NAFlex: Nucleic Acids Flexibility

Supplementary Tables

Base Pair Step Average Helical Parameters
Intra-Base Pair Average Helical Parameters
Base Pair Axis Average Helical Parameters
Base Pair Step Average Stiffness Constants

Average Helical Parameters and standard deviations for the unique base pair steps

Pablo D. Dans, Alberto Pérez, Ignacio Faustino, Richard Lavery and Modesto Orozco.
Exploring polymorphisms in B-DNA helical conformations.
Nucleic Acids Research. (2012) 40, 10668-10678..

(Supplementary table S3)

Amount of data(N), average values and standard deviation of the six intra-strand base pair parameters for the 10 unique bps.
For each step, the naked-DNA structures (first row), all the PDB structures (second row), and results from MD simulations with parmbsc0 (third row) are shown.
Values for simulations were obtained from time averages computed for individual steps in each sequence.
Rotational parameters are in degrees (Twist, Tilt, Roll), and translational ones (Shift, Slide, Rise) in Å.
Complementary steps (e.g. AG and CT) have the same average except for a change in sign of Shift and Tilt, and the same standard deviation.

Step	Amount of data	Twist	Tilt	Roll	Shift	Slide	Rise
AA	60	35.6±4.3	-1.4±2.7	1.0±3.8	0.0±0.3	-0.2±0.4	3.3±0.1
AA	850	33.4±5.9	-1.2±3.0	2.5±7.1	0.1±0.5	0.0±0.6	3.3±0.2
AA	1M	35.4±5.4	-2.6±4.1	0.3±5.6	-0.3±0.6	-0.3±0.6	3.3±0.3

TT	60	35.6±4.3	-1.4±2.7	1.0±3.8	0.0±0.3	-0.2±0.4	3.3±0.1
TT	850	33.4±5.9	-1.2±3.0	2.5±7.1	0.1±0.5	0.0±0.6	3.3±0.2
TT	1M	35.4±5.4	-2.6±4.1	0.3±5.6	-0.3±0.6	-0.3±0.6	3.3±0.3

AC	12	35.6±2.3	-0.5±2.2	0.4±3.6	-0.1±0.6	-0.2±0.3	3.3±0.1
AC	670	31.5±3.9	0.7±3.4	2.0±4.1	0.2±0.6	-0.6±0.4	3.2±0.2
AC	1M	32.0±5.1	-0.7±4.0	-0.6±5.9	0.1±0.7	-0.6±0.5	3.3±0.3

GT	12	35.6±2.3	-0.5±2.2	0.4±3.6	-0.1±0.6	-0.2±0.3	3.3±0.1
GT	670	31.5±3.9	0.7±3.4	2.0±4.1	0.2±0.6	-0.6±0.4	3.2±0.2
GT	1M	32.0±5.1	-0.7±4.0	-0.6±5.9	0.1±0.7	-0.6±0.5	3.3±0.3

AG	17	29.7±5.9	-0.4±4.0	5.7±4.9	0.4±0.4	0.3±0.8	3.4±0.3
AG	700	32.4±4.7	-1.1±3.6	3.2±5.7	0.1±0.7	-0.2±0.3	3.3±0.3
AG	1M	33.5±6.0	-2.5±4.2	3.1±5.9	-0.4±0.7	-0.6±0.7	3.4±0.3

CT	17	29.7±5.9	-0.4±4.0	5.7±4.9	0.4±0.4	0.3±0.8	3.4±0.3
CT	700	32.4±4.7	-1.1±3.6	3.2±5.7	0.1±0.7	-0.2±0.3	3.3±0.3
CT	1M	33.5±6.0	-2.5±4.2	3.1±5.9	-0.4±0.7	-0.6±0.7	3.4±0.3

AT	62	32.0±3.6	0.3±2.2	-1.2±3.1	0.1±0.4	-0.6±0.3	3.3±0.2
AT	890	30.0±4.7	0.2±2.9	1.6±5.3	0.0±0.5	-0.6±0.4	3.2±0.3
AT	1M	30.4±4.2	0.0±3.8	-0.5±5.1	0.0±0.7	-0.8±0.4	3.3±0.3

