2564
J. Phys. Chem. 1996, 100, 2564-2566
B to A Transition of DNA on the Nanosecond Time Scale Liqiu Yang and B. Montgomery Pettitt* Department of Chemistry, UniVersity of Houston, Houston, Texas 77204-5641 ReceiVed: October 17, 1995; In Final Form: December 6, 1995X
A 3.5-ns atomic-level computer simulation of a DNA solution was performed. We found that a dodecamer of DNA, which contains the recognition site for Eco RI endonuclease, transforms from B-form to A-form in 0.45 M salt water. This supports an earlier proposal on the A-DNA binding site for transcription factor IIIA.
The structural flexibility and polymorphism of nucleic acids are closely related to their genetic and biological functions. Most conformations of DNA and RNA in ViVo are widely accepted as B-type and A-type, respectively. Hamilton speculated that the DNA template remains in B-form during DNA replication but undergoes a reversible B f A transition during RNA transcription.1 The B f A transition has been found to occur in both eukaryotic and prokaryotic DNAs upon binding by small acid-soluble spore proteins;2 such a transition locks the DNA in the relatively more rigid A-form with much reduced ultraviolet (UV) photoreactivity.3 Freezing of the B f A transition, such as by DNA-binding drugs, may cause a malfunction of DNA biochemistry.4 Ivanov and Krylov recently reviewed existing experimental probes for the B f A transition and the thermodynamic and statistical mechanical aspects of the transition.5 The B f A transition is sequence specific (pro-G‚C) and environment dependent, preferring low relative humidity (i.e., high salt concentration) in fibers and high concentration of alcohols in low-salt solutions.6 Several recently published computer simulations of DNA in solution,7,8 crystal,9 and cluster10 did not indicate the occurrence of a B f A transition. However, one of the earliest simulations of DNA11 as well as some recently published simulations12 and unpublished simulations13 revealed the B f A tendency. Here we report a B f A transition of [d(CGCGAATTCGCG)]2 in high-salt solution from a 3.5-ns molecular dynamics simulation (Figure 1). This molecule represents the first B-DNA crystal structure solved14 (0 ns in Figure 1) and contains the recognition site for Eco RI endonuclease GAATTC. The entire system contains 758 DNA atoms, 38 Na+ ions, 16 Cl- ions, and 1801 water molecules in a 33 Å × 33 Å × 54 Å periodic box. The CHARMM 2315 all-hydrogen parameters (version 6.1, November 1993) were employed. The initialization (random placement of ions) and equilibration (200 ps) procedures are similar to those in ref 16. A 2-fs time step, velocity Verlet algorithm,17 and SHAKE bond constraints17 were used in the constant-energy production run at 298 ( 5 K. To calculate the long-range Coulomb forces accurately, we used the Ewald method,17 which has recently been used in simulations of peptides,18,19 triple-helical DNA,16 double-helical DNA,7,9 RNA hairpin loops,7 and proteins.7 We used an Ewald convergence parameter (κ) of 0.24 Å-1 and 709 lattice vectors in the reciprocal-space sum.17 Figure 1 depicts the displacement of base pairs from the center to the edge of the DNA helix as time progresses. The structure at 2.0 ns is “hollow” at the center (Figure 1), which is distinct from the initial B-DNA at 0 ns but similar to the ideal A-DNA X
Abstract published in AdVance ACS Abstracts, January 15, 1996.
0022-3654/96/20100-2564$12.00/0
Figure 1. Sketch plots of the DNA viewed along the helix axis at 0, 0.5, and 2.0 ns during the simulation, together with an ideal A-DNA built using QUANTA.33 The 486 heavy atoms of the DNA are shown as vertices and connected by lines representing covalent bonds.
Figure 2. The root-mean-square (r.m.s.) positional deviations per atom of the 410 nonterminal heavy atoms of the DNA as functions of time, best-fit to the A-DNA (thick curve) and B-DNA (thin curve) in Figure 1, respectively.
