Task 1

PDB-files with DNA structures:

  • gatc_a.pdb (A-form DNA)
  • gatc_b.pdb (B-form DNA)
  • gatc_z.pdb (Z-form DNA)

    • Task 2

    I chose B-form DNA. Nucleobase that was given to me is cytosine.

    Atoms facing the major groove C4,C5,C6,N4

    Atoms facing the minor groove C2,O2

    Cytosine
    A-form B-form Z-form
    Type of helix right right left
    Helix pitch (Å) 28.0 33.8 43.5
    Quantity of bases per coil 11 10 12
    Width of major groove (Å) 17 (9nt, A chain; 35nt, B chain) 17.2 (12nt, A chain; 26nt, B chain) 18.1 (6nt, A chain; 32nt, B chain)
    Width of minor groove (Å) 8 (9nt, A chain; 26nt, B chain) 11.7 (12nt, A chain; 33nt, B chain) 8.7 (13nt, A chain; 33nt, B chain)

    Task 3

    I got tRNA 1ffy

    Numbers of nucleotides that form stems in the secondary structure of a tRNA:

  • Strand I:1-7, Strand II:72-66
  • Strand I:49-55, Strand II:65-58
  • Strand I:36-44, Strand II:33-26
  • Strand I:10-13, Strand II:25-22