Supplementary Materials
Properties of the Nucleic-acid Bases in Free and Watson-Crick Hydrogen-bonded States:
Computational Insights into the Sequence-dependent Features of Double-helical DNA
A. R. Srinivasan,1 Ronald R. Sauers,1 Marcia O. Fenley,3,4 Alexander H. Boschitsch,5 Atsushi Matsumoto,1,6,7
‡
Andrew V. Colasanti,1, and Wilma K. Olson1,2,
1
*
Department of Chemistry & Chemical Biology
2
BioMaPS Institute for Quantitative Biology
Rutgers, the State University of New Jersey
Wright-Rieman Laboratories
610 Taylor Road
Piscataway, NJ 08854-8087, USA
3
4
Department of Physics
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306-4380, USA
5
Continuum Dynamics, Inc.
34 Lexington Avenue
Ewing, NJ 08618-2302, USA
6
Quantum Bioinformatics Team
Center for Computational Science and Engineering
7
Research Unit for Quantum Beam Life Science Initiative
Quantum Beam Science Directorate
Japan Atomic Energy Agency
8-1 Umemidai
Kizugawa
Kyoto, 619-0215, Japan
‡ Current address: Provid Pharmaceuticals Inc., 671 U.S. Route 1, North Brunswick, NJ 08902.
* To whom correspondence should be addressed: Tel: 732-445-3993; Fax: 732-445-5958; Email:
wilma.olson@rutgers.edu.
p. 2
Highlighted References
Frisch MJ, Trucks GW, Schlegel HB et al. (2003) Gaussian 03. Gaussian, Inc., Pittsburgh, PA
Frisch MJ, Trucks GW, Schlegel HB et al. (2001) Gaussian 98. Gaussian, Inc., Pittsburgh, PA
These suites of ab initio quantum chemistry programs successfully predict numerous properties of molecules
and reactions, in the gas phase and in solution, including the energies, structures, atomic charges, electrostatic
potentials, and normal modes of the nucleic acid bases discussed herein.
Boschitsch AH, Fenley MO, Zhou H-X (2002) Fast boundary element method for the linear Poisson-Boltzmann
equation. J Phys Chem B 106:2741-2754
Boschitsch AH, Fenley MO (2004) Hybrid boundary element and finite difference method for solving the nonlinear
Poisson-Boltzmann equation. J Comp Chem 25:935-955
The novel algorithms developed in these papers produce useful, highly detailed electrostatic potential surfaces
of nucleic acids and other biomolecules in a simulated aqueous salt environment.
Lu X-J, Olson WK (2003) 3DNA: a software package for the analysis, rebuilding, and visualization of threedimensional nucleic acid structures. Nucleic Acids Res 31:5108-5121
Lu X-J, Olson WK (2008) 3DNA: a versatile, integrated software system for the analysis, rebuilding, and
visualization of three-dimensional nucleic-acid structures. Nature Protocols 3:1213-1227
This versatile, integrated software system facilitates the analysis, reconstruction, and visualization of threedimensional nucleic-acid-containing structures.
Berman HM, Olson WK, Beveridge DL et al. (1992) The Nucleic Acid Database: a comprehensive relational
database of three-dimensional structures of nucleic acids. Biophys J 63:751-759
This relational database assembles and distributes information about the high-resolution structures of nucleic
acids.
p. 3
List of Supporting Tables
S1.
Residual atomic charges, in esu, of nucleic-acid bases in free and Watson-Crick paired forms.
S2.
Database identities, refinement information, sequences, base-pair contents, and literature citations of
high-resolution B-DNA structures surveyed in this study.
S3.
Comparative features of exocyclic amino groups in energy-optimized vs. observed DNA bases
S4.
Average surface electrostatic potential, in kcal mole–1e–1, of selected surface atoms on isolated DNA
bases and Watson-Crick base pairs
S5.
Mean step parameters and deformational properties of AA·TT and GG·CC dimers constructed from
optimized base pairs and subjected to configurational sampling
p. 4
Table S1.
