A-form, B-form of DNA. RNA structure

Task 1

Used programms: Terminal

The task was to use fiber command in 3DNA pack. Results are in .pdb files, presented below:

Download gatc-a.pdb , gatc-b.pdb , gatc-z.pdb files ↓

Task 2

Used programms: Jmol, Marvin Sketch

The first exercise was about selecting one of the nucleobases in B-form DNA structure (gatc-b.pdb file was used) and coloring its atoms depending on at which groove a particular atom points out (red color is for major groove, blue is for minor).

Figure 1.Marvin Sketch guanine.

	Major groove	Minor groove
C	C5, C6, C8	C2, C4
N	N1, N7	N2, N3, N9
O	O6	-

Table 1. Atom data.

In the second exercise I measured some DNA characteristics, using Jmol, and wrote them down in the table, presented below.

	A-form	B-form	Z-form
Helical rotation (left/right)	Right	Right	Left
Pitch/helical turn (Å)	28.03	33.75	43.5
Bp/turn	11	10+	12
Major groove width (Å)	16.81 \| Distance [DT]31:B.P #618 - [DC]12:A.P #228	17.21 \| Distance [DT]27:B.P #536 - [DA]10:A.P #187	22.91 \| Distance [DC]2:A.P #23 - [DG]23:B.P #452
Minor groove width (Å)	7.98 \| Distance [DT]3:A.P #44 - [DC]32:B.P #638	11.69 \| Distance [DC]12:A.P #228 - [DG]33:B.P #657	9.87 \| Distance [DC]10:A.P #187 - [DG]23:B.P #452

Table 2. A-, B-, Z-form DNA structural parameters.

Task 3

Part 1. Torsion angles (tRNA, DNA)

Used programms: Terminal, 3DNA pack, Excel

Table 3. tRNA strand I data

Base	α	β	γ	δ	ε	ζ	χ
2 C	-79,60	173,00	92,50	84,40	-112,00	-102,10	-171,40
3 C	-79,00	151,20	56,40	75,60	-114,00	-95,60	-149,10
4 G	-79,20	149,00	74,40	90,40	-168,90	-64,20	-152,60
5 A	-88,60	-160,90	66,20	77,30	-165,10	-65,00	-143,20
6 G	-68,60	178,60	63,60	85,60	179,00	-46,60	-162,60
7 G	-120,10	-142,60	63,20	76,80	40,50	175,30	-137,60
8 C	24,20	-138,10	40,20	86,90	-134,90	-97,00	-159,10
9 G	-29,00	152,90	23,00	76,50	-133,50	-80,10	-152,40
10 C	-77,70	137,10	92,40	77,00	-141,00	-71,10	-167,80
11 G	-95,60	-137,20	44,70	74,90	-139,50	-83,30	-147,60
12 G	-63,60	165,90	55,20	80,20	-148,20	-110,40	-159,70
13 U	-70,80	-166,90	37,30	73,00	-149,50	-72,60	-158,80
14 C	-21,70	173,60	37,40	84,80	-131,00	-84,70	-149,70
15 G	-38,20	149,80	32,90	72,20	-155,30	-69,00	-162,60
16 C	-44,10	-171,90	39,10	83,90	-151,00	-71,30	-142,40
17 A	-91,60	161,20	81,70	75,10	-170,90	-71,30	-158,70
18 G	-54,10	170,20	66,60	83,50	-152,30	-115,80	-171,80
19 G	103,80	-141,80	49,20	82,00	-131,10	-113,60	161,40
20 C	-79,70	174,20	80,10	103,30	-169,30	-41,50	-173,20
21 U	-103,90	-166,30	49,20	77,70	-162,90	-62,50	-148,00
22 C	-83,20	167,90	78,40	82,10	174,70	-99,00	-160,80
23 A	-60,30	174,00	55,40	83,50	-135,60	-50,70	-173,20
24 G	-48,40	165,40	57,60	81,90	-138,70	-159,80	-161,40
25 U	-41,50	125,40	58,80	87,30	-127,90	-127,30	-157,70
26 G	-112,50	-107,90	120,30	78,00	-90,00	-150,30	-140,20
27 G	-57,70	127,50	62,30	84,10	137,40	-72,60	-128,60
28 A	-126,80	159,40	119,40	93,70	-171,50	-52,00	-143,80
29 U	-31,80	138,90	59,90	85,80	-174,70	-11,60	175,00
Average:	-61,40	59,34	62,76	82,05	-104,90	-73,78	-132,06

