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2. Beskrive de kræfter (Watson-Crick baseparring og "base-stacking") som holder en DNA dobbelt helix sammen

2 types of forces are used to stabilize the DNA-double helix:

Watson-Crick base pairing:
Devlin, s.39, fig.2.16,17
Stryer, s.10

The relationship between bases in the double helix is described as complementarity.

Bases are complementary because every base of one strand is matched by a complementary hydrogen bonding to a base on the other strand. These complementary base pairs are called Watson-Crick base pairs.

Fx. for each adenine projecting towards the common axis of the double helix, a thymine must be projected from the opposite chain so as to fill exactly the space between strands by hydrogen bonding. No other base would fit.

• Adenosine and thymine are linked by two hydrogen bonds, while cytosine and guanine with three H-bonds.
   

• -NH and NH₂ groups are proton donors (have partial positive charge, because H has a small electronegativity - a less strong attraction to the shared electrons then N, that has a higher electro negativity), while -O=  and =N- groups are proton acceptors (have partially negative charge because they have a stronger attraction to shared electrons and have a free electron pair) for the hydrogen bond
   

• The hydrogen bond is not very strong bond in itself, but because of the double helix confirmation, as well as the huge lenght of the DNA molecule, it becomes strong enough to keep it all together
   

• Uracil (RNA) has the same donor and acceptor groups as thymidine, meaning an RNA molecule can make base pairing with a DNA molecule
   

• The complementary bases have a space confirmation that favors base stacking.

Base stacking:
Devlin, s. 34
Stryer, s.123-4

The faces of the base rings tend to avoid contact with water, unlike their edges that contain polar groups that interact with other polar groups (Watson-Crick base pairing) or surrounding water molecules.

Therefore, the faces of the rings interact with one another, in order to produce a stacked confirmation - base stacking. Base stacking introduces 2 types of bonds:

• hydrophobic bonds between the non-polar rings of the bases. These bonds reduce the hydrophobic surface area of the DNA molecule by exposing the more polar surfaces to the surrounding water.  This also causes release of water into the bulk solvent, which is entropically favorable.
   

•  Van der Waals forces or London dispersion forces - these forces are produced between hydrophobic molecules, when the electrons moving around the nucleus of one atom can cause a dipole in the electron density of the neighbor atom when the electron orbitals of the two atoms approach to a close distance . These induced dipoles are very temporary, but they still contribute to the stabilization on the bond. Because the strength of these electronic interactions is very dependent upon distance, no empty space remains between the stacked bases.

Polynucleotides adopt confirmations that maximize the favorable stacking interactions between neighboring bases.

When the two strands of DNA come close to each other, it is also because of base stacking that it is impossible for two purines or pyrimidines to make a hydrogen bonds together. Two purines fill up too much, while two pyrimidines too little. That way, gaps or bulges are created in the DNA which are unfavorable to base stacking.

On top of everything, the phosphate groups in the DNA backbone do not want to be close to eachother since they all have negative charges, which has a destabilizing effect on the molecule. This problem is solved by introducing catjones which bind with the negative backbone and stabilize the entire strucutre.

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