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Nucleic Acid Structure AnalysisNucleic Acid Structure Analysis

Dhananjay Bhattacharyya

Biophysics Division, Saha Institute of

Nuclear Physics, Kolkata

and

Manju Bansal

Molecular Biophysics Unit, Indian

Institute of Science, Bangalore

Nucleic Acid Backbone is Connected to Nucleic Acid Backbone is Connected to

Either of Four Different BasesEither of Four Different Bases

A

G

T

C

C3’-endo

C2’-endo

pseudorotation cycle of furanose ring in nucleosides

(Saenger, 1984)

tan P = (ττττ4 + ττττ1) – (ττττ3 + ττττ0) / 2 * ττττ2 *(sin 36o + sin 72o)

ττττI+2 = ττττmax cos (P+ i * 144o)

ττττmax = ττττ0 / cosP

Distribution of pseudorotation phase

angle (P) calculated from B-DNA

crystal structures

Torsion angles of DNA models

αααα ββββ γγγγ δδδδ εεεε ζζζζ χχχχ P

-51.7 174.8 41.7 79.0 -147.6 -75.2 -157.2 7.8

-29.9 136.4 31.1 143.4 -140.8 -160.5 -98.0 153.9

-43.3 142.2 47.8 140.6 -148.7 -149.5 -96.7 165.8

-61.9 -152.1 69.0 156.2 141.7 -100.5 -96.6 -167.5D-DNA

C-DNA

B-DNA

A-DNA

minor

groovemajor

groove

minor

groovemajor

groove

Netropsin like drugs bind in the B-DNA

narrow and deep minor groove

Actinomycin D like drugs make their place in between two

stacked base pairs by distorting the DNA double helix

DNA kinks by

90o at the dyad

location while

binding to two

subunits of

Catabolite

Activator

Protein (CAP)

TATA-box

binding

protein

transforms the

interfacing

DNA region to

A-DNA like

structure

Base Centered Parameters

• Torsion angles can not indicate structural features

• Torsion Angles are measured from dynamic backbone atoms

• Bases are more rigid and well defined in terms of thermal motion

• Axis system easily can be defined with respect to a base pair

Softwares for Calculation of Base

Pair Parameters

• NEWHELIX or FREEHELIX (Dickerson)

• NUPARM (1 & 2) (Bansal & Bhattacharyya)

• CURVES (Lavery)

• X3DNA (Olson)

• CEHS (Xiang-Jun Lu)

• CompDNA NGEOM (Zhurkin & Olson)

Standard Reference frame of a WatsonStandard Reference frame of a Watson--

Crick base pairCrick base pair

Definition and Nomenclature of Base Definition and Nomenclature of Base

Pair Doublet ParametersPair Doublet Parameters

Calculation of Base Pair Calculation of Base Pair

parameters by NUPARMparameters by NUPARM

Local Step Parameters:

Mean Local Helix Axis: Zm = Xm ×××× Ym,

where Xm = Xaxis1 + Xaxis2 and Ym = Yaxis1 + Yaxis2

M is Base Pair Center to Center Vector

Tilt : 2.0 * sin-1 ( -Zm • Y1) Roll: 2.0 * sin-1 ( Zm • X1)Twist: cos-1 (( X1 ×××× Zm) • ( X2 ×××× Zm)) Shift (Dx) M • XmSlide(Dy) M • YmRise(Dz) M • Zm

Y1

Y2

X1

X2

Base Pair parameters of DNA models

Tilt Roll Twist Shift Slide Rise Prop.

-0.05 13.15 30.04 0.06 -1.22 3.34 -10.64

-0.02 2.22 35.93 0.05 0.56 3.35 -15.14

0.43 -4.16 38.38 0.1 1.09 3.46 -11.09

0 -13.01 44.08 0 0.59 3.3 -7.97

A-DNA

B-DNA

C-DNA

D-DNA

Local Helical Parameters:

Local Helix Axis: Z* = X* ×××× Y*,

where X* = Xaxis1 - Xaxis2 and Y* = Yaxis1 - Yaxis2

M is Base Pair Center to Center Vector

Inclination : 2.0 * sin-1 ( -Z* • Y1) Tip: 2.0 * sin-1 ( Z* • X1)Twist: cos-1 (( X1 ×××× Z*) • ( X2 ×××× Z*)) X-translation (dx): M • X*Y-translation (dy): M • Y*Helical Rise(dz): M • Z*

A-DNA structural Parameters:

Roll ~ 12; Inclination ~20

Slide ~ -1.5; X-translation ~ -4.0

Rise ~ 3.2; Helical Rise ~2.63.3A

2.6A

Relation between the two frames

( ) ( ) ( ) ( ) ( ) ( )

