Structure of DNA

References (Part #2)

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DNA is a double stranded molecule composed of two polarized strands (of deoxyribonucleotide polymers) which run in opposite directions (termed antiparallel) and wind around a central, common axis -- one is entwined about the other such that an overall helical shape results (known as a plectonemic helix). Both are wound in a right-handed manner. This structure is to be contrasted with a paranemic helix, in which a pair of coils lie side by side without interwinding. The strands are occasionally distinguished as the Watson strand and the Crick strand.

In the case of the molecular structure of eukaryotic chromosomes in each human cel, 2 meztres of DNA is packaged into the cell nucleus. To access the information, it must be unwound as a double helix and needs to be "spread out" in the nucleus. However during cell division (mitosis), in order to move them around, they are packaged as follows into dense bundles:

• Nucleosome formation ("beads on a string"): 2.5 loops of DNA wrapped around core DNA
• Solenoid Formation "beaded string is coiled"): 6 nucleosomes per solenoid coil
• Supercoiling (coil of solenoids is itself coiled): coiled coil is then folded - as in mitotic chromosome, namely a 10,000 fold reduction in length

Each nucleotide base of one strand is paired with a nucleotide base on the other strand to create a stable structure of the two polymers. The pairing of the four types of bases (A, T, C, G) by hydrogen bonds is not random: an A pairs with a T and a G pairs with a C. The bases on the outside of the helix are exposed to solvent within two grooves along the helix, the "major groove" and the "minor groove". It is within these grooves that DNA interacts with other molecules. The three structural variation of these grooves ("A", "B" and "Z" DNA), which differ in the relationship between the bases and the helical axis, offer one mechanism by which reactivity of DNA is modulated:

• B-DNA : Fully hydrated DNA, the most common encountered in vivo. Owing to the location of the helical axis in the center of the base pairs, the edges of the base pairs are about equally deep in the interior.
• A-DNA : When B-DNA is dehydrated, there is a reversible structural change to A-DNA
• Z-DNA : Unlike B-DNA and A-DNA, Z-DNA is a left-handed helix. The conformational change from B-DNA to Z-DNA is one mechanism for relief of the torsional strain found in B-DNA in vivo, and may serve as a switch mechanism to regulate gene expression.

In circular double helix DNA (closed circular ccDNA), both strands are covalently joined to form a circular duplex molecule. The geometry of such an assembly is such that its number of coils cannot be changed without first breaking one of its strands. This topological "dilemma" is resolved within the cell -- to ensure proper biological functioning -- by specialized enzymes that unknot, untwist and unwind the DNA to enable replication and then reform the compact mode thereafter.

Heptad repeats: The coiled coil is a ubiquitous protein-folding motif. The accepted hallmark of the coiled coil is the seven-residue heptad repeat..A coiled-coil protein consists of two identical strands of amino acid sequences that wrap around each other. The amino acids in a coiled-coil structure reside on seven different structural positions on the coil, forming a heptad repeat (see The Heptad Repeat of The Coiled-coil Structure). Heptad repeats are characteristic of certain proteins. (see also images of David Gossard. Coiled Coils. 2003). Most coiled-coil sequences contain heptad repeats, namely seven residue patterns -- denoted abcdefg -- in which the a and d residues (core positions) are generally hydrophobic. As there are 3.6 residues to each turn of the alpha-helix, these a and d residues form a hydrophobic seam, which, as each heptad is slightly under two turns, slowly twists around the helix. The coiled-coil is formed by component helices coming together to bury their hydrophobic seams. As the hydrophobic seams twist around each helix, so the helices also twist to coil around each other, burying the hydrophobic seams and forming a supercoil. It is the characteristic interdigitation of side chains between neighbouring helices, known as knobs-into-holes packing, that defines the structure as a coiled coil (see Jenny Shipway. An Introduction to Coiled Coils. 2000) [more | more].

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