International Tables for Crystallography (2006). Vol. F, ch. 23.3, pp. 588-622   | 1 | 2 |
doi: 10.1107/97809553602060000716

Chapter 23.3. Nucleic acids

Contents

  • 23.3. Nucleic acids  (pp. 588-622) | html | pdf | chapter contents |
    • 23.3.1. Introduction  (p. 588) | html | pdf |
    • 23.3.2. Helix parameters  (pp. 588-596) | html | pdf |
      • 23.3.2.1. Backbone geometry  (p. 588) | html | pdf |
      • 23.3.2.2. Sugar ring conformations  (pp. 588-589) | html | pdf |
      • 23.3.2.3. Base pairing  (pp. 589-592) | html | pdf |
      • 23.3.2.4. Helix parameters  (pp. 592-593) | html | pdf |
      • 23.3.2.5. Syn/anti glycosyl bond geometry  (p. 596) | html | pdf |
    • 23.3.3. Comparison of A, B and Z helices  (pp. 596-602) | html | pdf |
      • 23.3.3.1. x displacement and groove depth  (pp. 596-597) | html | pdf |
      • 23.3.3.2. Glycosyl bond geometry  (p. 597) | html | pdf |
      • 23.3.3.3. Sugar ring conformations  (pp. 597-598) | html | pdf |
      • 23.3.3.4. Helical twist and rise, and propeller twist  (pp. 598-600) | html | pdf |
      • 23.3.3.5. Allowable RNA helices  (p. 600) | html | pdf |
      • 23.3.3.6. Biological applications of A, B and Z helices  (pp. 600-601) | html | pdf |
      • 23.3.3.7. `Watson–Crick' Z-DNA  (pp. 601-602) | html | pdf |
    • 23.3.4. Sequence–structure relationships in B-DNA  (pp. 602-609) | html | pdf |
      • 23.3.4.1. Sequence-dependent deformability  (pp. 603-607) | html | pdf |
        • 23.3.4.1.1. Minor groove width  (p. 603) | html | pdf |
        • 23.3.4.1.2. Helix bending  (pp. 603-607) | html | pdf |
      • 23.3.4.2. A-tract bending  (pp. 607-609) | html | pdf |
    • 23.3.5. Summary  (p. 609) | html | pdf |
    • Appendix 23.3.1. X-ray analyses of A, B and Z helices  (pp. 609-622) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 23.3.1.1. `Hot wire' painting of A-DNA by Irving Geis  (p. 589) | html | pdf |
      • Fig. 23.3.1.2. Infinite A-DNA helix  (p. 590) | html | pdf |
      • Fig. 23.3.1.3. Infinite B-DNA helix  (p. 590) | html | pdf |
      • Fig. 23.3.1.4. Infinite Z-DNA helix  (p. 591) | html | pdf |
      • Fig. 23.3.2.1. Unrolled schematic of A- or B-DNA, viewed into the minor groove  (p. 591) | html | pdf |
      • Fig. 23.3.2.2. Sugar–phosphate backbone of RNA and DNA polynucleotides  (p. 592) | html | pdf |
      • Fig. 23.3.2.3. Definition of torsion angles  (p. 592) | html | pdf |
      • Fig. 23.3.2.4. The three most common furanose ring geometries  (p. 592) | html | pdf |
      • Fig. 23.3.2.5. Potential plot of all furanose ring conformations  (p. 593) | html | pdf |
      • Fig. 23.3.2.6. Plot of observed sugar conformations in 296 nucleotides of A-DNA (crosses) and 280 of B-DNA (open circles)  (p. 594) | html | pdf |
      • Fig. 23.3.2.7. A·T and G·C base pairs with minor groove edge below and major groove edge above  (p. 594) | html | pdf |
      • Fig. 23.3.2.8. Alternative purines and pyrimidines, and possible base pairings  (p. 594) | html | pdf |
      • Fig. 23.3.2.9. Watson–Crick pairing of a purine (A or G) with a pyrimidine to its right (T or C), and Hoogsteen pairing of the same purine with a pyrimidine above it  (p. 594) | html | pdf |