)/(sinT

and

)/(sinR

where

RT)TRTR/cotT/)sin(

RTTRTR/cotT/)sin(

/

/

2

2

411221

411221

2

2

212

212

τ=

ρ=

−−−−−−Ω=θ

−−−−−−Ω=η

η=Inclination; θ=Tip; τ=Tilt; ρ=Roll; Ω=Twist

Base Pair step parameters of B-DNA

crystal structures (1BNA.pdb)

Tilt of Dickerson Dodecamer (1BNA.pdb)

-6

-4

-2

0

2

4

6

1 2 3 4 5 6 7 8 9 10 11

NUPARM

CURVES

X3DNA

Roll

-15

-10

-5

0

5

10

15

1 2 3 4 5 6 7 8 9 10 11

NUPARM

CURVES

X3DNA

Twist

25

30

35

40

45

1 2 3 4 5 6 7 8 9 10 11

NUPARM

CURVES

X3DNA

Slide

-1.5

-1

-0.5

0

0.5

1

1 2 3 4 5 6 7 8 9 10 11

NUPARM

CURVES

X3DNA

Base pair doublet parameters of A-DNA

structure (2ANA.pdb)

-2.5

-2

-1.5

-1

-0.5

0

0.5

1

1 2 3 4 5 6 7 NUPARM

CURVES

X3DNA

Roll of A-DNA structure (2ANA.pdb)

0

2

4

6

8

10

12

1 2 3 4 5 6 7

NUPARM

CURVES

X3DNA

Twist of 2ANA

26

31

36

41

1 2 3 4 5 6 7

NUPARM

CURVES

X3DNA

Slide

-3

-2

-1

01 2 3 4 5 6 7

NUPARM

CURVES

X3DNA

Tilt

Base pair doublet

parameters of TATA-

box DNA-TBP complex

(PDT012), calculated by

3DNA (Lu & Olson

2003)

Roll of 1CGP

-20

-10

0

10

20

30

40

50

16 18 20 22 24 26 28 30 32 34 36 38 40 42

Residue no.

Twist

20

25

30

35

40

45

16 18 20 22 24 26 28 30 32 34 36 38 40 42

Roll of TBP bound TATA box

-20

0

20

40

60

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

Nuparm

Curves

X3DNA

Twist

0

10

20

30

40

50

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

Nuparm

Curves

X3dna

Slide

-2

-1

0

1

2

3

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

Nuparm

Curves

X3dna

Tilt and Roll of

nucleosomal DNA (1M1A)

RiseSlideShift

TwistRollTilt

Distribution of base-pair step parameters in high

resolution DNA crystal structures

Red: A-DNA Green:B-DNA

Roll Variation in Crystal Structures

Roll of d(AA).d(TT) doublets

0

10

20

30

-15 -10 -5.4 -0.9 3.72 8.29 12.9

Roll

Oc

cu

rre

nc

e

Roll of d(CG).d(CG) doublets

0

10

20

30

40

-17 -10 -4.3 1.78 7.87 14 20.1

Roll

Oc

cu

rre

nc

e

Roll of d(GC).d(GC) doublets

0

5

10

15

20

-27 -21 -12 -5.4 1.15 7.68 14.2

Roll

Occu

rren

ce

Steric clash between

Purines of successive base

pairs can cause non-

parallel base pair

orientations (Calladine &

Drew 1982)

Minor Groove Width

Definition of Intra Base Pair

Parameters (IUPAC-IUB)

Definition of Intra Base Pair Definition of Intra Base Pair

Parameters (IUPACParameters (IUPAC--IUB)IUB)

Base pair parametersBase pair parameters

Buckle = 2 sin-1( Zm . Y1)

Opening = 2 sin-1( Zm . X1)

Propeller = cos-1 (( X1× Zm) . ( X

2× Zm))

