Journal:Acta Cryst D:S2059798318000050
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DNA is a structurally plastic molecule, and its biological function is enabled by adaptation to its binding partners. We identify the DNA structural polymorphisms by analyzing structures of short DNA stretches, dinucleotides. The reported paper describes in detail the analysis and the protocol of assigning distinct structural (conformational) classes called NtC (for Nucleotide Conformers) that describe the local DNA structure. To further facilitate understanding of the DNA structure, structurally similar NtC classes were grouped into 11 letters of a DNA “structural alphabet” called CANA (Conformational Alphabet of Nucleic Acids). Structural alphabet is a tool allowing to translate information about three-dimensional structure of a biopolymer into a linear sequence of letters of the alphabet simplifying thus the analysis of complex three dimensional object such as DNA in analysis of a sequence of symbols. | DNA is a structurally plastic molecule, and its biological function is enabled by adaptation to its binding partners. We identify the DNA structural polymorphisms by analyzing structures of short DNA stretches, dinucleotides. The reported paper describes in detail the analysis and the protocol of assigning distinct structural (conformational) classes called NtC (for Nucleotide Conformers) that describe the local DNA structure. To further facilitate understanding of the DNA structure, structurally similar NtC classes were grouped into 11 letters of a DNA “structural alphabet” called CANA (Conformational Alphabet of Nucleic Acids). Structural alphabet is a tool allowing to translate information about three-dimensional structure of a biopolymer into a linear sequence of letters of the alphabet simplifying thus the analysis of complex three dimensional object such as DNA in analysis of a sequence of symbols. | ||
| - | [[Image: AAA_BBB_BB2_40.png | + | [[Image:AAA_BBB_BB2_40.png|left|thumb|450px|Gallery of the CANA letters. Each letter is represented by 40 randomly selected structures of steps which represent one NtC class belonging to the letter in the golden set. A-like and mixed B/A conformers are drawn in pink and violet, B-like conformers in blue. The CANA letter AAA is represented by NtC AA00, BBB by BB00, and BB2 by BB07]] |
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Annotation of the structural properties of a few archetypal types of DNA structures revealed some unexpected features: | Annotation of the structural properties of a few archetypal types of DNA structures revealed some unexpected features: | ||
| - | (i) The Dickerson–Drew dodecamer (for example PDB entry <scene name='77/777977/Cv/5'>1bna</scene>), which is often considered to be a typical B-DNA duplex, is conformationally rich, with a high proportion of features mixing B and A forms. | + | (i) The Dickerson–Drew dodecamer (for example PDB entry <scene name='77/777977/Cv/5'>1bna</scene>; [[1bna]]), which is often considered to be a typical B-DNA duplex, is conformationally rich, with a high proportion of features mixing B and A forms. |
(ii) Our analysis of duplex models based on the fibre-diffraction data discloses the need for their critical evaluation before they are used for computer modeling. | (ii) Our analysis of duplex models based on the fibre-diffraction data discloses the need for their critical evaluation before they are used for computer modeling. | ||
| - | (iii) Conformational analysis of guanine quadruplexes (for example PDB entry <scene name='77/777977/Cv/8'>1jpq</scene>) demonstrates the universality of the most frequent B conformer, BB00, which builds the tetrad cores of these folded DNA in combination with more exotic conformers which have a base in syn orientation (NtC BB1S or BBS1). | + | (iii) Conformational analysis of guanine quadruplexes (for example PDB entry <scene name='77/777977/Cv/8'>1jpq</scene>; [[1jpq]]) demonstrates the universality of the most frequent B conformer, BB00, which builds the tetrad cores of these folded DNA in combination with more exotic conformers which have a base in syn orientation (NtC BB1S or BBS1). |
(iv) A Holliday junction (for example PDB entry <scene name='77/777977/Cv/12'>1dcw</scene>) is a DNA intermediate in homologous recombination. It contains four double-stranded DNA arms joined together by short links. The stems of the junctions are usually B-DNA duplexes with very few, if any, B-A and A-B conformers. The NtC class that can be associated with the junction proper is the recurrently occurring unstacked NS04. | (iv) A Holliday junction (for example PDB entry <scene name='77/777977/Cv/12'>1dcw</scene>) is a DNA intermediate in homologous recombination. It contains four double-stranded DNA arms joined together by short links. The stems of the junctions are usually B-DNA duplexes with very few, if any, B-A and A-B conformers. The NtC class that can be associated with the junction proper is the recurrently occurring unstacked NS04. | ||
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