Table 4. tRNA strand II data

#	Base	α	β	γ	δ	ε	ζ	χ
1	C	-96,00	-159,10	87,20	93,60	-80,00	89,60	-160,30
2	G	-94,10	-170,30	62,70	79,90	-160,20	-71,10	-158,50
3	G	-89,00	-161,10	54,00	87,50	-146,90	-76,80	-167,40
4	C	-3,60	159,20	42,60	84,00	-165,30	-73,70	-139,50
5	U	-89,70	-161,40	51,40	74,50	-150,30	-95,60	-166,90
6	C	-2,60	144,20	17,30	79,20	-146,60	-71,00	-164,80
7	C	-37,80	-172,00	38,90	77,30	-147,50	-103,60	-168,20
8	G	-70,40	165,10	55,60	73,60	-158,00	-69,50	-169,30
9	C	-64,80	161,00	51,80	77,00	-139,20	-78,50	-164,90
10	G	-87,60	-142,30	70,20	86,80	-151,10	-83,20	-147,70
11	C	-83,20	163,90	58,00	76,90	-163,20	-76,70	-173,10
12	C	-145,40	-131,80	68,90	81,40	-159,50	-67,70	-113,10
13	A	-80,90	-147,50	50,00	78,40	-157,70	-59,90	-146,90
14	G	-87,10	173,00	58,80	79,10	-153,60	-73,10	-179,90
15	C	-82,70	177,20	67,20	87,20	-145,00	-84,40	-169,20
16	G	-55,90	163,70	55,60	84,80	-147,50	-76,00	-175,70
17	U	-65,20	-157,70	51,70	77,00	-147,80	-84,30	-170,20
18	A	-57,50	143,50	57,40	70,00	-158,40	-67,30	173,00
19	C	-41,70	137,50	72,80	74,50	-124,70	-76,50	-176,00
20	G	-69,30	-171,40	38,00	77,10	-125,00	-80,00	-157,10
21	A	-78,00	163,00	49,20	74,00	-166,40	-67,40	-151,50
22	G	-76,40	112,60	136,20	87,40	-128,80	-79,00	-169,20
23	U	-44,30	145,60	43,70	80,60	-93,80	-137,00	-152,60
24	C	-18,80	-163,80	127,20	88,80	172,30	-163,00	-170,10
25	U	69,10	164,50	64,20	85,50	-164,40	-61,30	-171,30
26	U	-76,20	179,70	55,80	76,30	-135,60	-31,70	-144,40
27	C	162,70	122,90	84,50	110,60	-131,40	-87,70	177,70
28	C	-142,20	121,70	122,10	67,50	-140,10	-96,80	-176,50
29	A	-88,50	-176,60	44,10	82,90	56,20	89,70	-93,40
	Average:	-58,52068966	23,56206897	63,34827586	81,15172414	-126,1896552	-69,43103448	-136,1034483