CA	30	41.9±8.7	0.7±2.7	0.7±7.0	0.1±0.2	1.6±1.0	3.3±0.2
CA	730	35.9±5.5	0.3±3.9	4.6±6.8	-0.1±0.6	0.6±1.0	3.4±0.3
CA	1M	29.6±8.3	0.2±4.8	10.3±6.3	-0.2±0.7	-0.2±0.6	3.1±0.4

TG	30	41.9±8.7	0.7±2.7	0.7±7.0	0.1±0.2	1.6±1.0	3.3±0.2
TG	730	35.9±5.5	0.3±3.9	4.6±6.8	-0.1±0.6	0.6±1.0	3.4±0.3
TG	1M	29.6±8.3	0.2±4.8	10.3±6.3	-0.2±0.7	-0.2±0.6	3.1±0.4

CC	36	33.8±5.6	1.9±3.4	4.3±4.6	0.0±0.5	0.7±1.0	3.4±0.3
CC	560	33.7±4.6	0.9±4.7	4.3±5.5	0.1±0.7	-0.2±0.8	3.4±0.3
CC	1M	32.7±6.6	0.0±4.4	4.9±5.7	0.2±0.7	-0.7±0.9	3.5±0.3

GG	36	33.8±5.6	1.9±3.4	4.3±4.6	0.0±0.5	0.7±1.0	3.4±0.3
GG	560	33.7±4.6	0.9±4.7	4.3±5.5	0.1±0.7	-0.2±0.8	3.4±0.3
GG	1M	32.7±6.6	0.0±4.4	4.9±5.7	0.2±0.7	-0.7±0.9	3.5±0.3

CG	205	33.0±5.1	0.3±4.5	3.4±7.7	0.1±0.5	0.5±0.6	3.3±0.3
CG	860	32.5±5.7	-0.2±4.2	4.6±5.9	0.0±0.7	0.4±0.8	3.3±0.3
CG	1M	29.8±8.8	0.0±5.2	9.3±6.0	0.0±0.7	0.0±0.5	3.1±0.4

GA	35	38.9±3.9	-0.8±3.3	2.3±3.8	0.0±0.4	0.0±0.5	3.4±0.2
GA	805	35.4±4.7	-1.4±3.6	2.3±5.5	-0.2±0.6	-0.1±0.6	3.3±0.2
GA	1M	36.6±6.2	-1.6±4.5	1.6±5.9	-0.4±0.7	-0.3±0.7	3.4±0.3

TC	35	38.9±3.9	-0.8±3.3	2.3±3.8	0.0±0.4	0.0±0.5	3.4±0.2
TC	805	35.4±4.7	-1.4±3.6	2.3±5.5	-0.2±0.6	-0.1±0.6	3.3±0.2
TC	1M	36.6±6.2	-1.6±4.5	1.6±5.9	-0.4±0.7	-0.3±0.7	3.4±0.3

GC	125	39.7±4.4	-0.5±3.7	-5.2±6.0	-0.2±0.8	0.3±0.4	3.5±0.2
GC	940	35.0±5.2	-0.2±3.7	0.6±5.7	0.0±0.7	-0.1±0.6	3.3±0.3
GC	1M	35.7±5.1	0.0±4.0	-1.3±5.8	0.0±0.7	-0.4±0.6	3.5±0.3

TA	19	41.7±6.3	-0.1±3.5	1.4±5.0	-0.2±0.4	0.7±0.8	3.4±0.2
TA	680	35.7±7.5	0.1±3.6	3.2±7.2	0.0±0.6	0.3±1.0	3.4±0.4
TA	25000	28.9±8.4	0.0±5.1	10.0±7.4	0.0±0.9	-0.2±0.8	3.2±0.4

Units:
Translational Inter-BP Step Helical Parameters Shift/Slide/Rise in Å, Rotational Inter-BP Helical Parameters Tilt/Roll/Twist in degrees

Average Intra-Base Pair Helical Parameters and standard deviations for the AT, TA, CG, GC base pairs

R. Lavery, K. Zakrzewska, D. Beveridge, T.C. Bishop, D.A. Case, T. Cheatham III, S. Dixit, B. Jayaram, F. Lankas, C. Laughton, J.H. Maddocks, A. Michon, R. Osman, M. Orozco, A. Perez, T. Singh, N. Spackova, J. Sponer.
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.
Nucleic Acids Research. (2010) 38, 299-313.

