DNA is a structurally plastic molecule, and its biological function is enabled by adaptation to its binding partners. To identify the DNA structural polymorphisms that are possible in such adaptations, the dinucleotide structures of 60 000 DNA steps from sequentially nonredundant crystal structures were classified and an automated protocol assigning 44 distinct structural (conformational) classes called NtC (for Nucleotide Conformers) was developed. To further facilitate understanding of the DNA structure, the NtC were assembled into the DNA structural alphabet CANA (Conformational Alphabet of Nucleic Acids) and the projection of CANA onto the graphical representation of the molecular structure was proposed. The NtC classification was used to define a validation score called confal, which quantifies the conformity between an analyzed structure and the geometries of NtC. NtC and CANA assignment were applied to analyze the structural properties of typical DNA structures such as Dickerson-Drew dodecamers, guanine quadruplexes and structural models based on fibre diffraction. NtC, CANA and confal assignment, which is accessible at the website https://dnatco.org, allows the quantitative assessment and validation of DNA structures and their subsequent analysis by means of pseudo-sequence alignment. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:Acta_Cryst_D:2.

Institute of Biotechnology of the Czech Academy of Sciences BIOCEV Průmyslová 595 CZ 252 50 Vestec Czechia

Laboratory of Informatics and Chemistry Faculty of Chemical Technology University of Chemistry and Technology Prague Technická 5 CZ 166 28 Prague Czechia

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Adhireksan, Z., Davey, G. E., Campomanes, P., Groessl, M., Clavel, C. M., Yu, H., Nazarov, A. A., Yeo, C. H., Ang, W. H., Dröge, P., Rothlisberger, U., Dyson, P. J. & Davey, C. A. (2014). PubMed PMC

Ahlrichs, R., Bär, M., Häser, M., Horn, H. & Kölmel, C. (1989).

Ala-Kokko, L., Kontusaari, S., Baldwin, C. T., Kuivaniemi, H. & Prockop, D. J. (1989). PubMed PMC

Altona, C. & Sundaralingam, M. (1972). PubMed

Aymami, J., Coll, M., van der Marel, G. A., van Boom, J. H., Wang, A. H.-J. & Rich, A. (1990). PubMed PMC

Aymami, J., Nunn, C. M. & Neidle, S. (1999). PubMed PMC

Barabas, O., Ronning, D. R., Guynet, C., Hickman, A. B., Ton-Hoang, B., Chandler, M. & Dyda, F. (2008). PubMed PMC

Berman, H. M., Battistuz, T. PubMed

Berman, H. M., Westbrook, J., Feng, Z., Iype, L., Schneider, B. & Zardecki, C. (2002). PubMed

Boer, R., Russi, S., Guasch, A., Lucas, M., Blanco, A. G., Perez-Luque, R., Coll, M. & de la Cruz, F. (2006). PubMed

Čech, P., Kukal, J., Černý, J., Schneider, B. & Svozil, D. (2013). PubMed PMC

Černý, J., Božíková, P. & Schneider, B. (2016). PubMed PMC

Černý, J., Kabeláč, M. & Hobza, P. (2008). PubMed

Chen, L., Cai, L., Zhang, X. & Rich, A. (1994). PubMed

Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S. & Richardson, D. C. (2010). PubMed PMC

Chen, Y. & Rice, P. A. (2003). PubMed

Chevalier, B. S., Kortemme, T., Chadsey, M. S., Baker, D., Monnat, R. J. & Stoddard, B. L. (2002). PubMed

Clark, G. R., Pytel, P. D., Squire, C. J. & Neidle, S. (2003). PubMed

Collie, G. W., Promontorio, R., Hampel, S. M., Micco, M., Neidle, S. & Parkinson, G. N. (2012). PubMed

Conner, B. N., Yoon, C., Dickerson, J. L. & Dickerson, R. E. (1984). PubMed

Davis, I. W., Leaver-Fay, A., Chen, V. B., Block, J. N., Kapral, G. J., Wang, X., Murray, L. W., Arendall, W. B., Snoeyink, J., Richardson, J. S. & Richardson, J. S. (2007). PubMed PMC

Drew, H. R., Wing, R. M., Takano, T., Broka, C., Tanaka, S., Itakura, K. & Dickerson, R. E. (1981). PubMed PMC

Eichman, B. F., Vargason, J. M., Mooers, B. H. M. & Ho, P. S. (2000). PubMed PMC

Frederick, C. A., Williams, L. D., Ughetto, G., Van der Marel, G. A., Van Boom, J. H., Rich, A. & Wang, A. H.-J. (1990). PubMed

Frouws, T. D., Duda, S. C. & Richmond, T. J. (2016). PubMed PMC

Galindo-Murillo, R., Robertson, J. C., Zgarbová, M., Šponer, J., Otyepka, M., Jurečka, P. & Cheatham, T. E. (2016). PubMed PMC

Gao, Y.-G., Robinson, H., Wijsman, E. R., van der Marel, G. A., van Boom, J. H. & Wang, A. H.-J. (1997).