Table 5. DNA strand I data

#	Base	α	β	γ	δ	ε	ζ	χ
1	A	-53,00	-176,70	46,00	141,00	174,70	-97,60	-94,70
2	T	-47,70	-175,40	31,20	140,40	-158,50	-163,50	-86,20
3	C	-27,50	137,70	29,20	132,20	177,20	-97,90	-104,50
4	T	-60,90	-169,40	46,60	133,30	-172,30	-135,20	-114,00
5	G	56,40	-172,00	-72,40	169,90	143,70	-115,80	-125,70
6	G	-169,20	-92,80	120,20	114,60	-177,90	-95,70	-125,90
7	T	-56,00	-162,30	39,30	131,80	177,40	-96,90	-116,00
8	C	-53,60	-176,40	39,20	123,90	-160,30	-110,40	-126,60
9	C	26,40	-153,10	-59,90	147,80	-154,10	-92,10	-118,60
10	G	-52,60	160,20	43,00	140,20	-164,80	-147,40	-93,30
11	A	-32,70	153,40	34,90	130,00	-172,60	-103,60	-118,00
12	C	-50,00	171,40	48,10	136,00	-170,90	-115,60	-112,80
13	C	-59,60	-163,00	32,40	125,40	126,80	-34,10	-119,20
14	A	-121,00	-135,50	55,70	147,00	-128,70	173,70	-101,00
15	G	99,20	-142,90	-170,10	142,70	-165,70	-78,60	-148,70
16	A	-70,50	-167,10	41,50	134,00	-171,80	-99,50	-108,40
17	T	-47,40	169,30	39,30	137,20	-170,30	-151,10	-100,00
	Average:	-42,34	-64,39	20,25	136,91	-68,71	-91,84	-112,56

Table 6. DNA strand II data

#	Base	α	β	γ	δ	ε	ζ	χ
1	T	-65,30	-177,00	42,10	117,40	0,00	0,00	-93,40
2	A	-63,50	-175,70	45,50	137,00	-168,10	-106,30	-109,10
3	G	-61,40	152,90	59,90	140,60	-169,70	-98,10	-134,70
4	A	-78,40	-169,10	48,00	140,20	-159,40	-150,10	-112,60
5	C	-52,10	162,10	57,10	139,50	-174,00	-93,30	-131,10
6	C	-65,30	179,50	45,50	138,00	-169,10	-140,80	-117,70
7	A	-59,00	161,10	40,90	141,10	-175,40	-89,70	-113,60
8	G	-52,20	109,90	30,00	147,60	-137,90	166,00	-51,80
9	G	-72,90	174,30	51,20	151,20	-79,70	-176,30	-90,40
10	C	34,30	-167,90	-58,50	145,80	-157,70	-85,20	-131,10
11	T	-54,80	-175,00	45,80	133,90	-169,50	-123,90	-117,20
12	G	-78,70	-162,30	51,40	136,60	177,40	-101,80	-117,80
13	G	-42,90	168,00	61,60	149,20	179,50	-97,50	-127,70
14	T	-60,70	-170,50	36,70	126,30	176,20	-106,20	-124,50
15	C	-51,30	159,00	35,30	126,70	-175,60	-89,80	-118,50
16	T	-34,30	149,70	40,20	120,20	-161,90	-139,00	-93,20
17	A	168,20	-138,80	92,00	125,60	-165,10	-109,80	-107,40
	Average:	-40,61	4,72	42,63	136,29	-90,00	-90,69	-111,28

Deformations

tRNA: 12C (α), 22G (γ)
DNA: 6G (α), 15G (β)

Comparison

Comparing with torsion angles, A-, B-, Z-forms of DNA, I must say that tRNA in some angles is close to A-form and DNA is close to B-form.

Part 2. H-bonds. tRNA structure

Used programms: Terminal, 3DNA pack

tRNA stems

    Acceptor stem
 1   (0.023) ....>C:...1_:[..G]G-----C[..C]:..72_:C<.... (0.006)     |
 2   (0.005) ....>C:...2_:[..C]C-----G[..G]:..71_:C<.... (0.017)     |
 3   (0.016) ....>C:...3_:[..C]C-----G[..G]:..70_:C<.... (0.016)     |
 4   (0.025) ....>C:...4_:[..G]G-----C[..C]:..69_:C<.... (0.013)     |
 5   (0.015) ....>C:...5_:[..A]A-----U[..U]:..68_:C<.... (0.017)     |
 6   (0.015) ....>C:...6_:[..G]G-----C[..C]:..67_:C<.... (0.012)     |
 7   (0.014) ....>C:...7_:[..G]G-----C[..C]:..66_:C<.... (0.013)     |
     