Shear = -Xm . M

Stagger = Ym . M

Stretch = Zm . M

Xm = (XXXX1111 + XXXX2222) / | (XXXX1111 + XXXX2222) |

Ym = (YYYY1111 + YYYY2222) / | (YYYY1111 + YYYY2222) |

Zm = (XXXX1111 + XXXX2222) x (YYYY1111 + YYYY2222)/ | (XXXX1111 + XXXX2222) | | (YYYY1111 + YYYY2222) |

Y1

Y2 X2

X1

Base Pair Parameters of Dickerson DodecamerBuckle

-15

-10

-5

0

5

10

15

1 2 3 4 5 6 7 8 9 10 11 12

NUPARM

CURVES

X3DNA

Open Angle

-10

-5

0

5

10

15

1 2 3 4 5 6 7 8 9 10 11 12

Nuparm

Curves

X3dna

Propeller

-25

-20

-15

-10

-5

0

5

1 2 3 4 5 6 7 8 9 10 11 12Nuparm

Curves

X3dna

Stagger

-0.5

0

0.5

1

1 2 3 4 5 6 7 8 9 10 11 12

Nuparm

Curves

X3dna

Shear

-1

-0.5

0

0.5

1 2 3 4 5 6 7 8 9 10 11 12Nuparm

Curves

X3dna

Stretch

-1

0

1

2

3

4

1 2 3 4 5 6 7 8 9 10 11 12

Nuparm

Curves

X3dna

Possibility of Unusual Base

Pairing in RNA

Possibility of Unusual Base

Pairing in RNA

Unusual Basepairs Observed By Leontis (Leontis

et al., Nucl. Acids Res., 2003, 31, 3450.)

RNA structures show wide

variability of Base Pairing Types

• Some of these base pairs are significantly different from standard Watson-Crick types

• These unusual base pairs are also seen in DNA, such as in G-quadrates or triple helices

• Standard reference frame (axis system) applicable to WC type does not give meaningful results

Base Pair FinderBase Pair FinderBase Pair Finder

Took a base edge

Identify the H-bonding centers (N3G & N2G)

Look for H-bond partner through distance

calculation (N6A & N7A)

Calculate pseudo-angles (such as C6G-N3G-

N6A, N3G-N6A-N1A, N1G-N2G-N7A, N2G-

N7A-N9A in figure) for

planarity

Confirm orientation through angle calculation

Calculate E=Σi(di-3.0)2 + ½Σk(θk-π)2; i are for

two H-bond distances and k are for four pseudo

angles

Gives rise to:

6959 A:U W-W(C);

21965 G:C W-W(C) and

2786 G:U W-W(C) base pairs

G:U W:W Cis (2769)

U:U W:W Cis (360)

A:G W:W Cis (404)

A:G H:S Trans (2323)

A:U H:W Trans (1193)

A:A H:H Trans (437)

Axis System of Bases

G:C Base Pair Using W:W base edges in Cis Orientation

Buckle

0

1000

2000

3000

4000

5000

-48 -31 -13 4.83 22.6 40.4

Open

0

1000

2000

3000

4000

5000

-16 -11 -5.1 0.37 5.89 11.4 16.9

Propeller

0

1000

2000

3000

4000

5000

-42 -28 -13 1.13 15.5 29.9

Shear

0

2000

4000

6000

8000

-1.6 -1.3 -0.9 -0.6 -0.3 0.01 0.33 0.65 0.97 1.29 1.61

Stagger

0

2000

4000

6000

-2 -1.6 -1.3 -0.9 -0.5 -0.1 0.3 0.69 1.08 1.47 1.86

Stretch

0

2000

4000

6000

2.26 2.45 2.65 2.84 3.04 3.23 3.43

Distribution of Base Pair Parameters for A:U Distribution of Base Pair Parameters for A:U Distribution of Base Pair Parameters for A:U Distribution of Base Pair Parameters for A:U

HHHH----W (Trans) Base Pair (freq: 1164)W (Trans) Base Pair (freq: 1164)W (Trans) Base Pair (freq: 1164)W (Trans) Base Pair (freq: 1164)

Buckle

0

50

100

150

200

250

-71 -51 -31 -11 9.53 29.8 50

Open

0

100

200

300

-30 -21 -11 -1.9 7.63 17.1 26.6

Propeller

050

100150200250

-45 -32 -19 -5.3 7.97 21.3 34.5

Shear

0100200300400

-1.9 -1.3 -0.6 0.05 0.7 1.36 2.01

Stagger

050

100150200250300

-2.1 -1.2 -0.4 0.47 1.31 2.16

Stretch

0

100

200

300

2 2.26 2.52 2.78 3.04 3.3 3.56

Telomeric DNA (PDB ID: 1JPQ)

Tilt Roll Twist Shift Slide Rise Cup

--------------------------------------------------------------------------------

LC 1 G:G 19 27.23 -10.46 166.15 1.78 -0.28 2.97 -3.59 W:H C

LC 2 G:G 20 3.15 7.09 -112.63 -5.31 0.18 3.61 -7.16 H:W C

LC 3 G:G 21 3.19 3.74 76.95 -0.29 -5.42 3.20 31.84 W:H C

LC 4 G:G 12 29.27 35.74 102.57 4.26 1.34 6.44 17.26 W:H C

LC 5 T: 0 -16.15 35.76 64.60 -0.51 2.68 -4.74 0.00 :