structure. Figures 2 and 3 demonstrate that, after a B f A transition, the DNA structure remains more A-like for at least 2 ns near the end of the simulation. The original parameters in Figure 3 (the unscaled F(t)’s) averaged from 1.5 ns to the end of the simulation are (a) sugar pucker pseudorotation phase angle ) (13 ( 5)°, i.e., C3′-endo; (b) rotation per residue around helix axis ) (30 ( 1)°; (c) rise per residue along helix axis ) 2.8 ( 0.1 Å; (d) intrastrand distance between adjacent phosphorus atoms ) 5.9 ( 0.1 Å; © 1996 American Chemical Society
B to A Transition of DNA
Figure 3. Key conformation-defining parameters of nonterminal DNA residues as functions of time in a linearly scaled form: (a) pseudorotation, (b) twist, (c) rise, (d) P-P distance, and (e) tilt or inclination. For a parameter F at time t, we plot f(t) ) [F(t) - FB-DNA]/(FA-DNA FB-DNA), such that f(t) ) 0 and f(t) ) 1 correspond to B-DNA and A-DNA in Figure 1, respectively.
and (e) base-pair tilt6 or inclination20 toward helix axis ) (11 ( 3)°. Comparisons of these values to those of B-DNA and A-DNA in ref 6 and Figure 1 indicate that the B f A transition is nearly complete in the simulation. The nanosecond time scale for DNA transition that we report here seems realistic. Nuclear magnetic resonance (NMR) measurements in solution revealed a possible two-state isomerization between the B-DNA and a non-B-DNA with a time constant of 1-2 ns, accompanied by local angular motions up to (35° from the average geometry.21 The A-DNA structure in pure salt water that we find here is likely to have biological relevance. Arnott et al. envisaged that RNA synthetases and DNA replicases would be compatible only with DNA targets of A-type and B-type, respectively.22 Rhodes and Klug, on the basis of nuclease digestion experiments, proposed specifically that the binding site for transcription factor IIIA (TFIIIA) has an A-DNA form.23 X-ray diffraction experiments in DNA crystal24 supported the Rhodes-Klug proposal of an A-DNA for the TFIIIA binding site; however, circular dichroism (CD),25,26 NMR,26 and UV footprinting3 experiments in solution suggested the site to be a B-DNA. More recent CD studies reached a conclusion that the TFIIIA binding site in solution has an intermediate structure between A-DNA and B-DNA.27 Unlike in the other studies,3,25,26 the conclusion of ref 27 is based upon direct comparisons of the TFIIIA binding site with the best-known A-DNA and B-DNA in the same set of experiments. The dodecamer [d(CGCGAATTCGCG)]2 was selected to be the B-DNA defining molecule in certain solution conditions in ref 27. Raman spectroscopy28 and NMR29 studies reveal, however, that the dodecamer structure in solution is different from the B-DNA in the crystal. The solution structure is characterized by an increase in the C3′-endo (i.e., A-DNA) population28 and an average rotation per residue of 20°, which is closer to that of A-DNA than B-DNA but much smaller than both.29 There is considerable evidence from Raman spectroscopy,28 NMR,29 and the present simulation that the dodecamer in solution exhibits a B f A tendency to varying degrees,
J. Phys. Chem., Vol. 100, No. 7, 1996 2565 leading to a more A-like TFIIIA binding site, as proposed originally by Rhodes and Klug.23 The experimental characterizations of the dodecamer structure are quite different;27-29 the lack of a consensus among experiments precludes a unique test for the accuracy of our computer simulation. As compared to the experiments,27-29 our simulation has higher DNA concentration (28 mM) and salt concentration (1.1 M in Na+ and 0.45 M in Cl-). The B f A transition in the simulation may be salt induced (although ion distributions are similar in the two states) or even possibly affected by the force field. CD and NMR studies of poly(G‚C) showed that, however, about 4 M NaCl is required to induced completed R f L,30 B f “alternating B”,31 and B f Z32 