    T-stem
 8   (0.006) ....>C:..49_:[..C]C-----G[..G]:..65_:C<.... (0.011)     |
 9   (0.016) ....>C:..50_:[..G]G-----C[..C]:..64_:C<.... (0.014)     |
10   (0.015) ....>C:..51_:[..C]C-----G[..G]:..63_:C<.... (0.019)     |
11   (0.011) ....>C:..52_:[..G]G-----C[..C]:..62_:C<.... (0.017)     |
12   (0.015) ....>C:..53_:[..G]G-----C[..C]:..61_:C<.... (0.013)     x
    
    Anticodon stem
13   (0.014) ....>C:..39_:[..U]U-----A[..A]:..31_:C<.... (0.024)     |
14   (0.010) ....>C:..40_:[..C]C-----G[..G]:..30_:C<.... (0.024)     |
15   (0.020) ....>C:..41_:[..G]G-----C[..C]:..29_:C<.... (0.006)     |
16   (0.017) ....>C:..42_:[..C]C-----G[..G]:..28_:C<.... (0.012)     |
17   (0.014) ....>C:..43_:[..A]A-----U[..U]:..27_:C<.... (0.020)     |
    
    D-stem
19   (0.014) ....>C:..10_:[..G]G-----C[..C]:..25_:C<.... (0.015)     |
20   (0.012) ....>C:..11_:[..C]C-----G[..G]:..24_:C<.... (0.025)     |
21   (0.013) ....>C:..12_:[..U]U-----A[..A]:..23_:C<.... (0.015)     |
22   (0.010) ....>C:..13_:[..C]C-----G[..G]:..22_:C<.... (0.019)     |
    

Stabilising h-bonds

23   (0.019) ....>C:..14_:[..A]A-**--U[..U]:...8_:C<.... (0.006)     |
24   (0.012) ....>C:..15_:[..G]G-**+-C[..C]:..48_:C<.... (0.031)     |
25   (0.011) ....>C:..16_:[..U]U-**+-U[..U]:..59_:C<.... (0.016)     x
26   (0.019) ....>C:..18_:[..G]G-**+-U[..U]:..55_:C<.... (0.009)     |
27   (0.026) ....>C:..19_:[..G]G-----C[..C]:..56_:C<.... (0.014)     x
28   (0.013) ....>C:..73_:[..A]A-**+-C[..C]:..74_:C<.... (0.017)     +
29   (0.016) ....>C:..45_:[..U]U-**--A[..A]:...9_:C<.... (0.017)     +

7 non-Watson-Crick base-pairs

18   (0.019) ....>C:..44_:[..G]G-**--A[..A]:..26_:C<.... (0.022)     |
23   (0.019) ....>C:..14_:[..A]A-**--U[..U]:...8_:C<.... (0.006)     |
24   (0.012) ....>C:..15_:[..G]G-**+-C[..C]:..48_:C<.... (0.031)     |
25   (0.011) ....>C:..16_:[..U]U-**+-U[..U]:..59_:C<.... (0.016)     x
26   (0.019) ....>C:..18_:[..G]G-**+-U[..U]:..55_:C<.... (0.009)     |
28   (0.013) ....>C:..73_:[..A]A-**+-C[..C]:..74_:C<.... (0.017)     +
29   (0.016) ....>C:..45_:[..U]U-**--A[..A]:...9_:C<.... (0.017)     +

The 23, 24, 29 bp are also non-Watson-Crick despite their "common" pairing. that is because of a different kind of interaction between them. In the Fig.2 there is an exapmle of such pair:

Figure 2. Non-canonical GC pairing

Back to term 3 page 🚶