Residual atomic charges, in esu, of nucleic-acid bases in free and Watson-Crick paired
forms.†
Purine
Atom
Free
Adenine
N1
C2
H2
N3
C4
C5
C6
N6
H61
H62
N7
C8
H8
N9
C1´
H1C1´
H2C1´
H3C1´
–0.8316
0.6585
0.0347
–0.7795
0.5241
–0.0703
0.7657
–0.8117
0.3643
0.3501
–0.5818
0.2194
0.1267
–0.1424
0.0084
0.0583
0.0366
0.0706
–0.7495
0.5662
0.0716
–0.7470
0.4933
–0.0227
0.7216
–0.8876
0.4339
0.3903
–0.6003
0.2267
0.1218
–0.1498
0.0399
0.0658
0.0279
0.0451
Guanine
N1
H1
C2
N2
H21
H22
N3
C4
C5
C6
O6
N7
C8
H8
N9
C1´
H1C1´
H2C1´
H3C1´
–0.8967
0.4473
0.9656
–0.8687
0.3695
0.3551
–0.7611
0.4105
–0.0760
0.8724
–0.6592
–0.5253
0.1367
0.1394
–0.0654
–0.0466
0.0700
0.0543
0.0781
–0.9123
0.5174
0.9845
–0.9123
0.4186
0.3745
–0.7794
0.3743
–0.0357
0.8515
–0.7406
–0.5416
0.1130
0.1367
–0.0223
–0.0553
0.0494
0.0542
0.0878
†Structures
Paired
Paired
Free
Atom
Pyrimidine
–0.1612
0.8381
–0.6413
–0.7790
0.3995
0.8905
–0.6869
–0.2249
–0.1337
0.0640
0.0469
0.0680
–0.0636
0.1963
–0.0789
0.0670
0.0742
0.0777
–0.1129
0.8476
–0.6559
–0.7918
0.4063
0.8665
–0.6470
–0.1808
–0.1162
0.0635
0.0424
0.0635
–0.1144
0.2081
–0.1962
0.0907
0.1358
0.0907
N1
C2
O2
N3
H3
C4
O4
C5
C5M
H51
H52
H53
C6
H6
C1´
H1C1´
H2C1´
H3C1´
Thymine
–0.2366
0.9694
–0.7103
–0.9998
1.1582
–1.1693
0.5703
0.4541
–0.6905
0.2122
0.1840
0.1524
–0.1091
0.0834
0.0729
0.0962
–0.2442
1.0039
–0.6951
–0.8906
0.9500
–0.8817
0.3820
0.3539
–0.6436
0.2111
0.1530
0.1550
–0.0795
0.0608
0.0896
0.0754
N1
C2
O2
N3
C4
N4
H41
H42
C5
H5
C6
H6
C1´
H1C1´
H2C1´
H3C1´
Cytosine
of free and paired bases obtained from calculations based on second-order Møller-Plesset perturbation theory within
the Gaussian 98 and Gaussian 03 suites of programs [1, 2] starting with standard nucleic-acid base [3] and base-pair [4] models.
Partial atomic charges computed at the MP2/6-311+G**//MP2/6-31G* level of model chemistry and fitted to the electrostatic
potential obtained through the CHelpG (CHarges from electrostatic potentials using a Grid-based method) scheme [5] as
incorporated in Gaussian.
p. 5
Table S2.
Database identities, refinement information, sequences, base-pair contents, and literature citations of high-resolution B-DNA structures
surveyed in this study.
NDB_ID†
Resolution (Å)
R-value (%)
DNA sequence
A·T
G·C
Reference
BD0001
1.6
17.3
5´-d(ApCpCpGpApCpGpTpCpGpGpT)-3´
2
6
1
BD0005
1.75
21.8
5´-d(CpGpCpGpApApTpTpCpGpCpG)-3´
4
4
2
BD0006
1.15
17.22
5´-d(GpGpCpCpApApTpTpGpG)-3´
4
4
4
3
BD0007