(Supplementary table S3)

Base Pair	Shear	Stretch	Stagger	Buckle	Propeller	Opening
AT	0.10±0.29	0.03±0.12	0.07±0.42	3.7±11.7	-12.9±9.0	3.1±5.5
GC	0.02±0.31	0.03±0.11	0.10±0.39	2.8±12.3	-9.1±9.2	1.1±3.3
TA	0.10±0.29	0.03±0.12	0.07±0.42	3.7±11.7	-12.9±9.0	3.1±5.5
CG	0.02±0.31	0.03±0.11	0.10±0.39	2.8±12.3	-9.1±9.2	1.1±3.3

Units: Translational Intra-BP Helical Parameters Shear/Stretch/Stagger in Å, Rotational Intra-BP Helical Parameters Buckle/Propeller/Opening in degrees.

Average Base Pair Axis Helical Parameters and standard deviations for the AT, TA, CG, GC base pairs

(Supplementary table S3)

Base Pair	Xdisp	Ydisp	Inclination	Tip
AT	-1.45±0.82	0.10±0.53	6.7±5.5	0.2±5.0
GC	-1.43±0.96	0.00±0.56	6.9±5.2	0.5±4.9
TA	-1.45±0.82	0.10±0.53	6.7±5.5	0.2±5.0
CG	-1.43±0.96	0.00±0.56	6.9±5.2	0.5±4.9

Units: Translational BP Axis Helical Parameters Xdisp/Ydisp in Å, Rotational BP Axis Helical Parameters Inclination/Tip in degrees.

