Early NMR Study Finds Two Distinct Phosphate Environments in DNA Backbone

Shindo, Simpson and Cohen, writing in The Journal of Biological Chemistry in 1979, reported that the backbone of a repeating synthetic DNA sequence shows two chemically distinct phosphate environments rather than one uniform structure.

The researchers worked with a 145-base-pair fragment of poly(dA-dT), a synthetic polydeoxyribonucleotide made of alternating adenine and thymine building blocks. They generated this fragment by digesting a lab-made chromatin complex, built from nucleosome core histones and the synthetic DNA, with an enzyme called micrococcal nuclease. Using phosphorus nuclear magnetic resonance (NMR), a technique that detects the chemical surroundings of phosphorus atoms, they found two signals of equal strength, separated by 24 Hz, that persisted at every temperature below the point where the DNA strands separate (the melting temperature). This did not happen in longer versions of the same repeating sequence.

The authors interpreted this as evidence that the phosphate groups along the DNA backbone sit in two alternating chemical environments, hinting that the double helix's shape can vary locally depending on the underlying sequence. The study is a structural chemistry experiment on an artificial DNA construct; it does not examine biological activity, cells, tissue, or any therapeutic application, and the abstract gives no further detail beyond the NMR measurements.