1.1
16.2
5´-d(CpGpCpGpApApTAFpTpCpGpCpG)-3´
BD0009
1.6
19.6
5´-d(CpGpCpGpAOCH3pApTpCpCpGpCpG)-3´
2
5
2
6
BD0010
2
23.2
5´-d(CpGpCpGpAOCH3pApTpTpCpGpCpG)-3´
BD0012
1.2
17.9
5´-d(CpGpCpGpApApTAFpTpCpGpCpG)-3´
4
7
4
7
2
8
6
9
BD0013
1.5
18.6
5´-d(CpGpCpGpApApTAFpTpCpGpCpG)-3´
BD0014
1.45
21.72
5´-d(CpGpCpGpApApTpTpCpGpCpG)-3´
4
5´-d(CpBrUpCpCpBrUpCpCpGpCpGpCpG)-3´
BD0017
1.8
21
5´-d(CpGpCpGpCp GpGpApG)-3´
BD0018
1.3
18.2
5´-d(GpCpGpApApTpTpCpGpCpG)-3´
4
2
10
BD0019
1.7
19.4
5´-d(GpGpCpGpApApTpTpCpGpCpG)-3´
4
2
10
4
BD0021
1.55
20.31
5´-d(CpCpApGpGXL1pCpCpTpGpG)-3´
BD0023
0.74
10.5
5´-d(CpCpApGpTpApCpTpGpG)-3´
1
1
12
BD0029
1.82
20.9
5´-d(CpGpCpGpApApTpTpCpGpCpG)-3´
4
4
13
BD0030
0.95
16
5´-d(CpGpCpGpApApTAFpTpCpGpCpG)-3´
4
14
2
6
1
15
11
BD0031
1.6
21.8
5´-d(CpGpCpGpAOCH3pApTpTpCpGpCpG)-3´
BD0032
1.8
22.4
5´-d(CpGpCpGpApApTpTpCpGpCpG)-3´
1
BD0033
0.98
14.09
5´-d(CpCpApApCpGpTpTpGpG)-3´
2
16
BD0034
0.98
11.83
5´-d(CpCpApApCpGpTpTpGpG)-3´
2
16
p. 6
NDB_ID†
Resolution (Å)
R-value (%)
DNA sequence
A·T
G·C
Reference
BD0035
0.98
14.05
5´-d(CpCpApGpCpGpCpTpGpG)-3´
1
1
16
BD0036
0.98
12.14
5´-d(CpCpApGpCpGpCpTpGpG)-3´
1
1
16
BD0037
0.89
13.5
5´-d(GpCpGpApApTpTpCpG)-3´
4
BD0038
1.43
19.8
5´-d(CpGpCpGpApApTLCpCTLpCpGpCpG)-3´
BD0041
1.2
14.1
5´-d(CpGpCpGpApApTpTpCpGpCpG)-3´
BD0043
1.57
21
17
2
18
4
19
5´-d(CpGpCpGpApApTpUFORpCpGpCpG)-3´
2
20
2
20
4
BD0044
1.55
20.7
5´-d(CpGpCpGpApApTpUFORpCpGpCpG)-3´
BD0045
1.85
24
5´-d(CpGpCpGpApApTpUFORpCpGpCpG)-3´
2
20
2
20
BD0046
1.8
20.8
5´-d(CpGpCpGpApApTpUFORpCpGpCpG)-3´
BD0048
1.6
22.4
5´-d(CpGpCpGpApApTpTpCOCH3pGpCpGP)-3´
BD0050
2
24
5´-d(GpGpCpGpCpC)-3´
BD0051
1.6
18.4
5´-d(CpCpTpTpTpApApApGpG)-3´
6
23
2
24
2
21
2
22
BD0053
1.6
21.8
5´-d(CpGpCpApApApTpTpCOCH3pGpCpG)-3´
BD0054
1.2
16.3
5´-d(CpGpCpGpApApTpTpCpGpCpG)-3´
4
BD0055
2
13.4
5´-d(CpCpApApIpApTpTpGpG)-3´
1
BD0060
1.2
16
5´-d(CpGpCpGpApApTTFpTpCpGpCpG)-3´
BD0066
1.6
21.6
5´-d(CpGpCpApApTpTpGpCpG)-3´
1
BD0067
1.53
19.9
5´-d(CpGpCpApApApTpTpTpGpCpG)-3´
6
2
29
BD0070
1.6
20.7
5´-d(CpGpCpTpGpGpApApApTpTpTpCpCpApGpC)-3´
3
2
30
BD0071
0.89
12.63
5´-d(CpTpTpTpTpApApApApG)-3´
6
31
2
32
33
4
25
26
4
27
28
BD0072
1.65
22.1
5´-d(CpGpCpGpApApTpTpC5FpGpCpG)-3´
BD0073
2
23.7
5´-d(CpCpApTpTpApApTpGpG)-3´
6
BD0077
1.5
25.3
5´-d(CpCpGpTpTpApApCpGpG)-3´
4
2
34
BD0079
0.99
29
5´-d(CpCpApGpCpGpCpTpGpG)-3´
1
2
34
p. 7
NDB_ID†
Resolution (Å)
R-value (%)
DNA sequence
A·T
G·C
Reference
BD0080
1.05
27.6
5´-d(CpCpGpTpCpGpApCpGpG)-3´
