Beyond the double helix: DNA structural diversity and the PDB

Stephen Neidle
2021 Journal of Biological Chemistry  
The determination of the double helical structure of DNA in 1953 remains the landmark event in the development of modern biological and biomedical science. This structure has also been the starting point for the determination of some 2000 DNA crystal structures in the subsequent 67 years. Their structural diversity has extended to the demonstration of sequence-dependent local structure in duplex DNA, to DNA bending in short and long sequences and in the DNA wound round the nucleosome, to
more » ... nded duplex DNAs. Beyond the double helix itself, in circumstances where DNA sequences are or can be induced to unwind from being duplex, a wide variety of topologies and forms can exist. Quadruplex structures, based on four-stranded cores of stacked G-quartets, are prevalent though not randomly distributed in the human and other genomes, and can play roles in transcription, translation and replication. Yet more complex folds can result in DNAs with extended tertiary structures and enzymatic/catalytic activity. The PDB is the depository of all these structures and the resource where structures can be critically examined and validated, as well as compared one with another in order to facilitate analysis of conformational and base morphology features. This review will briefly survey the major structural classes of DNAs and illustrate their significance, together with some examples of how the use of the PDB by for example, data mining, has illuminated DNA structural concepts.
doi:10.1016/j.jbc.2021.100553 pmid:33744292 fatcat:fkhh7heumre2xp45kugv72uwoe