Cравнительный анализ канонической ДНК и стеблей тРНК
Анализ структур ДНК
PDB-файлы со сгенерированными структурами
Задание 2
Видно, что у экспериментальной структуры значения ширины могут варьироваться. Для упрощения измерения для таблицы с параметрами ДНК будут на сгенерированных структурах.
| А-форма | В-форма | Z-форма | |
| Тип спирали | Правая | Правая | Левая |
| Шаг спирали(Å) | 28.0 | 33.8 | 43.5 |
| Число оснований на виток | 11 | 10 | 12 |
| Ширина большой бороздки | 16.5 | 20.6 | 22.9 |
| Ширина малой бороздки | 9.6 | 13.2 | 9.9 |
Красным отмечены атомыб смотрящие в большую бороздку(с DA30/C8 по DA30/N6)
Синим отмечены атомы, смтрящие в малую бороздку(с DA30/C2 по DA30/C4)
Анализ структуры тРНК
Координаты стеблей
Strand I Strand II Helix
1 (0.011) ....>C:.501_:[..G]G-----C[..C]:.572_:C<.... (0.008) |
2 (0.008) ....>C:.502_:[..G]G-*---U[..U]:.571_:C<.... (0.007) |
3 (0.005) ....>C:.503_:[..C]C-----G[..G]:.570_:C<.... (0.004) |
4 (0.005) ....>C:.504_:[..C]C-----G[..G]:.569_:C<.... (0.008) |
5 (0.007) ....>C:.505_:[..C]C-----G[..G]:.568_:C<.... (0.009) |
6 (0.006) ....>C:.506_:[..C]C-----G[..G]:.567_:C<.... (0.004) |
7 (0.004) ....>C:.507_:[..A]A-----U[..U]:.566_:C<.... (0.004) |
8 (0.008) ....>C:.549_:[..G]G-----C[..C]:.565_:C<.... (0.003) |
9 (0.006) ....>C:.550_:[..G]G-----C[..C]:.564_:C<.... (0.005) |
10 (0.005) ....>C:.551_:[..G]G-----C[..C]:.563_:C<.... (0.002) |
11 (0.003) ....>C:.552_:[..G]G-----C[..C]:.562_:C<.... (0.004) |
12 (0.008) ....>C:.553_:[..G]G-----C[..C]:.561_:C<.... (0.004) |
13 (0.007) ....>C:.554_:[..U]U-**--A[..A]:.558_:C<.... (0.003) |
14 (0.009) ....>C:.555_:[..U]U-**+-G[..G]:.518_:C<.... (0.014) x
15 (0.006) ....>C:.538_:[..A]A-**--C[..C]:.532_:C<.... (0.006) |
16 (0.007) ....>C:.539_:[..G]G-----C[..C]:.531_:C<.... (0.003) |
17 (0.009) ....>C:.540_:[..G]G-----C[..C]:.530_:C<.... (0.007) |
18 (0.003) ....>C:.541_:[..C]C-----G[..G]:.529_:C<.... (0.006) |
19 (0.008) ....>C:.542_:[..C]C-----G[..G]:.528_:C<.... (0.007) |
20 (0.007) ....>C:.543_:[..G]G-----C[..C]:.527_:C<.... (0.009) |
21 (0.011) ....>C:.544_:[..A]A-**--G[..G]:.526_:C<.... (0.009) |
22 (0.012) ....>C:.510_:[..G]G-----C[..C]:.525_:C<.... (0.005) |
23 (0.005) ....>C:.511_:[..U]U-----A[..A]:.524_:C<.... (0.006) |
24 (0.005) ....>C:.512_:[..C]C-----G[..G]:.523_:C<.... (0.010) |
25 (0.007) ....>C:.513_:[..U]U-*---G[..G]:.522_:C<.... (0.013) |
26 (0.005) ....>C:.508_:[..U]U-**--A[..A]:.546_:C<.... (0.007) |
27 (0.009) ....>C:.514_:[..A]A-**--A[..A]:.521_:C<.... (0.013) |
28 (0.024) ....>C:.515_:[..G]G-**+-C[..C]:.548_:C<.... (0.013) x
29 (0.012) ....>C:.519_:[..G]G-----C[..C]:.556_:C<.... (0.003) +
Стебли тРНК
- 501-507 и 572-566
- 549-553 и 565-/561
- 538-544 и 532-526
- 510-514 и 525-521
Неканонические пары
2 G-*---U [2] O6 - N3 2.85 N1 - O2 2.91
13 U-**--A [2] O2 - N6 3.17 N3 - N7 3.19
14 U-**+-G [1] O2 - N2 2.70
15 A-**--C [1] N6 - O2 3.15
21 A-**--G [2] N6 - O6 3.10 N1 - N1 2.88
25 U-*---G [2] O2 - N1 2.65 N3 - O6 2.96
26 U-**--A [3] O3'- O2' 2.87 O2'- N3 3.22 O2 * N1 3.55
27 A-**--A [2] N6 - N3 3.03 N1 - O2' 2.74
28 G-**+-C [2] N1 - O2 3.24 N2 - N3 2.95
Дополнительные водородные связи
13 (0.007) ....>C:.554_:[..U]U-**--A[..A]:.558_:C<.... (0.003) |
14 (0.009) ....>C:.555_:[..U]U-**+-G[..G]:.518_:C<.... (0.014) x
28 (0.024) ....>C:.515_:[..G]G-**+-C[..C]:.548_:C<.... (0.013) x
29 (0.012) ....>C:.519_:[..G]G-----C[..C]:.556_:C<.... (0.003) +