Influence of packing interactions on the average conformation of B-DNA in crystalline structures

• Published in: Acta crystallographica. Section D, Biological crystallography. Biological crystallography., 1999-04, Vol.55 (4), p.810-819
• Main Authors: Tereshko, V., Subirana, J. A.
• Format: Article
• Language: English
• Subjects: B-DNA; Crystallography, X-Ray; DNA - chemistry; Nucleic Acid Conformation; nucleic acids; Oligodeoxyribonucleotides - chemistry; Oligonucleotides; Packing interactions; Thermodynamics
• ISSN: 1399-0047; 0907-4449; 1399-0047
• DOI: 10.1107/S0907444999000591

The molecular interactions in crystals of oligonucleotides in the B form have been analysed and in particular the end‐to‐end interactions. Phosphate–phosphate interactions in dodecamers are also reviewed. A strong influence of packing constraints on the average conformation of the double helix is found. There is a strong relationship between the space group, the end‐to‐end interactions and the average conformation of DNA. Dodecamers must have a B‐form average conformation with 10 ± 0.1 base pairs per turn in order to crystallize in the P212121 and related space groups usually found. Decamers show a wider range of conformational variation, with 9.7–10.6 base pairs per turn, depending on the terminal sequence and the space group. The influence of the space group in decamers is quite striking and remains unexplained. Only small variations are allowed in each case. Thus, crystal packing is strongly related to the average DNA conformation in the crystals and deviations from the average are rather limited. The constraints imposed by the crystal lattice explain why the average twist of the DNA in solution (10.6 base pairs per turn) is seldom found in oligonucleotides crystallized in the B form.