor, solvent interaction.  Macromolecular 
structure is highly dependent on the solution in which it resides.  
Hydrophobicity, pH, temperature, salinity, etc. all play an important role 
in helping 'determine' macromolecular structure.

As you can see, it is very complex.  The fact that DNA forms a double 
helix is not dependent on base molecular weights or the Fibonacci 
sequence.  Rather, it is a complex culmination of several factors.  We 
simply can't point to one factor that strictly determines tertiary 
structure of a protein or DNA organization.  This is evident by the 
plethora of analytical and theoretical techniques currently in use 
to 'predict' structure.

Hope this answers your question.  If not, just post back to MadSci asking 
for me.

cheers,
/frank hays

REFERENCES:

Principles of Physical Biochemistry, van Holde, Johnson, and Ho: 1998 
Prentice Hall ISBN 0-13-720459-0 http://www.ic
r.ac.uk/structbi/computing/linux_res.html http://www.se.iucr
.org/struc/linux/structure.html