Average Stiffness Constants for the unique base pair steps

Base Pair	Shift	Slide	Rise	Tilt	Roll	Twist
AATT
	1.72017	0.19796	0.32533	-0.01249	0.00576	0.05913
	0.19797	2.12618	0.75074	-0.00581	-0.05309	-0.10162
	0.32534	0.75074	7.64359	-0.18348	-0.04547	-0.14850
	-0.01249	-0.00581	-0.18349	0.03738	0.00211	0.00597
	0.00576	-0.05309	-0.04547	0.00211	0.01961	0.00742
	0.05913	-0.10162	-0.14850	0.00597	0.00742	0.02761
	-0.18750	-0.41750	3.32750	-2.01750	2.73750	33.57250
ACGT
	1.28288	0.13127	0.29502	-0.02780	0.00302	0.03646
	0.13127	2.97699	2.10518	-0.02280	0.03038	-0.10881
	0.29502	2.10518	8.83137	0.04907	0.10478	-0.14741
	-0.02780	-0.02280	0.04907	0.03776	0.00378	0.00418
	0.00302	0.03038	0.10479	0.00378	0.02306	0.00708
	0.03646	-0.10881	-0.14742	0.00418	0.00708	0.03551
	0.05000	-0.73571	3.37143	-1.06286	0.00857	33.38429
AGCT
	1.39990	0.27887	0.27572	-0.03917	0.02080	0.07408
	0.27887	1.78493	0.99427	-0.00395	-0.01181	-0.06894
	0.27572	0.99427	7.04130	-0.15259	-0.02113	-0.14069
	-0.03917	-0.00395	-0.15259	0.03699	0.00410	0.00630
	0.02080	-0.01181	-0.02113	0.00410	0.01912	0.00500
	0.07408	-0.06894	-0.14069	0.00630	0.00500	0.02797
	-0.32750	-0.65000	3.38750	-2.70500	2.83250	32.05750
ATAT
	1.04661	0.00000	0.00000	0.03066	0.00000	0.00000
	0.00000	3.76524	2.16877	0.00000	-0.03029	-0.04352
	0.00000	2.16877	9.33735	0.00000	0.06011	-0.09916
	0.03066	0.00000	0.00000	0.03494	0.00000	0.00000
	0.00000	-0.03029	0.06011	0.00000	0.02157	0.00877
	0.00000	-0.04352	-0.09916	0.00000	0.00877	0.03122
	0.00000	-0.77333	3.14333	0.00000	1.47000	28.59333
CATG
	1.05328	0.07552	0.23196	-0.03375	0.00158	-0.01277
	0.07552	1.79677	0.52999	-0.00472	0.02114	-0.03759
	0.23197	0.53000	6.30474	0.01221	-0.07708	-0.14400
	-0.03375	-0.00472	0.01221	0.02498	-0.00127	0.00137
	0.00158	0.02114	-0.07708	-0.00127	0.01647	0.00541
	-0.01277	-0.03759	-0.14399	0.00137	0.00541	0.01534
	-0.32600	-0.22200	3.20800	0.42800	9.24600	28.43600
CCGG
	1.43205	-0.29768	-0.35747	-0.08468	-0.01448	-0.03982
	-0.29768	1.57310	1.18241	-0.00677	0.01068	-0.09303
	-0.35748	1.18243	7.85985	0.25771	0.00156	-0.11971
	-0.08468	-0.00677	0.25771	0.04202	0.00134	0.00022
	-0.01448	0.01068	0.00156	0.00134	0.02012	0.00493
	-0.03982	-0.09303	-0.11970	0.00022	0.00493	0.02602
	0.11125	-0.76000	3.55625	-0.43625	4.58000	34.18625
CGCG
	1.05459	0.00000	0.00000	-0.07841	0.00000	0.00000
	0.00000	1.91048	0.56341	0.00000	0.02388	-0.05037
	0.00000	0.56342	6.11191	0.00000	-0.04625	-0.14832
	-0.07841	0.00000	0.00000	0.02587	0.00000	0.00000
	0.00000	0.02388	-0.04625	0.00000	0.01562	0.00319
	0.00000	-0.05037	-0.14832	0.00000	0.00319	0.01400
	0.00000	-0.07250	3.25875	0.00000	6.45000	31.88875
CTAG
	1.39990	-0.27887	-0.27572	-0.03917	-0.02080	-0.07408
	-0.27887	1.78493	0.99427	0.00395	-0.01181	-0.06894
	-0.27572	0.99427	7.04130	0.15259	-0.02113	-0.14069
	-0.03917	0.00395	0.15259	0.03699	-0.00410	-0.00630
	-0.02080	-0.01181	-0.02113	-0.00410	0.01912	0.00500
	-0.07408	-0.06894	-0.14069	-0.00630	0.00500	0.02797
	0.32750	-0.65000	3.38750	2.70500	2.83250	32.05750
GATC
	1.31766	0.29517	0.40655	-0.04665	0.00977	0.01782
