The Dickerson-Drew B-DNA Dodecamer Revisited at Atomic Resolution

Tereshko, Valentina; Minasov, G.; Egli, Martin

doi:10.1021/ja9832919

Cited by 171 publications

(188 citation statements)

References 19 publications

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“…The crystallographic evidence in favor of this proposition is based entirely on cryogenic diffraction data (36)(37)(38). 23 Na and 87 Rb magnetic relaxation dispersion studies (39,40) of DNA in solution at ambient temperatures indicate that ion binding is weak (partial occupancy) and relatively short-lived (submicrosecond at 277 K), so the thermodynamic and kinetic parameters should fall in the range of values examined here.…”

Section: Discussionmentioning

confidence: 86%

Biomolecular cryocrystallography: Structural changes during flash-cooling

Halle

2004

Proc. Natl. Acad. Sci. U.S.A.

189

143

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To minimize radiation damage, crystal structures of biological macromolecules are usually determined after rapid cooling to cryogenic temperatures, some 150 -200 K below the normal physiological range. The biological relevance of such structures relies on the assumption that flash-cooling is sufficiently fast to kinetically trap the macromolecule and associated solvent in a room-temperature equilibrium state. To test this assumption, we use a two-state model to calculate the structural changes expected during rapid cooling of a typical protein crystal. The analysis indicates that many degrees of freedom in a flash-cooled protein crystal are quenched at temperatures near 200 K, where local conformational and association equilibria may be strongly shifted toward low-enthalpy states. Such cryoartifacts should be most important for strongly solvent-coupled processes, such as hydration of nonpolar cavities and surface regions, conformational switching of solventexposed side chains, and weak ligand binding. The dynamic quenching that emerges from the model considered here can also rationalize the glass transition associated with the atomic fluctuations in the protein.protein structure ͉ protein hydration ͉ protein glass transition ͉ x-ray diffraction

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Section: Discussionmentioning

confidence: 86%

Biomolecular cryocrystallography: Structural changes during flash-cooling

Halle

2004

Proc. Natl. Acad. Sci. U.S.A.

189

143

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“…The second reason is that the interaction among duplexes which are stabilized by the divalent cations are very different in the presence of Ca 2ϩ (Figs. 2 and 3) than in the presence of Mg 2ϩ (11).…”

Section: Discussionmentioning

confidence: 89%

Structure of d(CGCGAATTCGCG) in the Presence of Ca2+Ions

Liu¹,

Subirana²

1999

Journal of Biological Chemistry

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The dodecamer d(CGCGAATTCGCG) was the first oligonucleotide to be crystallized as a B-DNA duplex. Its structure was analyzed in detail in the early 1980s. Here we show that, in the presence of Ca 2؉ , it crystallizes in a different way (R3 space group). The dodecamers form parallel columns of straight duplexes with ten base pairs in the B form. The terminal cytosines in each molecule are disordered, whereas the terminal guanines are placed in the minor groove of neighbor duplexes. The central GAATTC region is practically identical to that found in the classic structure of the same dodecamer crystallized in the P2 1 2 1 2 1 space group in the presence of Mg 2؉ and spermine. Its structure is thus independent of the crystallization conditions which have been used.The first detailed structure of a DNA oligonucleotide in the B-form determined by single crystal x-ray diffraction methods was published in this journal in 1982 (1). The structure of a bromine derivative was compared with that previously determined (2, 3) for the native dodecamer at different temperatures. Its features were analyzed in detail in several other publications (4 -7). Many other derivatives from the same oligonucleotide and related sequences, alone and in association with drugs, have also been studied. Coordinates and references may be found in the Nucleic Acid Database (8). Most of them are in practically identical unit cells in the P2 1 2 1 2 1 space group. The original work (1-3) was a landmark in the study of DNA because it confirmed unequivocally the double helical structure of B-form DNA and, at the same time, showed many features of conformation as a function of sequence. More recently, the same dodecamer has been crystallized under various ionic conditions (9 -13). A high resolution (1.4 Å) was obtained (9) in the presence of Na ϩ /Mg 2ϩ /spermine, giving a structure essentially similar to those first reported by Dickerson and co-workers (1-3). Given the higher resolution of that structure (9), we used it for comparison with our results.Most of the work described in the previous paragraph was carried out with crystals obtained in the presence of Mg 2ϩ and spermine. Recently we discovered (14) that, in the presence of a high concentration of Ca 2ϩ ion, this oligonucleotide could crystallize in the R3 space group. Here we report the results we have obtained under the latter crystallization conditions at a higher resolution than that previously reported (14). Our results show that the central sequence GAATTC is practically identical in both cases, whereas the conformation of the terminal CGC/GCG sequences is much more variable because of the interaction with neighbor molecules in the crystal. EXPERIMENTAL PROCEDURESCrystallization-The crystal was grown by the vapor diffusion hanging drop method. The crystallization solution contained 0.4 mM dodecamer (NH 4 ϩ salt), 300 mM CaCl 2 , 10% MPD (2-methyl-2,4-pentanediol), and 20 mM cacodylic acid (pH 7.0). The concentration of monovalent cations (Na ϩ from the buffer and NH 4 ϩ from the dodecame...

