Energy associated with different structures

References (Part #5)

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The energy of the molecule changes if there is a change in pitch (that is, the number of bases per full turn) or bending of the double helix ring. Even a small change in the pitch of the DNA results in a large increase in energy

• Minimum energy: Linear DNA assumes the B configuration because it is the one of minimum energy. Linear molecules of DNA assume a configuration known as the b-configuration. Deviation from this relaxed state increases the energy of the DNA molecule, although circular DNA of large diameter increases it least.
  
  
• Higher energy: In the ring form too, the DNA double helix tries to attain the state of minimum energy. The DNA ring approximates the b-configuration of the linear molecule while trying to attain the state of minimum energy. This packaging of DNA deforms it physically, thereby increasing its energy. Such an increase in stored (potential) energy within the molecule is then available to drive reactions such as the unwinding events that occur during DNA replication and transcription. Too much stored energy is not necessarily a good thing, though. In nature, this problem is addressed by having DNA form supercoils, in which the helical axis of the DNA curves itself into a coil. Supercoiling or the formation of a superhelix structure minimizes the excess energy that builds up when DNA molecules are deformed during the packing process.
  
  
• At this point, it's a good idea to mention that supercoiling is not necessarily the only solution to the problem of normalizing the number of base pairs per helix in an unwound piece of DNA. You could also separate the two strands by breaking the hydrogen bonds between complementary bases in contiguous base pairs until the remaining DNA has the correct number of base per per turn. In terms of energy needed, though, it requires a lot more energy to break the H-bonds than to supercoil. Nevertheless, strand separation does occur during replication and transcription and it turns out that it is the physics of the underwinding that facilitates the strand separation. Cruciform structures also require some unpairing of the base pairs and, again, it is the underwinding that maintains the required strand separation.