Table 2. Mechanical properties calculated from all simulations performed.
| Simulations | A: bending persistence (nm) | S: stretch modulus S(pN) | C: torsional persistence length(nm) | Slope of link vs. force (rad/pN) | Slope of extension vs. link (nm/turn) | g: link-extension coupling 1 (pN·nm)1 | g: link-extension coupling 2 (pN·nm)2 |
| DNA | |||||||
| Experiment3 | 45(2) | 1000(200) | 109(4) | 0.064 | 0.44(0.1) | −90(20)4 | −70(20) |
| default5 | 54.7(0.6) | 1956.9(102.1) | 28.8(0.1) | 0.202(0.001) | 0.473(0.015) | −131.0(7.5) | −147.4(9.0) |
| default_frag6 | 54.5(0.6) | 1993.4(106.1) | 28.7(0.1) | 0.206(0.001) | 0.461(0.017) | −135.0(7.9) | −146.3(9.5) |
| 2.8_all | 39.4(0.5) | 1504.8(90.8) | 40.5(0.3) | 0.227(0.001) | 0.743(0.025) | −156.7(10.6) | −177.9(12.3) |
| 2.8_all_frag | 39.1(0.4) | 1517.8(78.4) | 40.4(0.3) | 0.229(0.001) | 0.757(0.030) | −158.2(9.2) | −182.9(11.9) |
| 2.0_noprot | 50.0(0.5) | 2146.7(115.2) | 27.0(0.1) | 0.218(0.002) | 0.483(0.025) | −143.7(8.5) | −164.9(12.2) |
| 2.0_noprot_frag | 50.0(0.6) | 2122.9(146.0) | 27.0(0.2) | 0.218(0.001) | 0.496(0.014) | −142.4(10.8) | −167.5(12.5) |
| poly(A)/poly(T) default | 111.1(0.8) | 4373.4(190.8) | 97.7(0.4) | 0.040(0.000) | 0.307(0.017) | −210.6(9.5) | −214.0(15.1) |
| poly(A)/poly(T) 2.8_all | 38.5(0.4) | 2403.1(170.3) | 38.1(0.1) | 0.086(0.004) | 0.351(0.014) | −97.2(8.2) | −134.3(11.0) |
| poly(G)/poly(C) default | 62.0(0.6) | 1500.3(59.5) | 28.9(0.2) | 0.260(0.001) | 0.540(0.008) | −123.1(5.4) | −129.0(5.5) |
| poly(G)/poly(C) 2.8_all | 51.5(0.6) | 1315.1(57.3) | 53.7(0.3) | 0.243(0.001) | 1.037(0.017) | −188.4(9.5) | −217.0(10.1) |
| Z-DNA | 175.4(1.0) | 2618.5(59.0) | 126.9(0.3) | 0.001(0.000) | 0.012(0.015) | −4.0(0.7) | −4.9(6.4) |
| RNA | |||||||
| Experiment3 | 57(2) | 350(100) | 100(2) | N/A | −0.85(0.04) | N/A | 47(14) |
| default | 66.3(0.9) | 979.0(40.5) | 53.0(0.2) | 0.161(0.001) | 0.797(0.011) | −116.5(5.2) | −124.2(5.4) |
| default_frag | 66.5(0.8) | 983.1(37.9) | 52.7(0.2) | 0.161(0.001) | 0.802(0.016) | −116.2(4.8) | −125.5(5.4) |
| 2.8_all | 46.9(0.7) | 776.7(36.5) | 42.4(0.3) | 0.165(0.001) | 0.650(0.020) | −76.7(3.8) | −80.3(4.5) |
| 2.8_all_frag | 46.9(0.7) | 773.1(35.7) | 42.8(0.3) | 0.164(0.001) | 0.648(0.008) | −76.8(3.8) | −79.8(3.8) |
| 2.0_noprot | 76.3(1.1) | 996.9(42.2) | 49.7(0.2) | 0.220(0.001) | 1.030(0.009) | −146.7(7.0) | −163.5(7.1) |
| 2.0_noprot_frag | 75.8(0.9) | 1034.0(39.3) | 49.9(0.2) | 0.219(0.001) | 1.045(0.004) | −151.2(6.5) | −171.9(6.6) |
| poly(A)/poly(U) default | 82.0(0.9) | 1354.0(51.3) | 57.6(0.3) | 0.120(0.001) | 0.689(0.014) | −133.8(5.6) | −148.4(6.4) |
| poly(A)/poly(U) 2.8_all | 59.1(0.8) | 1049.2(48.5) | 69.2(0.3) | 0.145(0.001) | 0.981(0.026) | −146.7(7.5) | −163.9(8.8) |
| poly(G)/poly(C) default | 86.4(0.9) | 1197.1(41.7) | 62.9(0.4) | 0.179(0.001) | 1.050(0.018) | −175.6(7.1) | −200.0(7.8) |
| poly(G)/poly(C) 2.8_all | 51.7(0.7) | 706.2(29.4) | 34.8(0.1) | 0.246(0.003) | 0.831(0.006) | −82.1(3.8) | −93.4(4.0) |
The values in parenthesis are the corresponding fitting errors.
1
Computed from the slope of link vs. force plots.
2
Computed from the slope of extension vs. link plots.
3
Data from Lipfert et al., unpublished data.
4
Data from Gore et al. Nature 2006 (ref. [14]).
5
See Table 1 for detailed description for each parameter set.
6
“_frag” stands for using fragment picking sampling method.