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- Task 1: In this task an EMBOSS "einverted" programm was used to find inverted repeats in nucleotide structure of given tRNA (1GTR - PDB ID). Second program was RNAfold in ViennaRNA package, based on Zuker algorithm. All results are presented in the following table.
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| RNA segment |
find_pair |
einverted |
RNAfold |
| Acceptor stem |
- 5'-2-7-3'
- 5'-66-71-3'
- 6 pairs
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all 6 pairs |
all 6 pairs |
| D-stem |
- 5'-49-55-3'
- 5'-18,58,61-65-3'
- 4 pairs
|
0/4 |
3/4 |
| Anticodon stem |
- 5'-37-44-3'
- 5'-26-33-3'
- 6 pairs
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4/6 |
5/6 |
| T-stem |
- 5'-10-15-3'
- 5'-48,21,45,23-25-3'
- 6 pairs
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0/6 |
5/6 |
| Total canonical pairs |
22 |
10 |
19 |
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- 1GTR RNA secondary strucrute derived with Zuker algorithm.
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- Task 2: DNA-protein contacts are determined as close proximity of corresponding atoms in both structures. Polar contact involves nitrogen or oxygen atoms at the distance 3.5 Å or less, nonpolar contact - sulfur or phosphorus, 4.5 Å. The results are presented below.
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| DNA structure |
Polar |
Nonpolar |
Total |
| 2'-deoxyribose |
4 |
36 |
40 |
| Phosphoric acid residue |
11 |
0 |
11 |
| Major groove |
5 |
6 |
11 |
| Minor groove |
1 |
0 |
1 |
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- Defined sets:
- O - atoms in 2'-deoxyribose
- O - atoms in phosphoric acid residue
- N - atoms in nytrogen bases
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- Task 3: The result of nucplot programe usage:
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- Task 4: According to the previous picture we can conclude that ARG23 has the biggest number of contacts - 2. The most significant links are between aminoacids and nitrogen bases, our AGR23 has exactly such ones, allowing us to choose him as the most important in DNA recognition
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- There were two ARG23 observed - cpk 100, DNA - cpk 50, one arginin is too far from DNA to form connections (it is well observed on pic2), but the second one has two links:
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