LC 6 T: 0 -22.93 -47.04 32.85 -3.12 -1.74 6.70 0.00 :

LC 7 T: 0 13.70 49.51 -26.95 -5.01 2.20 -6.66 4.15 :

LC 8 G:G 22 4.93 -0.61 77.93 -0.08 -6.03 3.48 5.51 W:H C

LC 9 G:G 13 -2.23 2.03 -23.71 -0.30 1.56 3.45 -12.68 W:H C

LC 10 G:G 20 -9.71 5.20 76.81 -0.58 -5.84 3.51 18.36 W:H C

LC 11 G:G 15 5.29 10.56 41.20 1.51 -3.27 11.16 -10.69 W:H C

LC 12 G:G 8 10.97 -6.79 167.70 1.28 0.00 3.13 -6.78 W:H C

LC 13 G:G 9 5.44 8.01 -112.14 -5.24 0.18 3.57 -6.16 H:W C

LC 14 G:G 10 48.09 -10.89 164.64 2.30 0.23 2.65 0.48 W:H C

LC 15 G:G 11 32.96 5.30 12.22 -1.75 2.36 5.49 17.91 H:W C

LC 16 T: 0 -14.90 39.32 66.47 -0.81 3.01 -4.72 0.00 :

LC 17 T: 0 -25.02 -45.62 48.09 -2.27 -0.58 6.85 0.00 :

LC 18 T: 0 -119.01 -37.81 19.04 0.52 7.74 2.68 -3.17 :

LC 19 G:G 1 6.30 -5.64 -102.33 -0.18 -6.97 3.62 6.03 H:W C

LC 20 G:G 10 9.11 14.38 156.06 0.55 9.80 2.20 4.72 H:W C

LC 21 G:G 3 -5.30 -4.41 -101.92 0.38 -6.79 3.43 -11.89 H:W C

LC 22 G:G 8

Inter Base Pair parameters of 1JPQ

Buckle Open Propel Stagger Shear Stretch

--------------------------------------------------------------------

BL 1 G:G 19 -0.75 -2.56 4.64 0.06 2.50 2.86 W:H C

BL 2 G:G 20 -4.34 -2.52 -2.46 -0.25 -2.43 2.83 H:W C

BL 3 G:G 21 -11.50 -3.93 2.12 -0.07 2.41 2.95 W:H C

BL 4 G:G 12 20.34 -4.54 -0.60 -0.23 2.44 2.91 W:H C

BL 5 T: 0 0.00 0.00 0.00 0.00 0.00 0.00 :

BL 6 T: 0 0.00 0.00 0.00 0.00 0.00 0.00 :

BL 7 T: 0 0.00 0.00 0.00 0.00 0.00 0.00 :

BL 8 G:G 22 0.39 -4.33 -6.90 0.08 2.43 2.89 W:H C

BL 9 G:G 13 5.90 -6.09 -3.94 -0.12 2.37 2.95 W:H C

BL 10 G:G 20 -6.78 -3.20 -7.45 0.02 2.46 2.86 W:H C

BL 11 G:G 15 11.58 -7.34 -15.29 -0.52 2.38 3.03 W:H C

BL 12 G:G 8 0.88 -4.43 6.63 -0.01 2.46 2.86 W:H C

BL 13 G:G 9 -5.90 -6.09 -3.94 -0.12 -2.37 2.95 H:W C

BL 14 G:G 10 -12.06 -6.09 1.20 -0.15 2.37 2.90 W:H C

BL 15 G:G 11 -11.58 -7.34 -15.29 -0.52 -2.38 3.03 H:W C

BL 16 T: 0 0.00 0.00 0.00 0.00 0.00 0.00 :

BL 17 T: 0 0.00 0.00 0.00 0.00 0.00 0.00 :

BL 18 T: 0 0.00 0.00 0.00 0.00 0.00 0.00 :

BL 19 G:G 1 0.75 -2.56 4.64 0.06 -2.50 2.86 H:W C

BL 20 G:G 10 6.78 -3.20 -7.45 0.02 -2.46 2.86 H:W C

BL 21 G:G 3 11.50 -3.93 2.12 -0.07 -2.41 2.95 H:W C

BL 22 G:G 8 -0.39 -4.33 -6.90 0.08 -2.43 2.89 H:W C

Intra Base Pair Parameters of 1JQP

Twist

Slide

ShearPropeller

Open angle

Thanks

• Dr. Sudip Kundu (CU)

• Anirban Ghosh (IISc)

• Shayantani Mukherjee (SINP)

• Jhuma Das (SINP)

• Arvind Marathe (IISc)

• Sukanya Halder (SINP)

http://www.saha.ac.in/biop/bioinformatics.html