Structure of a B-DNA dodecamer

Dickerson, Richard E.; Drew, Horace R.

doi:10.1016/0022-2836(81)90357-0

Cited by 883 publications

(434 citation statements)

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“…These phenomena can be explained, at least qualitatively, with the aid of the Calladine/Dickerson C3 sum function [34,351. The crystal structure data [36] the steric clash between purine bases of opposite strands of the duplex, produced by the propellor twist, can be alleviated by several mechanisms. One of these proposed mechanisms is the separation of purines by sliding one or both of the base pairs concerned along its long axis so that the purine is pulled out of the base-pair stack.…”

Section: The Important Backbone Torsion Angle B (C5'-c4'-mentioning

confidence: 99%

Conformational analysis of the B and Z forms of the d(m⁵C‐G)₃ and d(br⁵C‐G)₃ hexamers in solution

Orbons

Altona

1986

European Journal of Biochemistry

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The B and the Z forms of the DNA hexamers d(m5C-G)3 and d(b~-%-G)~ were investigated by means of NMR spectroscopy. It is demonstrated that the low-salt form of d(m5C-G)3 is a B DNA structure. The form, which becomes increasingly predominant when increasing amounts of MgC12 and/or methanol are added to the solution, has Z DNA characteristics. It is shown that the major geometrical features of the Z form of d(mSC-G)3 in the crystal structure are maintained in solution, with the dC residues S sugar conformation, y ' and the base in the anti orientation and the dG residues N (except the 3'-terminal residue), yf and syn. Neither the Z form of the methylated nor that of the brominated compound resembles the Z form, in which the deoxy guanosine sugar rings adopt a Cl'-exo conformation. Substitution of m5C by br5C causes no perceptible conformational changes in either the B or in the Z forms.The polymorphism exhibited by the DNA double helix [I, 21 has fascinated investigators from many fields of research for a long time. It is becoming clear that the character of the bases (purine R or pyrimidine Y) and their sequence determine the conformational possibilities of a given DNA species. For example, the peculiar inversion of the CD spectrum of poly d(G,C) . poly d(G,C) upon addition of salt [3] and/or alcohols [4,5] appeared limited to polymer duplex species that contain alternating dC-dG sequences and few others (dA-dC, dT-dG). This inversion was later shown to be a consequence of the conversion of the right-handed B DNA form into the lefthanded Z DNA species 16, 71. Detailed NMR and CD studies have revealed that Z DNA can be stabilized chemically in several ways. For instance, methylation [8,9] or bromination [lo-121 at the C-5 position of cytosine, or bromination at the C-8 position of guanine [13, 141 shifts the equilibrium between the B and Z forms towards the latter DNA species.Up till now information concerning the detailed geometry of Z DNA has come almost exclusively from X-ray crystallography 1151. In contrast to the classical B form, Z DNA has only a minor groove, which resembles the minor groove of B DNA. The major groove of B DNA constitutes an outer surface of Z DNA and exposes the cytosine C-5 and guanine N-7 and C-8 atoms. The major geometrical characteristics of Z DNA in the crystal can be summarized as follows: (a) the pyrimidines ( Y ) adopt a standard conformation with S-type sugar pucker, base anti (Fig. l ) and g + orientation about torsion angle y (Fig. 2); (b) the purines (R) prefer This paper is number 46 in a series Nucleic Acid Constituents from this laboratory; for part 45 see the preceding paper in this journal.Abbreviations. Me,NCI, tetramethylammonium chloride; NOE, nuclear Overhauser effect; NOESY, two-dimensional nuclear Overhauser spectroscopy; COSY, correlated spectroscopy. N-type sugars, base syn (Fig. I) and a g' rotamer about y ; (c) the phosphodiester bonds adopt the (+, a+ rotamer combination for the Y-R step and usually l -, a' for the R-Y step. It should be mentioned here that spe...

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Section: The Important Backbone Torsion Angle B (C5'-c4'-mentioning

confidence: 99%

Conformational analysis of the B and Z forms of the d(m⁵C‐G)₃ and d(br⁵C‐G)₃ hexamers in solution

Orbons

Altona

1986

European Journal of Biochemistry

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“…That the T (5)-H 6 resonance intensities are reproduced better by a structure different from that of the other base protons might be rationalized by noting that this residue is the first pyrimidine after a series of purine residues. In their X-ray crystallographic study of the influence of base sequence on helix structure in the dodecamer [d(CGCGAATTCGCG)],, Dickerson and Drew [6] reported several structural deviations or purine-pyrimidine sequences relative to purine-purine or pyrimidine-pyrimidine sequences. The six internal residues in the Dickerson sequence and in the [7] have performed Xray analysis of the EcoRI endonuclease co-crystallized with the tridecamer [d(TCGCGAATTCGCG)I2 (again, the central six-base sequence is the EcoRI site) and found that at the GAA-TTC junction, there is a kink.…”

Section: Theoretical (Upper Triangle) Andexperimental (Lower Triangmentioning

confidence: 99%

Investigation of the solution structure of a DNA octamer [d(GGAATTCC)]₂ using two‐dimensional nuclear Overhauser enhancement spectroscopy

