Conformation-based refinement of 18-mer DNA structures

0574529 - BTÚ 2024 RIV GB eng J - Journal Article
Svoboda, Jakub - Berdár, Daniel - Kolenko, Petr - Černý, Jiří - Nováková, Zora - Pavlíček, Jiří - Schneider, Bohdan
Conformation-based refinement of 18-mer DNA structures.
Acta Crystallographica Section D-Biological Crystallography. Roč. 79, JUL 2023 (2023), s. 655-665. ISSN 1399-0047. E-ISSN 2059-7983
R&D Projects: GA MŠMT(CZ) LTAUSA18197; GA MŠMT EF16_019/0000778
Institutional support: RVO:86652036
Keywords : DNA structure * dnatco.datmos.org * structure validation * structure refinement * base pairing
OECD category: Biochemistry and molecular biology
Impact factor: 2.2, year: 2022
Method of publishing: Open access
https://scripts.iucr.org/cgi-bin/paper?S2059798323004679

Nine new crystal structures of CG-rich DNA 18-mers with the sequence 5'-GGTGGGGGC-XZ-GCCCCACC-3', which are related to the bacterial repetitive extragenic palindromes, are reported. 18-mer oligonucleotides with the central XZ dinucleotide systematically mutated to all 16 sequences show complex behavior in solution, but all ten so far successfully crystallized 18-mers crystallized as A-form duplexes. The refinement protocol benefited from the recurrent use of geometries of the dinucleotide conformer (NtC) classes as refinement restraints in regions of poor electron density. The restraints are automatically generated at the dnatco.datmos.org web service and are available for download. This NtC-driven protocol significantly helped to stabilize the structure refinement. The NtC-driven refinement protocol can be adapted to other low-resolution data such as cryo-EM maps. To test the quality of the final structural models, a novel validation method based on comparison of the electron density and conformational similarity to the NtC classes was employed.
Permanent Link: https://hdl.handle.net/11104/0345411