Forms of DNA

References (Part #3)

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• Supercoiled (or "knotted"): Double stranded circular (or linear) DNA can have tertiary or higher order structure. Superhelicity is therefore sometimes referred to as DNA's tertiary structure. Supercoils refer to the DNA structure in which double-stranded circular DNA twists around each other. This is termed supercoiling, supertwisting or superhelicity -- meaning the coiling of a coil, also understood in terms of knots. Only topological closed domains (such as a covalently closed circle) can undergo supercoiling. A linear molecule can have topological domains as long as there is a region of the DNA bounded by constraints on the rotation of the DNA double helix. Eukaryotic DNAs in association with nuclear proteins acquire superhelical conformation in chromosomes.
  
  Adding a twist to the DNA (as catalyzed by an enzyme), imposes a strain. A DNA segment so strained that is closed into a circle would then contort into a figure of eight (or its topological equivalents) -- the simplest supercoil. This is the shape that a circular DNA assumes to accomodate one too many or one too few helical twists. For each additional helical twist that is accomodated, the lobes will show one more roation about their axis. Such superhelicity results in more compact structures. In any other naturally found geometry, the DNA is either under- or overwound. Its helical axis does not lie in a plane or on the surface of a sphere because of writhing and twisting of it. This is the physical solution to the potential (torsional) energy minimization problem. Supercoiling can therefore be :
  • negative (right-handed): Supercoils formed by deficit in link are called negative supercoils. They result from underwinding, unwinding or subtractive twisting of the DNA helix (due to a deficit in link). The two lobes of the figure of eight then appear rotated counterclockwise with respect to each other. All naturally occuring double stranded DNAs are negatively supercoiled. Negative supercoiling facilitates DNA-strand separation during replication, recombination and transcription. All the naturally occuring double stranded DNAs are negatively supercoiled (including bacterial and viral circular duplex DNAs).
  • positive (left-handed): Supercoils formed by an increase in link are called positive supercoils. They result from tighter winding or overwinding of the DNA helix (due to an increase in link) resulting in extra helical twists. The two lobes of the figure of eight then appear rotated clockwise with respect to each other. This would compact DNA as effectively as negative supercoiling, but would make strand separation much more difficult.
  • In non-dividing eukaryotic cells, chromosomal DNA is wrapped around a nucleosome core which consists of highly basic proteins called histones. The DNA is wrapped around the nucleosome in a left-handed solenoidal arrangement. This negative supercoiling is one of the forms taken up by underwound DNA.
    
    
• Relaxed: Circular DNA without any superhelical twist is known as a relaxed molecule. DNA in its relaxed (ideal) state usually assumes the B configuration. In a relaxed double-helical segment of DNA, the two strands twist around the helical axis once every 10.6 base pairs of sequence. Relaxed, closed circular DNA, is defined as DNA which has no supercoils when constrained to lie flat in a plan. The following structures are consistent with the relaxed state: (a) Linear DNA (either straight or curved) (b) Closed circular DNA, provided its axis lies in a plane or on the surface of a sphere

Supercoiling is thus vital to two major functions. It helps pack large circular rings of DNA into a small space by making the rings highly compact. It also helps in the unwinding of DNA required for its replication and transcription. Supercoiled DNA is thus the biological active form. The normal biological functioning of DNA occurs only if it is in the proper topological state.

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