	0.29517	1.87898	1.00952	0.00116	-0.01328	-0.09736
	0.40656	1.00952	8.48201	-0.25663	-0.01013	-0.12376
	-0.04665	0.00116	-0.25663	0.03758	-0.00252	0.00117
	0.00977	-0.01328	-0.01012	-0.00252	0.02025	0.00861
	0.01782	-0.09736	-0.12376	0.00117	0.00861	0.02441
	-0.21400	-0.29000	3.37200	-0.49800	2.13600	36.47000
GCGC
	1.17900	0.00000	0.00000	-0.08357	0.00000	0.00000
	0.00000	2.58821	2.05067	0.00000	0.08753	-0.07364
	0.00000	2.05063	9.46559	0.00000	0.15720	-0.18431
	-0.08357	0.00000	0.00000	0.03618	0.00000	0.00000
	0.00000	0.08753	0.15720	0.00000	0.02569	0.00442
	0.00000	-0.07364	-0.18431	0.00000	0.00442	0.02238
	0.00000	-0.28800	3.41000	0.00000	-1.07600	36.07200
GGCC
	1.43205	0.29768	0.35747	-0.08468	0.01448	0.03982
	0.29768	1.57310	1.18241	0.00677	0.01068	-0.09303
	0.35748	1.18243	7.85985	-0.25771	0.00156	-0.11971
	-0.08468	0.00677	-0.25771	0.04202	-0.00134	-0.00022
	0.01448	0.01068	0.00156	-0.00134	0.02012	0.00493
	0.03982	-0.09303	-0.11970	-0.00022	0.00493	0.02602
	-0.11125	-0.76000	3.55625	0.43625	4.58000	34.18625
GTAC
	1.28288	-0.13127	-0.29502	-0.02780	-0.00302	-0.03646
	-0.13127	2.97699	2.10518	0.02280	0.03038	-0.10881
	-0.29502	2.10518	8.83137	-0.04907	0.10478	-0.14741
	-0.02780	0.02280	-0.04907	0.03776	-0.00378	-0.00418
	-0.00302	0.03038	0.10479	-0.00378	0.02306	0.00708
	-0.03646	-0.10881	-0.14742	-0.00418	0.00708	0.03551
	-0.05000	-0.73571	3.37143	1.06286	0.00857	33.38429
TATA
	0.64315	0.00000	0.00000	-0.01544	0.00000	0.00000
	0.00000	1.24864	0.53653	0.00000	0.02038	-0.04224
	0.00000	0.53653	6.07971	0.00000	-0.07916	-0.14834
	-0.01544	0.00000	0.00000	0.01900	0.00000	0.00000
	0.00000	0.02038	-0.07916	0.00000	0.01464	0.00831
	0.00000	-0.04224	-0.14835	0.00000	0.00831	0.01759
	0.00000	-0.14667	3.26667	0.00000	8.31667	32.66000
TCGA
	1.31766	-0.29517	-0.40655	-0.04665	-0.00977	-0.01782
	-0.29517	1.87898	1.00952	-0.00116	-0.01328	-0.09736
	-0.40656	1.00952	8.48201	0.25663	-0.01013	-0.12376
	-0.04665	-0.00116	0.25663	0.03758	0.00252	-0.00117
	-0.00977	-0.01328	-0.01012	0.00252	0.02025	0.00861
	-0.01782	-0.09736	-0.12376	-0.00117	0.00861	0.02441
	0.21400	-0.29000	3.37200	0.49800	2.13600	36.47000
TGCA
	1.05328	-0.07552	-0.23196	-0.03375	-0.00158	0.01277
	-0.07552	1.79677	0.52999	0.00472	0.02114	-0.03759
	-0.23197	0.53000	6.30474	-0.01221	-0.07708	-0.14400
	-0.03375	0.00472	-0.01221	0.02498	0.00127	-0.00137
	-0.00158	0.02114	-0.07708	0.00127	0.01647	0.00541
	0.01277	-0.03759	-0.14399	-0.00137	0.00541	0.01534
	0.32600	-0.22200	3.20800	-0.42800	9.24600	28.43600
TTAA
	1.72017	-0.19796	-0.32533	-0.01249	-0.00576	-0.05913
	-0.19797	2.12618	0.75074	0.00581	-0.05309	-0.10162
	-0.32534	0.75074	7.64359	0.18348	-0.04547	-0.14850
	-0.01249	0.00581	0.18349	0.03738	-0.00211	-0.00597
	-0.00576	-0.05309	-0.04547	-0.00211	0.01961	0.00742
	-0.05913	-0.10162	-0.14850	-0.00597	0.00742	0.02761
	0.18750	-0.41750	3.32750	2.01750	2.73750	33.57250

Units:
Diagonal Shift/Slide/Rise in kcal/(mol*Å²), Diagonal Tilt/Roll/Twist in kcal/(mol*degree²)
Out of Diagonal: Shift/Slide/Rise in kcal/(mol*Å), Out of Diagonal Tilt/Roll/Twist in kcal/(mol*degree)