Gehring, K., Leroy, J.-L. & Guéron, M. (1993). PubMed

Glas, A. F., Maul, M. J., Cryle, M., Barends, T. R., Schneider, S., Kaya, E., Schlichting, I. & Carell, T. (2009). PubMed PMC

Gleghorn, M. L., Davydova, E. K., Rothman-Denes, L. B. & Murakami, K. S. (2008). PubMed PMC

Goedecke, K., Pignot, M., Goody, R. S., Scheidig, A. J. & Weinhold, E. (2001). PubMed

Haider, S., Parkinson, G. N. & Neidle, S. (2002). PubMed

Han, H. & Hurley, L. H. (2000). PubMed

Harper, A., Brannigan, J. A., Buck, M., Hewitt, L., Lewis, R. J., Moore, M. H. & Schneider, B. (1998). PubMed

Hays, F. A., Teegarden, A., Jones, Z. J. R., Harms, M., Raup, D., Watson, J., Cavaliere, E. & Ho, P. S. (2005). PubMed PMC

Howerton, S. B., Nagpal, A. & Dean Williams, L. (2003). PubMed

Ivani, I. PubMed PMC

Johnson, S. J. & Beese, L. S. (2004). PubMed

Joosten, R. P., Womack, T., Vriend, G. & Bricogne, G. (2009). PubMed PMC

Jurečka, P., Černý, J., Hobza, P. & Salahub, D. R. (2007). PubMed

Kneale, G., Brown, T., Kennard, O. & Rabinovich, D. (1985). PubMed

Kollman, P., Keepers, J. W. & Weiner, P. (1982).

Kondo, J., Yamada, T., Hirose, C., Okamoto, I., Tanaka, Y. & Ono, A. (2014). PubMed

Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J. & Higgins, D. G. (2007). PubMed

Larsen, T. A., Kopka, M. L. & Dickerson, R. E. (1991). PubMed

Levitt, M. (1992). PubMed

Liu, Y. & West, S. C. (2004). PubMed

Lu, X.-J. & Olson, W. K. (2008). PubMed PMC

McAuley-Hecht, K. E., Leonard, G. A., Gibson, N. J., Thomson, J. B., Watson, W. P., Hunter, W. N. & Brown, T. (1994). PubMed

Mondragón, A. & Harrison, S. C. (1991). PubMed

Moore, M. H., Hunter, W. N., Langlois d’Estaintot, B. L. & Kennard, O. (1989). PubMed

Nicoludis, J. M., Miller, S. T., Jeffrey, P. D., Barrett, S. P., Rablen, P. R., Lawton, T. J. & Yatsunyk, L. A. (2012). PubMed

Parkinson, G. N., Lee, M. P. & Neidle, S. (2002). PubMed

Patikoglou, G. A., Kim, J. L., Sun, L., Yang, S.-H., Kodadek, T. & Burley, S. K. (1999). PubMed PMC

Pérez, A., Marchán, I., Svozil, D., Sponer, J., Cheatham, T. E. III, Laughton, C. A. & Orozco, M. (2007). PubMed PMC

Salomon-Ferrer, R., Case, D. A. & Walker, R. C. (2013).

Schäfer, A., Huber, C. & Ahlrichs, R. (1994).

Schellenberg, M. J., Appel, C. D., Adhikari, S., Robertson, P. D., Ramsden, D. A. & Williams, R. S. (2012). PubMed PMC

Schneider, B., Božíková, P., Čech, P., Svozil, D. & Černý, J. (2017). PubMed PMC

Silverman, A. P., Bu, W. M., Cohen, S. M. & Lippard, S. J. (2002). PubMed

Spingler, B., Whittington, D. A. & Lippard, S. J. (2001). PubMed

Sriram, M., Van der Marel, G. A., Roelen, H. L. P. F., Van Boom, J. H. & Wang, A. H.-J. (1992). PubMed

Sunami, T., Chatake, T. & Kono, H. (2017). PubMed PMC

Svozil, D., Kalina, J., Omelka, M. & Schneider, B. (2008). PubMed PMC

Swan, M. K., Johnson, R. E., Prakash, L., Prakash, S. & Aggarwal, A. K. (2009). PubMed PMC

Szulik, M. W., Pallan, P. S., Nocek, B., Voehler, M., Banerjee, S., Brooks, S., Joachimiak, A., Egli, M., Eichman, B. F. & Stone, M. P. (2015). PubMed PMC

Tao, J., Perdew, J. P., Staroverov, V. N. & Scuseria, G. E. (2003). PubMed

Temperini, C., Messori, L., Orioli, P., Di Bugno, C., Animati, F. & Ughetto, G. (2003). PubMed PMC

Thorpe, J. H., Gale, B. C., Teixeira, S. C. M. & Cardin, C. J. (2003). PubMed

Todd, A. K. & Neidle, S. (2011). PubMed PMC

Unger, R., Harel, D., Wherland, S. & Sussman, J. L. (1989). PubMed

Williams, R. S., Moncalian, G., Williams, J. S., Yamada, Y., Limbo, O., Shin, D. S., Groocock, L. M., Cahill, D., Hitomi, C., Guenther, G., Moiani, D., Carney, J. P., Russell, P. & Tainer, J. A. (2008). PubMed PMC

Wing, R. M., Pjura, P., Drew, H. R. & Dickerson, R. E. (1984). PubMed PMC

Xia, S., Wang, J. & Konigsberg, W. H. (2013). PubMed PMC

Zgarbová, M., Šponer, J., Otyepka, M., Cheatham, T. E., Galindo-Murillo, R. & Jurečka, P. (2015). PubMed

Conformation-based refinement of 18-mer DNA structures

Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks

Developing Community Resources for Nucleic Acid Structures

Structural variability of CG-rich DNA 18-mers accommodating double T-T mismatches

Structural alphabets for conformational analysis of nucleic acids available at dnatco.datmos.org

A unified dinucleotide alphabet describing both RNA and DNA structures

A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)

Enriched Conformational Sampling of DNA and Proteins with a Hybrid Hamiltonian Derived from the Protein Data Bank