The physical properties of the DNA double helix are unlike those of any other natural or synthetic polymer. The molecule's characteristic base stacking and braided architecture lend it unusual stiffness: it takes about 50 times more energy to bend a double-stranded DNA (dsDNA) molecule into a circle than to perform the same operation on single-stranded DNA (ssDNA). Moreover, the phosphates in DNA's backbone make it one of the most highly charged polymers known. The protein machinery involved in copying, transcribing and packaging DNA has adapted to exploit these unique physical properties (see article by Alberts, pages 431). For example, RNA polymerases (which synthesize RNA from a DNA template) and helicases (which unwind the double helix to provide single-stranded templates for polymerases) have evolved as motors capable of moving along torsionally constrained DNA molecules. DNA-binding proteins can use the polymer's electrostatic potential to cling to DNA while they diffuse along the molecule in search of their target sequences. Topoisomerases break and rejoin the DNA to relieve torsional strain that accumulates ahead of the replication fork. During the past ten years, direct manipulation of single molecules of DNA has expanded our understanding of the mechanical interactions between DNA and proteins, following a pattern in which basic investigations of DNA elasticity have laid the groundwork for real-time, single-molecule assays of enzyme mechanism.
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