Sequence-dependent persistence length of long DNA

DNA is a common model system for studying polymer physics at the single molecule level, making an accurate measurement of the DNA persistence length important for interpreting experimental data. While it well known that the bending energy at short length scales (around 100 base pairs) is a strong function of the underlying sequence, how this behavior propagates into the persistence length of the chain at long length scales remains unclear. Using a high-throughput genome mapping technique, we have obtained over 50 million measurements of the extension of human DNA segments in a 41 nm x 41 nm nanochannel. The analyzed DNA segments are between 2.5 and 393 kilobase pairs in size with % GC content ranging from 32.5% to 60%. While the fractional extension of the chain only changes by a small amount as a function of % GC content, Odijk’s theory for stretching of a wormlike chain in channel confinement implies that the underlying persistence length increases by 20% over this range. We have developed a statistical terpolymer model, which contains no adjustable parameters, that captures the experimental phenomena.