A- and B- forms of DNA. Structure of RNA

Task 1

A-, B-, and Z-forms of DNA were constructed using 3DNA software.

The following programs were used to build the models:

A-DNA: fiber -seq="GATCGATCGATCGATCGATC" -a gatc-a.pdb

fiber -seq="GATCGATCGATCGATCGATC" -b gatc-b.pdb

fiber -z gatc-z.pdb Number of repeats=25

links to the resulting structures

A-DNA B-DNA Z-DNA

Task 2

For this exercise, I chose T27 in the B-DNA. Atoms directed toward the small groove are highlighted in blue, and atoms directed toward the large groove are highlighted in red

Sorry! — Orientation of atoms in the thymine molecule in B-DNA

Atoms that are oriented toward the large groove:[DT]27:B.7, [DT]27:B.O4

Atoms that are oriented toward the small groove:[DT]27:B.N1, [DT]27:B.O2

	A-DNA	B-DNA	Z-DNA
Helix type	right-handed	right-handed	left-handed
Helix pitch, Å	28,03	33,75	42,81
Number of bases per turn	11	10	12
Width of the large groove, Å	16,81 [DC]12:A.P - [DT]31:B.P	17,21 [DG]13:A.P-[DA]30:B.P	14,73 [DC}12:A.P-[DC]90:B.P
Width of the small groove, Å	9,48[DT]7:A.P-[DG]29:B.P	11,69 [DT]31:B.P-[DA]14:A.P	7,20 [DG]9:A.P-[DG]95:B.P

Task 3

Coordinates of tRNA stems:

	Strand 1	Strand 2
2-7	66-71
49-53	61-65
37-44	26-33
10-12	23-25

Non-canonical base pairs:

55U-18G

38U-32U

44C-26A

13A-45A

14A-21A

19G-56C is additional hydrogen bond that maintains the tertiary structure of tRNA