Broido

James

Zon

et al. 1985

European Journal of Biochemistry

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Proton two-dimensional nuclear Overhauser enhancement (2 D NOE) spectra in the pure absorption phase were obtained at 500 MHz for [d(GGAATTCC)], in aqueous solution at a series of mixing times. The experimental data were analyzed by comparison with theoretical spectra calculated using the complete 70 x 70 relaxation matrix including all proton dipole-dipole interactions and spin diffusion [Keepers, J. W. &James, T. L. (1984) J . M a p . Reson. 57,404-4261. The theoretical spectra at each mixing time were calculated using two structures: a standard B-form DNA structure and an energy-minimized structure based on the similarity of the six internal residues of the title octamer with those of the dodecamer [d(CGCGAATTCGCG)],, for which the crystal structure has been determined. Neither the standard B-form nor the energy-minimized structure will yield theoretical 2 D NOE spectra which accurately reproduce all peak intensities in the experimental spectra. However, many features of the experimental spectra can be represented by both the B-form and the energy-minimized structure. Sequencedependent structural characteristics are manifest in the 2 D NOE spectra, in particular at the purine-pyrimidine junction as noted previously in the crystal structure. On the whole, the energy-minimized structure appears to yield theoretical 2 D NOE spectra which mimic many, if not all, aspects of the experimental spectra. All 2 D NOE data were consistent with nanosecond correction times as implied by proton spin-lattice relaxation time measurements. But better fits of some of the 2 D NOE data using small variations in an effective isotropic correlation time suggest that there may be some local variations in mobility within the octamer duplex structure in solution.With recent advances in DNA synthesis enabling the preparation of DNA oligomers of known, specific sequence [l -41, X-ray crystallographers are examining DNA oligomers of different sequences and reporting details of sequence-dependent crystalline conformations [3, 5 -81. Questions regarding the structure of these DNA fragments in solution are also being addressed. These questions focus on the extent of preservation of the crystal structures in solution and on the manner in which the solution and crystal structures differ. On a more general level, discussion also focusses on whether or not it is accurate to speak of a molecular structure in solution and by what means may such a structure be determined. The continuing development of high-resolution NMR technology has both spurred such questions and been of great use in the quest for answers. Two-dimensional NMR (2D NMR), in particular, has developed to the point that proton spectra of biomolecules, spectra with perhaps hundreds of lines and once thought to be undecipherable, can now, in many cases, be totally assigned [I, 4,9 -111. Following assignment, both oneand two-dimensional NMR techniques enable spectroscopists to start probing in detail the solution conformations of these molecules.Correspondence to T. L. James, Departmen...

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“…A second alternative for homology pairing may arise from the base-pair dependent conformation of DNA. 17,18 It has been well established that DNA wraps on histones at defined sequence tracts, 19 the base sequence simultaneously encoding the nucleosome positioning. 20 This may arise from base-pair sequence dependence in the bending of DNA, 21,22 but also from the base pair dependence of DNA structure.…”

Section: Introductionmentioning

confidence: 99%

Which way up? Recognition of homologous DNA segments in parallel and antiparallel alignments

Lee

Wynveen

Albrecht

et al. 2015

The Journal of Chemical Physics

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Homologous gene shuffling between DNA molecules promotes genetic diversity and is an important pathway for DNA repair. For this to occur, homologous genes need to find and recognize each other. However, despite its central role in homologous recombination, the mechanism of homology recognition has remained an unsolved puzzle of molecular biology. While specific proteins are known to play a role at later stages of recombination, an initial coarse grained recognition step has, however, been proposed. This relies on the sequence dependence of the DNA structural parameters, such as twist and rise, mediated by intermolecular interactions, in particular, electrostatic ones. In this proposed mechanism, sequences that have the same base pair text, or are homologous, have lower interaction energy than those sequences with uncorrelated base pair texts. The difference between the two energies is termed the "recognition energy." Here, we probe how the recognition energy changes when one DNA fragment slides past another, and consider, for the first time, homologous sequences in antiparallel alignment. This dependence on sliding is termed the "recognition well." We find there is a recognition well for anti-parallel, homologous DNA tracts, but only a very shallow one, so that their interaction will differ little from the interaction between two nonhomologous tracts. This fact may be utilized in single molecule experiments specially targeted to test the theory. As well as this, we test previous theoretical approximations in calculating the recognition well for parallel molecules against MC simulations and consider more rigorously the optimization of the orientations of the fragments about their long axes upon calculating these recognition energies. The more rigorous treatment affects the recognition energy a little, when the molecules are considered rigid. When torsional flexibility of the DNA molecules is introduced, we find excellent agreement between the analytical approximation and simulations. C 2015 AIP Publishing LLC. [http://dx

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Structure of a B-DNA dodecamer

Cited by 883 publications

References 12 publications

Conformational analysis of the B and Z forms of the d(m⁵C‐G)₃ and d(br⁵C‐G)₃ hexamers in solution

Conformational analysis of the B and Z forms of the d(m⁵C‐G)₃ and d(br⁵C‐G)₃ hexamers in solution

Investigation of the solution structure of a DNA octamer [d(GGAATTCC)]₂ using two‐dimensional nuclear Overhauser enhancement spectroscopy

Which way up? Recognition of homologous DNA segments in parallel and antiparallel alignments

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Structure of a B-DNA dodecamer

Cited by 883 publications

References 12 publications

Conformational analysis of the B and Z forms of the d(m5C‐G)3 and d(br5C‐G)3 hexamers in solution

Conformational analysis of the B and Z forms of the d(m5C‐G)3 and d(br5C‐G)3 hexamers in solution

Investigation of the solution structure of a DNA octamer [d(GGAATTCC)]2 using two‐dimensional nuclear Overhauser enhancement spectroscopy

Which way up? Recognition of homologous DNA segments in parallel and antiparallel alignments

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Conformational analysis of the B and Z forms of the d(m⁵C‐G)₃ and d(br⁵C‐G)₃ hexamers in solution

Conformational analysis of the B and Z forms of the d(m⁵C‐G)₃ and d(br⁵C‐G)₃ hexamers in solution

Investigation of the solution structure of a DNA octamer [d(GGAATTCC)]₂ using two‐dimensional nuclear Overhauser enhancement spectroscopy