Journal:Acta Cryst D:S2059798318000050
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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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