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“…Hydrogen atoms were merged with the attached heavy atoms, and a cutoff of 4 A Å was used (very similar results were obtained for 3 A Å or 5 A Å). For the five central nominal water sites in the primary spine of hydration of A 2 T 2 , we thus obtained ϭ 1.3 Ϯ 0.2 MHz, with no significant difference between two crystal structures (5,7). Although this estimate is crude, it is reassuring to note that QCCs for oxygencoordinated Na ϩ derived from 23 Na NMR studies of cryptands (39) and inorganic solids (40) as well as from molecular simulations (41,42) generally fall in the range of 1-2 MHz.…”

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confidence: 76%

“…Nevertheless, it has been argued on the basis of indirect crystallographic evidence that the primary solvation sites of the so-called ''spine of hydration'' in the narrow minor groove of the [d(CGCGAATTCGCG)] 2 duplex (hereafter referred to as A 2 T 2 ) are not exclusively occupied by water molecules but are partly substituted by Na ϩ ions (5,6). However, a subsequent atomic-resolution (1.1 Å) study of the same duplex (but with a 4-fold higher Mg 2ϩ ͞Na ϩ ratio in the crystallizing solution) did not find any evidence, direct or indirect, for the presence of Na ϩ ions in the minor groove (7). Another study (8) found that the Mg 2ϩ salt of the cross-linked A 2 T 2 duplex (with virtually no monovalent ions present in the crystal) has essentially the same structure (at 1.43-Å resolution) as the Na ϩ salt of the native duplex (at 1.9 Å) (9).…”

mentioning

confidence: 99%

Sequence-specific binding of counterions toB-DNA

Денисов

Halle

2000

Proc. Natl. Acad. Sci. U.S.A.

170

154

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Recent studies by x-ray crystallography, NMR, and molecular simulations have suggested that monovalent counterions can penetrate deeply into the minor groove of B form DNA. Such groovebound ions potentially could play an important role in AT-tract bending and groove narrowing, thereby modulating DNA function in vivo. To address this issue, we report here 23 Na magnetic relaxation dispersion measurements on oligonucleotides, including difference experiments with the groove-binding drug netropsin. The exquisite sensitivity of this method to ions in long-lived and intimate association with DNA allows us to detect sequencespecific sodium ion binding in the minor groove AT tract of three B-DNA dodecamers. The sodium ion occupancy is only a few percent, however, and therefore is not likely to contribute importantly to the ensemble of B-DNA structures. We also report results of ion competition experiments, indicating that potassium, rubidium, and cesium ions bind to the minor groove with similarly weak affinity as sodium ions, whereas ammonium ion binding is somewhat stronger. The present findings are discussed in the light of previous NMR and diffraction studies of sequence-specific counterion binding to DNA.

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The Dickerson-Drew B-DNA Dodecamer Revisited at Atomic Resolution

Cited by 171 publications

References 19 publications

Biomolecular cryocrystallography: Structural changes during flash-cooling

Biomolecular cryocrystallography: Structural changes during flash-cooling

Structure of d(CGCGAATTCGCG) in the Presence of Ca2+Ions

Sequence-specific binding of counterions toB-DNA

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