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3D Structures of Biological Macromolecules Part 2: Nucleic Acids

3D Structures of Biological Macromolecules Part 2: Nucleic Acids. Jürgen Sühnel jsuehnel@fli-leibniz.de. Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena Centre for Bioinformatics Jena / Germany. Supplementary Material: www.fli-leibniz.de/www_bioc/3D/. Molecules of Life.

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3D Structures of Biological Macromolecules Part 2: Nucleic Acids

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  1. 3D Structures of Biological Macromolecules Part 2: Nucleic Acids Jürgen Sühnel jsuehnel@fli-leibniz.de Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena Centre for Bioinformatics Jena / Germany Supplementary Material: www.fli-leibniz.de/www_bioc/3D/

  2. Molecules of Life

  3. Nucleic Acids DNA genomic information (nucleosomes, chromatin) RNA messenger RNA, ribosomal RNA, transfer RNA, ribozymes, small RNAs, noncoding RNAs, RNAi (gene silencing), aptamers (alternatives to antibodies) PNA peptide nucleic acids mimic nucleic acids

  4. New Roles for RNA

  5. New Roles for RNA Couzin J. Breakthrough of the year. Small RNAs make big splash.Science.2002, 298, 2296-2297.

  6. From Gene to Protein

  7. History

  8. History

  9. Nucleic Acid Structure

  10. Nucleobases

  11. Chain Direction in Nucleic Acids /web.siumed.edu/~bbartholomew/course_material/nucleic_acids.html; no longer active)

  12. Chain Direction in Nucleic Acids

  13. Nucleic Acid Backbone

  14. Nucleic Acid Backbone Torsion Angles

  15. Ribonucleotides and Deoxyribonucleotides

  16. Nucleic Acid Base Pairs The ten possible purine-pyrimidine base pairs. Source: Ignacio Tinoco, Jr. in Gesteland, R. F. and Atkins, J. F. (1993) THE RNA WORLD. Cold Spring Harbor Laboratory Press.

  17. Nucleic Acid Base Pairs The seven possible homo-purine base pairs. Source: Ignacio Tinoco, Jr. in Gesteland, R. F. and Atkins, J. F. (1993) THE RNA WORLD. Cold Spring Harbor Laboratory Press.

  18. Nucleic Acid Base Pairs The four possible hetereo-purine base pairs. Source: Ignacio Tinoco, Jr. in Gesteland, R. F. and Atkins, J. F. (1993) THE RNA WORLD. Cold Spring Harbor Laboratory Press.

  19. Nucleic Acid Base Pairs The seven possible pyrimidine-pyrimidine base pairs.

  20. DNA Hydration www.lsbu.ac.uk/water/nucleic.html

  21. Nucleic Acid Base Pairs – Water-mediated Pairs

  22. Nucleic Acid Base Pairs – Water-mediated Pairs

  23. Nucleic Acid Base Pairs – Water-mediated Pairs

  24. Nucleic Acid Base Pairs with C-H…O/N Interactions

  25. Nucleic Acid Base Pairs with C-H…O/N Interactions

  26. Non-Canonical Base Pair Database http://prion.bchs.uh.edu/bp_type/

  27. Selected Base Triples

  28. Base Triples in tRNA Base triads in the crystal structure of yeast phenylalanine transfer RNA (PDB code: 4tna).

  29. Base Tetrads in a DNA Tetraplex Parallel-stranded DNA tetraplex formed from the Tetrahymena telomeric sequence d(TTGGGGT) solved by NMR spectroscopy (PDB code: 139d). The structure contains four stacked G-tetrads in the center and additional T-tetrads.

  30. Base Polyads

  31. Base Polyads Base triads and a heptad in the crystal structure of a pseudoknot from beet western yellow virus (BWYV) involved in frameshifting (PDB code: 437d). The heptad is formed from two triads linked by A25.

  32. HBexplore – H-bond Analysis in Proteins and Nucleic Acids www.imb-jena.de/www_bioc/hbx/hbx.html

  33. Geometrical Parameters for Base Pairs in Nucleic Acids ndbserver.rutgers.edu/archives/report/tsukuba_sup/bp_step_hel.html

  34. Nucleic Acid Structure

  35. Nucleic Acid Structure – Sugar Conformation

  36. Nucleic Acid Structure – Sugar Conformation

  37. Nucleic Acid Structure – Sugar Conformation

  38. Nucleic Acid Structure P:         P is the pitch of the helix corresponding to the distance between a base and the base obtained after walking along the DNA one full turn of 360°. n:         n is the number on nucleotides within one pitch. h:         distance between base planes. online-media.uni-marburg.de/chemie/bioorganic/vorlesung1/kapitel1e.html?/chemie/bioorganic/vorlesung1/k1e-20.html

  39. DNA Conformations A B Z www.rcsb.org/pdb/molecules/pdb23_3.html

  40. Ideal DNA Conformations and a Real B-DNA Structure

  41. Nucleic Acid Conformations • B-DNA is found at low salt concentrations. It is believed to be the native conformation occurring in chromatin. • In the cell nucleus DNA is complexed with about an equivalent mass of protein to form a structure • known as chromatin. Chromatin is a periodic structure made up of repeating, regularly spaced • subunits, the subunit being the nucleosome. Within the nucleosomes the major part of DNA is • wrapped around histones. The remaining DNA joining each nucleosome is known as linker DNA. • A-DNA In solutions with higher salt concentrations or with alcohol added A-DNA is found. • Z-DNA occurs for alternating poly(dG-dC) sequences in solutions with high salt concentrations or alcohol. • RNA occurs (contrary to DNA) almost exclusively in the A-conformation (or in a related A'-form). • There are further nucleic acid conformations like C-DNA, H-DNA or others which are not discussed • here. • Geometrical features: • The distance between two subsequent base pairs along the helical axis is called helical rise (h). • The pitch (p) is the length of the helix axis for one complete helix turn. • The turn angle per nucleotide or twist angle (t) is given by 360° / number of nucleotides per turn. • C2'-endo and C3'-endo are descriptions of sugar conformations. • The most frequently occurring nucleic acid model conformations are characterized by the following geometrical • parameters : • A-DNA • right-handed helix; sugar pucker: C3'-endo; number of nucleotides per pitch: 11; h: 2.56 Å; t: +32.7°. • B-DNA • right-handed helix; sugar pucker: C2'-endo; number of nucleotides per pitch: 10; h: 3.38 Å; t: +36° . • Z-DNA • left-handed helix; G: syn conformation; sugar pucker: C3'-endo; C: anti conformation, sugar pucker: C2' • endo; number of nucleotides per pitch: 6x2; h: 3.7x2 Å; t= -30°x2 (for Z-DNA the repeat unit is the dimer • (G-C)2.

  42. Nucleic Acid Conformations

  43. Nucleic Acid Conformations - B-DNA

  44. Nucleic Acid Conformations - B-DNA

  45. Nucleic Acid Conformations – B-DNA

  46. Nucleic Acid Conformations – B-DNA

  47. First Single-crystal DNA Structure (B-DNA) Drew-Dickerson structure H. R. Drew, R. M. Wing, T. Takano, C. Broka, S. Tanaka, K. Itakura, R. E. Dickerson Structure Of A B-/DNA Dodecamer. Conformation And Dynamics Proc. Nat. Acad. Sci. Usa V. 78 2179 1981

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