Structure of a B-DNA dodecamer: conformation and dynamics.

Abstract

The crystal structure of the synthetic DNA dodecamer d (CpGpCpGpApApTpTpCpGpCpG) has been refined to a residual error ofR = 17.8% at 1.9-A resolution (two-o'data In the 28 years since a double helix model for B-DNA was proposed by Watson and Crick (2), direct evidence for its structure has been based on refinement of models having standard bond parameters against x-ray diffraction data from oriented fibers (3-6). This has had two disadvantages: loss of information because of rotational disorder about the fiber axis, and lack of information about the effect ofspecific base sequences, aside from a limited number of experiments on homopolymers and alternating copolymers. Recent advances in triester methods of DNA synthesis have made possible the preparation of molecules ofpredetermined base sequence, in quantities and purities suitable for single-crystal x-ray analysis. This paper presents the results ofa structure analysis and refinement ofa complete turn of right-handed B-DNA, with the sequence d(CpGpCpGpApApTpTpCpGpCpG). A preliminary report of the partially refined structure has appeared (7).Our structure analysis of the dodecamer C-G-C-G-A-A-T-T-C-G-C-G is a logical extension of the earlier analyses of C-G-C-G-C-G (8) and C-G-C-G (9). Both of the latter adopted a lefthanded zigzag or Z helix, a totally unexpected conformation whose relevance to biological DNA of more varied sequence became particularly interesting. In December 1979 we were fortunate in growing large single crystals of dodecamer, synthesized at Pasadena and Duarte. This sequence is ofparticular significance because it contains an EcoRI restriction site, G-A-A-T-T-C, and because it brackets a Z-incompatible A-A-T-T segment with two Z-compatible C-G-C-G ends, offering a test of the tendency of mixed-sequence DNA to adopt the Z conformation. In spite of favorable salt conditions, the central A-A-T-T segment apparently is sufficient to counteract the Z-forming tendencies ofthe tetrameric C-G-C-G ends, resulting in a classical Watson-Crick B helix throughout.Structure analysis and refinementThe dodecamer crystallizes in space group P212121 with a = 24.87 A, b = 40.39 A, c = 66.20 A, and two single strands or one double helix per asymmetric unit. Two isomorphous heavy atom derivatives were obtained by de novo triester synthesis with 5-bromodeoxycytidine at the third position along each strand and by diffusion of the anticancer agent cisplatin [cisdichlorodiamminoplatinum(II)] into pregrown crystals. Phases from this analysis were used to obtain a starting model for restrained least-squares refinement (10).Initial energy parameters for DNA as obtained from Michael Levitt were modified so that conformational energy would restrain the molecule to a sterically acceptable structure but would allow the x-ray data to determine this structure. Internal sugar ring bond angles were set to the average oftheir C2'-endo and C3'-endo values but were left flexible enough that other conformations could be obtained (11). The residual error or R factor for 2...

The puzzling unsolved mysteries of liquid water: Some recent progress

“…Specifically, Kumar et al [50] studied the dynamic and thermodynamic behavior of lysozyme and DNA in hydration TIP5P water, by means of the software package GROMACS [64] for: (i) an orthorhombic form of hen egg-white lysozyme [65] and (ii) a Dickerson dodecamer DNA [66] at constant pressure P ¼ 1 atm, several constant temperatures T, and constant number of water molecules N (NPT ensemble).…”

Possible conformations of double-helical polynucleotides containing incorrect base pairs

“…The data of Tables 1 and 3 (15) and for the A-familv -the limit values of the corresmonding angles of phenylalanine tRNA double-helical fragments in crystals of two different classes (16,17). Ranges Analysis of the short interatomic distances for conformations whose characteristics are given in Tables 1-4 shows that deviation of the double Table 5.…”

A Physical Picture of Atomic Motions within the Dickerson DNA Dodecamer in Solution Derived from Joint Ensemble Refinement against NMR and Large-Angle X-ray Scattering Data

“…In this paper, we seek to derive a physical picture of motions in DNA using a similar approach based upon ensemble refinement against NOE, J coupling, RDC and CSA NMR data, and solution large-angle X-ray scattering data. The duplex DNA investigated is the Dickerson dodecamer [d(CGCGAATTCGCG) 2 (33)] which has served as a model system for numerous experimental and theoretical studies and for which extensive solution data are available. In particular, a large amount of high-quality NOE, RDC, CSA, and J coupling NMR data have been measured (12,15), and the large-angle solution X-ray scattering spectrum (28) is inconsistent with the structure obtained by refinement against the most NMR data (15).…”