2
4
34
BD0081
1.65
23.3
5´-d(CpCpGpCpCpGpGpCpGpG)-3´
6
34
BD0082
2
26.4
5´-d(CpCpGpApTpApTpCpGpG)-3´
4
2
34
BD0084
1.75
31.4
5´-d(CpCpGpApGpCpTpCpGpG)-3´
2
4
34
BD0087
0.94
42.8
5´-d(CpCpGpApApTpTpCpGpG)-3´
1
1
34
BDJ008
1.3
16.4
5´-d(CpCpApApGpAppTpTpGpG)
1
BDJ017
1.6
16
5´-d(CpCpApGpGpCpCpTpGpG)-3´
1
BDJ019
1.4
16
5´-d(CpCpApApCpGpTpTpGpG)-3´
2
BDJ025
1.5
16.1
5´-d(CpGpApTpCpGpApTpCpG)-3´
4
BDJ031
1.5
15.7
5´-d(CpGpApTpTpApApTpCpG)-3´
6
38
BDJ036
1.7
17.8
5´-d(CpGpApTpApTpApTpCpG)-3´, Calcium
6
39
BDJ037
2
16.5
5´-d(CpGpApTpApTpApTpCpG)-3´, Magnesium
6
39
BDJ051
2
19.6
5´-d(CpApTpGpGpCpCpApTpG)-3´
2
4
40
BDJ052
1.9
17.9
5´-d(CpCpApApGpCpTpTpGpG)-3´, Calcium
4
2
41
BDJ060
1.7
20
5´-d(CpTpCpTpCpGpApGpApG)-3´
2
4
42
BDJ061
1.95
17
5´-d(CpCpApCpTpApGpTpGpG)-3´
4
2
43
BDJ081
1.85
23.3
5´-d(CpApApApGpApApApApG)-3´
15
3
44
BDJB44
1.3
15.2
5´-d(CpCpApApCpIpTpTpGpG)-3´, monoclinic
1
BDL001
1.9
17.8
5´-d(CpGpCpGpApApTpTpCpGpCpG)-3´, 290 K
4
4
46
BDL005
1.9
14.9
4
4
47
35
1
36
35
2
37
45
5´-d(CpGpCpGpApApTpTpCpGpCpG)-3´, 290 K,
(anisotropic thermal motion model)
BDL020
1.9
18.8
5´-d(CpGpCpGpApApTpTpCpGpCpG)-3´, 290 K, (re-refinement)
4
4
48
BDL084
1.4
19.7
5´-d(CpGpCpGpApApTpTpCpGpCpG)-3´
4
4
49
BDLB13
2
16.9
5´-d(CpGpCpGpApACH3pTpTpCpGpCpG)-3´
4
50
p. 8
NDB_ID†
Resolution (Å)
R-value (%)
DNA sequence
A·T
BDLB26
2
18.5
5´-d(CpGpCpGCH3pApApTpTpTpGpCpG)-3´
2
BDLB84
1.55
20.8
5´-d(CpGpCpGpApApTFlOpTFlO pCpGpCpG)-3´
2
52
4
52
†
G·C
Reference
51
BDLB85
1.55
21.8
5´-d(CpGpCpGpApApTFlOpTpCpGpCpG)-3´
UD0023
1.97
22.3
5´-d(TpCpGpGpTpApCpCpGpA)-3´
1
4
53
UD0024
2
24.6
5´-d(CpCpGpGpTpApCpCpGpG)-3´
1
4
53
UD0025
1.8
20.3
5´-d(CpCpGpGpTpApCpCpGpG)-3´
1
4
53
UD0026
1.5
20.69
5´-d(TpCpGpGpTpApCpCpGpA)-3´
1
4
54
UD0028
1.7
22.9
5´-d(CpCpGpGpCpGpCpCpGpG)-3´
5
55
UD0029
2
23.6
5´-d(CpCpApGpTpApCpTpGpG)-3´
1
1
55
UD0030
1.9
21.5
5´-d(CpCpApGpTpApCpBrUpGpG)-3´
1
UDJ049
2
20.9
5´-d(GpGpCpCpApApTpTpGpG)-3´
4
55
1
56
NDB_ID refers to the identification code of the B-DNA structure in the Nucleic Acid Database (Berman, H. M., Olson, W. K., Beveridge, D. L., Westbrook, J., Gelbin, A., Demeny, T.,
Hsieh, S.-H., Srinivasan, A. R., Schneider, B. (1992) “The Nucleic Acid Database: a comprehensive relational database of three-dimensional structures of nucleic acids.” Biophys. J. 63,
751-759).
p. 9
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p. 11
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p. 12
Table S3.
