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- Task 1: There were build A- B- and Z- DNA forms by using 3DNA fiber programm, results converted in pdb format are presented below:
- gatc-a.pdb
- gatc-b.pdb
- gatc-z.pdb
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- Task 2.1: On the following pictures is presented thymine from B-DNA form, taken from the first task. Atoms turned to the minor groove marked blue, to the major - red.
Example (atom nubmers from pdb file are presented in brackets):
- Atoms N1(219) N2(222) and C3(220) are turned to the side of the minor groove.
- Atoms C4(223) C5(225) and C6(227) are turned to the side of the major groove.
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- Task 2.2: In the following table are presented main parameters of different DNA forms:
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A-form |
B-form |
Z-form |
| Spiral type |
right-spinned |
right-spinned |
left-spinned |
| Spiral step (angstrom) |
28,03 |
33,75 |
43,5 |
| Bases per one loop |
11 |
10 |
12 |
| Major groove width |
16,81 11:a.p - 32:b.p |
17,21 7:a.p - 31:b.p |
16,08 17:a.p - 26:b.p |
| Minor groove width |
7,98 8:a.p - 27:b.p |
11,69 15:a.p - 30:b.p |
7,2 11:a.p - 33:b.p |
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- Task 3.1: Torsion angles of given tRNA (1gtr) and DNA (1rh6) molecules were calculated using 3DNA packet.
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- Comparing of average values of provided tRNA with different DNA forms revealed its similarity to A-DNA.
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- Greatest deviations in torsion angles values for tRNA were observed in folowing nucleotides:
- Strand 1: 4G, 8G, 10G, 14A, 18C, 25A - one angle; 6A, 22G - two angles
- Strand 2: 12A, 15U, 25A, 26A - one angle
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- Greatest deviations in torsion angles values for DNA were observed in folowing nucleotides:
- Strand 1: 4G, 6A, 10T, 12T - one angle; 7G - three angles
- Strand 2: 3A, 7C, 9G - one angle; 2T - four angles
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- All the calculated values are presented in the file below:
- Torsion angles
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- Task 3.2: On the following picture information about tRNA structure is presented:
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- Non-Watson-Crick base pairs observed: U-G (55-18), U-U (38-32), C-A (44-26), A-A (13-45, 14-21)
- Non-stem base interactions in tRNA: G-C (19-56)
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