transitions. Unpublished simulation results, using a cutoff method for Coulomb forces, did not reveal an obvious effect of the salt concentration (0-0.5 M MgCl2) on the B f A transition of the dodecamer.13 Current work employing the Ewald method for Coulomb forces and experiments using the same DNA and salt concentration will help us to reach a firmer conclusion on concentration effects. In conclusion, the present DNA simulation showed a nanosecond B f A transition of DNA supporting existing evidence on the polymorphism of DNA. Acknowledgment. We thank Dr. P. E. Smith and Dr. S. Weerasinghe for valuable assistance and discussions, Mr. M. Sabripour and Mr. H. D. Blatt for help in using the new CHARMM parameters, Prof. A. D. MacKerell for sharing ref 13 prior to publication, and Dr. D. M. York for discussions about DNA dodecamer simulations prior to publication. References and Notes (1) Hamilton, L. D. Nature 1968, 218, 633-637. (2) Mohr, S. C.; Sokolov, N. V. H. A.; He, C.; Setlow, P. Proc. Natl. Acad. Sci. USA 1991, 88, 77-81. (3) Becker, M. M.; Wang, Z. J. Biol. Chem. 1989, 264, 4163-4167. (4) Fritzsche, H. Nucleic Acids Res. 1994, 22, 787-791. (5) Ivanov, V. I.; Krylov, D. Y. Meth. Enzymol. 1992, 211, 111-127. (6) Saenger, W. Principles of Nucleic Acid Structure; SpringerVerlag: New York, 1984. (7) Cheatham, T. E., III; Miller, J. L.; Fox, T.; Darden, T. A.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 4193-4194. (8) McConnell, K. J.; Nirmala, R.; Young, M. A.; Ravishanker, G.; Beveridge, D. L. J. Am. Chem. Soc. 1994, 116, 4461-4462. (9) York, D. M.; Yang, W.; Lee, H.; Darden, T.; Pedersen, L. J. Am. Chem. Soc. 1995, 117, 5001-5002. (10) Miaskiewicz, K.; Osman, R.; Weinstein, H. J. Am. Chem. Soc. 1993, 115, 1526-1537. (11) Levitt, M. Cold Spring Harbor Symp. Quant. Biol. 1983, 47, 251262. (12) Kumar, S.; Duan, Y.; Kollman, P. A.; Rosenberg, J. M. J. Biomol. Struct. Dyn. 1994, 12, 487-525. (13) MacKerell, A. D. J. Am. Chem. Soc., submitted. (14) Drew, H. R.; Wing, R. M.; Takano, T.; Broka, C.; Tanaka, S.; Itakura, K.; Dickerson, R. E. Proc. Natl. Acad. Sci. USA 1981, 78, 21792183. (15) Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217. (16) Weerasinghe, S.; Smith, P. E.; Mohan, V.; Cheng, Y.-K.; Pettitt, B. M. J. Am. Chem. Soc. 1995, 117, 2147-2158. (17) Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Oxford University: New York, 1987. (18) Smith, P. E.; Pettitt, B. M. J. Chem. Phys. 1991, 95, 8430-8441. (19) Schreiber, H.; Steinhauser, O. Biochemistry 1992, 31, 5856-5860. (20) Dickerson, R. E.; Bansal, M.; Calladine, C. R.; Diekmann, S.; Hunter, W. N.; Kennard, O.; Lavery, R.; Nelson, H. C. M.; Olson, W. K.; Saenger, W.; Shakked, Z.; Sklenar, H.; Soumpasis, D. M.; Tung, C. S.; von Kitzing, E.; Wang, A. H.-J.; Zhurkin, V. B. J. Mol. Biol. 1989, 205, 787-791. (21) Hogan, M. E.; Jardetsky, O. Biochemistry 1980, 19, 3460-3468. (22) Arnott, S.; Fuller, W.; Hodgson, A.; Prutton, I. Nature 1968, 220, 561-564. (23) Rhodes, D.; Klug, A. Cell 1986, 46, 123-132. (24) McCall, M.; Brown, T.; Hunter, W. N.; Kennard, O. Nature 1986, 322, 661-664.
2566 J. Phys. Chem., Vol. 100, No. 7, 1996 (25) Gottesfeld, J. M.; Blanco, J.; Tennant, L. L. Nature 1987, 329, 460-462. (26) Aboul-ela, F.; Varani, G.; Walker, G. T.; Tinoco, I., Jr. Nucleic Acids Res. 1986, 16, 3559-3572. (27) Fairall, L.; Martin, S.; Rhodes, D. EMBO J. 1989, 8, 1809-1817. (28) Peticolas, W. L.; Thomas, G. A.; Wang, Y. J. Mol. Liquids 1989, 41, 367-388. (29) Nerdal, W.; Hare, D. R.; Reid, B. R. Biochemistry 1989, 28, 1000810021.
Yang and Pettitt (30) Pohl, F. M.; Jovin, T. M. J. Mol. Biol. 1972, 67, 375-396. (31) Patel, D. J.; Canuel, L. L.; Pohl, F. M. Proc. Natl. Acad. Sci. USA 1979, 76, 2508-2511. (32) Patel, D. J.; Kozlowski, S. A.; Nordheim, A.; Rich, A. Proc. Natl. Acad. Sci. USA 1982, 79, 1413-1417. (33) QUANTA, Molecular Simulations Inc., release 4.0, 1994.
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