Comparative features of exocyclic amino groups in energy-optimized vs. observed DNA
bases.†
Base
Adenine
Prediction
Neutron [6]
Neutron [7]
Infrared [8]
X-ray
Guanine
Prediction
X-ray
Cytosine
Prediction
Neutron [9]
Infrared [10]
X-ray
†
Torsion angles (deg)
C5–C6–N6–H62
±21.4
–11.6 (11.6)
13.1
2.8
–
–
N1–C6–N6–H61
19.2
11.6 (–11.6)
±5.3
±6.9
–
–
C4–C5–C6–N6
±177.1
–178.1 (178.0)
±178.6
±179.4
~ 160°
177.3 (±2.2)
C2–N1–C6–N6
176.8
178.1 (–178.1)
178.9
±179
~ –160°
–178.1 (±1.3)
free
pair
pair
N3–C2–N2–H22
±11.7
–16.3 (16.3)
–
N1–C2–N2–H21
43.9
23.0 (–22.6)
–
C6–N1–C2–N2
177.0
176.2 (–176.3)
–179.9 (±1.6)
C4–N3–C2–N2
±175.5
–175.9 (176.0)
178.6 (±2.2)
free
C5–C4–N4–H42
28.1
N3–C4–N4–H41
±15.0
C2–N3–C4–N4
±176.5
C6–C5–C4–N4
177.0
free
pair
free
free
free
pair
pair
free
free
pair
–5.6 (5.8)
±0.1
–
–
7.1 (–7.2)
±3.9
~ 16°
–
–179.8 (179.8)
179.2
–
–178.9 (±2.5)
–179.7 (179.7)
±177.7
–
178.9 (±2.3)
Predicted base nonplanarity obtained from calculations based on second-order Møller-Plesset perturbation theory compared to
experimental findings. Numerical values in parentheses correspond to base pairs in a secondary, higher energy minimum with
positive propeller twist. (The minimum-energy base-pair structure has negative propeller twist; see text). Observations come
from neutron-diffraction studies of unpaired (free) bases,[6, 7, 9] infrared measurements of the vibrational transition moments
of free bases,[8, 10] and analyses of ultra-high resolution (0.99 Å or better resolution) B-DNA crystal structures (Table S2).
Mean values and standard deviations (subscripted values in parentheses) based on the designated torsions in 27 A·T pairs from
16 different structures and 36 G·C pairs from 15 different structures.
p. 13
Table S4.
Average surface electrostatic potential, in kcal mole–1e–1, of selected surface atoms on
isolated DNA bases and Watson-Crick base pairs.1
Purine
Atom2
potential
Atom2
Base-pair
potential
edge3
potential
Pyrimidine
potential
G·C
0.13
G(N1)
–0.14
WC
–0.08
C(N3)
–0.24
0.19
G(N2)§
–0.19
WC,m
–0.17
C(O2)
–0.40
0.05
G(N3)
–0.14
m
–0.33
G(O6)
–0.40
WC,M
–0.06
C(N4)4
0.04
–0.29
G(N7)
–0.38
M
0.18
C(C5)
0.16
A·T
1
–0.14
A(N1)
0.06
WC
–0.04
T(N3)
0.06
–0.09
A(N3)
–0.16
m
–0.18
T(O2)
–0.11
–0.07
A(N6)§
–0.17
WC,M
–0.20
T(O4)
–0.18
–0.11
A(N7)
–0.23
M
Electrostatic potentials of specific atomic sites calculated by taking the average of the potential determined at accessible points
in the aqueous milieu surrounding the given atoms. Sampled points reside on the surface of spheres 1.0 Å beyond the van der
Waals’ radii of the selected atoms. The potential is determined by treating the DNA solute as a low dielectric region with a
dieleletric constant of 2 to mimic solute polarizability and the exterior solvent region with a dielectric constant of 80, and then
solving the Poisson equation (at 298 K and zero ionic strength) with a fast-multipole accelerated boundary-element method [11,
12]. The static atomic point-charge distribution is represented by the derived partial charges. The set of atomic radii R (in Å)
used to define the molecular surface is based on the Parse parameter set [13]: RH = 1.0: RC = 1.7; RN = 1.5; RO = 1.4. The
dielectric interface separating solute and solvent regions is defined by the solvent-excluded molecular surface [14], obtained
with a solvent-probe radius of 1.4 Å. The MSMS algorithm [15] is used to tessellate the solvent-excluded surface, which is
represented by up to 10,000 curved triangular elements. A second-order multipole and Taylor series are invoked and the
maximum number of boundary elements per terminal octree box is set to 2. All other default code parameters are employed
[12].