      • Fig. 23.3.2.10. Definitions of local reference axes ( x , y , z ) at the first two base pairs of an n -base-pair double helix  (p. 595) | html | pdf |
      • Fig. 23.3.2.11. Local helix parameters involving rotations  (p. 595) | html | pdf |
      • Fig. 23.3.2.12. Local helix parameters involving translations  (p. 595) | html | pdf |
      • Fig. 23.3.2.13. Syn versus anti orientation about the glycosyl bond connecting sugar and base  (p. 595) | html | pdf |
      • Fig. 23.3.3.1. The A-DNA stereo pair drawing from which Fig. 23.3.1.2 was derived  (p. 596) | html | pdf |
      • Fig. 23.3.3.2. The B-DNA stereo pair drawing from which Fig. 23.3.1.3 was derived  (p. 597) | html | pdf |
      • Fig. 23.3.3.3. The Z-DNA stereo pair drawing from which Fig. 23.3.1.4 was derived  (p. 598) | html | pdf |
      • Fig. 23.3.3.4. Glycosyl conformation and chain sense  (p. 599) | html | pdf |
      • Fig. 23.3.3.5. The role of the C2′-OH in RNA helix geometry  (p. 600) | html | pdf |
      • Fig. 23.3.3.6. Interconversion of a B to a Z helix  (p. 601) | html | pdf |
      • Fig. 23.3.3.7. Z(WC)-DNA, or `Watson–Crick Z-DNA'  (p. 601) | html | pdf |
      • Fig. 23.3.4.1. Structure of C-A-A-A-G-A-A-A-A-G  (p. 602) | html | pdf |
      • Fig. 23.3.4.2. Relationship between minor groove width and propeller twist  (p. 602) | html | pdf |
      • Fig. 23.3.4.3. Structure of the 1:1 complex of netropsin with C-G-C-G-A-A-T-T-C-G-C-G  (p. 603) | html | pdf |
      • Fig. 23.3.4.4. Structure of the 2:1 complex of a di-imidazole lexitropsin with C-A-T-G-G-C-C-A-T-G  (p. 604) | html | pdf |
      • Fig. 23.3.4.5. DNA duplex (red and blue strands) looped around IHF or integration host factor  (p. 604) | html | pdf |
      • Fig. 23.3.4.6. Roll-angle plots for sequence-specific DNA–protein complexes with lacI (top) and purR (bottom)  (p. 606) | html | pdf |
      • Fig. 23.3.4.7. Bending via roll at T-A steps in TBP or the TATA-binding protein (top) and in γδ-resolvase (bottom)  (p. 606) | html | pdf |
      • Fig. 23.3.4.8. Representative base-pair steps from B-DNA single-crystal X-ray analyses  (p. 607) | html | pdf |
      • Fig. 23.3.4.9. Slide versus roll plots for six of the ten possible base-pair steps  (p. 608) | html | pdf |
    • Tables
      • Table 23.3.2.1. Average torsion-angle properties of A-, B- and Z-DNA (°)  (p. 593) | html | pdf |
      • Table 23.3.2.2. Sugar ring conformations, pseudorotation angles and torsion angle δ  (p. 593) | html | pdf |
      • Table 23.3.3.1. Comparison of structures of A, B and Z helices  (p. 599) | html | pdf |
      • Table 23.3.4.1. Sequence-dependent differential deformability in B-DNA. I. The Major Canon  (p. 605) | html | pdf |
      • Table 23.3.4.2. Sequence-dependent differential deformability in B-DNA. II. The Minor Canon  (p. 606) | html | pdf |
      • Table A23.3.1.1. X-ray analyses of A helices, DNA and RNA  (pp. 609-613) | html | pdf |
      • Table A23.3.1.2. X-ray analyses of B-DNA helices and their complexes with minor-groove-binding drug molecules  (pp. 613-619) | html | pdf |
      • Table A23.3.1.3. X-ray analyses of Z helices  (pp. 619-622) | html | pdf |