2 Atoms, which are significantly neutralized by Watson-Crick base-pair formation (i.e., the average surface electrostatic potential
differs by 0.10 kcal mole–1e–1 or more), are highlighted in boldface.
3 WC: Watson-Crick hydrogen-bonded edge; m: minor-groove edge; M: major-groove edge.
4 Value omits contribution of pendant hydrogens.
p. 14
Table S5.
Dimer
Mean step parameters and deformational properties of AA·TT and GG·CC dimers
constructed from optimized base pairs and subjected to configurational sampling.1
Tilt (°)
Roll (°)
Twist (°)
Shift (Å)
Slide (Å)
Rise (Å)



Dx
Dy
Dz
Emin
ln z
Free optimized base pairs2
AA·TT
–0.3 (±1.5)
1.0 (±4.9)
34.0 (±3.5)
0.02 (±0.51)
0.15 (±0.60)
3.26 (±0.10)
–26.1
6.3
GG·CC
0.2 (±1.6)
–1.5 (±3.8)
33.7 (±3.5)
–0.09 (±0.52)
0.29 (±0.58)
3.23 (±0.07)
–27.5
6.0
Free B-DNA base pairs2
AA·TT
–0.1 (±1.7)
1.0 (±4.0)
33.3 (±3.2)
–0.01 (±0.46)
0.20 (±0.51)
3.21 (±0.05)
–27.2
5.6
GG·CC
0.2 (±1.6)
–1.2 (±3.7)
33.7 (±3.5)
–0.09 (±0.51)
0.35 (±0.62)
3.22 (±0.07)
–27.6
6.1
Observed base-pair steps3
AA·TT
–1.2 (±2.5)
0.6 (±4.7)
34.8 (±3.7)
0.08 (±0.38) –0.18 (±0.37)
3.23 (±0.16)
GG·CC
–0.2 (±3.4)
5.1 (±4.0)
33.3 (±4.1)
–0.10 (±0.69) –0.43 (±0.65)
3.41 (±0.22)
1
Boltzmann-averaged step parameters and standard deviations computed over 124,215 configurational states where:  = [–3°,
 = [–18°, +18°] at 3° intervals;  = [30°, 42°] at 2° intervals; Dx = [–1 Å, +1 Å] at 0.5 Å intervals; Dy
= [–2.4 Å, +2.4 Å] at 0.4 Å intervals; Dz = [3.2 Å, 3.6 Å] at 0.2 Å intervals. Emin is the minimum energy between free base
pairs, expressed in kcal/mole, and z =
 exp(–Ei/RT)
is the configurational partition function evaluated over all states i
sampled at 298 K. Energy contributions based on an updated nucleic-acid force field that accounts for the sequencedependent conformational features of the Dickerson-Drew dodecamer in both the solid state and the aqueous liquidcrystalline phase [16]. Thymine C5 and C1´ methyl groups treated as united atoms with a van der Waals’ radius of 2.39 Å.
Dielectric constant set to 4 throughout.
2
Optimized base pairs assigned the base-pair parameters in Table 1 found from ab initio calculations; B-DNA base pairs
assigned the mean parameters found in high-resolution X-ray structures. Atoms assigned partial atomic charges from Table
S1. Standard deviations of roll vs. tilt and twist, and shift and slide compared to rise mimic observed deformations. The
relative bending, twisting, and sliding of AA·TT and GG·CC base-pair steps, however, differs from experiment. If the
charges are reduced in half, to simulate interactions with solvent, the fraction of GG·CC pairs assuming positive rather than
negative values of roll increases from 0.35 to 0.39 and the fraction of AA·TT pairs decreases from 0.58 to 0.57.
3
Data based on the analysis, within 3DNA [17], of 421 AA·TT and 317 GG·CC steps in 239 DNA-protein crystal complexes
of 2.5 Å or better resolution without chemical modifications, mismatches, or drugs from the Nucleic Acid Database [18]. The
dataset includes 101 structures of double-helical DNA bound to enzymes, 121 duplexes in the presence of regulatory
proteins, 16 complexes with structural proteins, and one DNA associated with a multifunctional protein [19]. Structures
filtered to exclude over-represented complexes in order to obtain a balanced sample of spatial and functional forms. Mean
values and standard deviations (subscripted values in parentheses) exclude terminal base pairs, side groups attached to nicked
backbone strands, and base pairs that stacked against modified or mispaired 3´- and 5´-nucleotides.
p. 15
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