Formation of (C.G)*G Triplets in a B-DNA Duplex with Overhanging Bases

Vlieghe, D.; Meervelt, Luc Van; Dautant, Alain; Gallois, B.; Précigoux, G.; Kennard, Olga

doi:10.1107/s0907444996003216

Cited by 14 publications

(19 citation statements)

References 33 publications

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“…It is evident that the central AATT sequence contains a quite rigid spine of hydration, first described by Drew and Dickerson (1), which is very stable. The minor groove is also very narrow in all three cases, although in the nonamer case it is about 0.6 Å wider at the center, as already reported (12).…”

Section: The Atomic Coordinates For Both Crystal Structures Are Availsupporting

confidence: 65%

“…The characteristic triplet interaction of this nonamer (12) is shown in the figure. Comparison of the duplex structure of d(GCGAATTCG) with the data obtained at a lower resolution (12) does not show any significant difference (root mean square excluding phosphates between both structures is 0.33 Å). The main difference is that in our study four phosphate groups are disordered and have at least a double conformation.…”

Section: The Atomic Coordinates For Both Crystal Structures Are Availmentioning

confidence: 99%

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Water and Ions in a High Resolution Structure of B-DNA

Soler-López¹,

Malinina²,

Liu³

et al. 1999

Journal of Biological Chemistry

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A detailed picture of hydration and counterion location in the B-DNA duplex d(GCGAATTCG) is presented. Detailed data have been obtained by single crystal x-ray diffraction at atomic resolution (0.89 Å) in the presence of Mg 2؉ . The latter is the highest resolution ever obtained for a B-DNA oligonucleotide. Minor groove hydration is compared with that found in the Na ؉ and Ca 2؉ crystal forms of the related dodecamer d(CGCGAAT-TCGCG). High resolution data (1.45 Å) of the Ca 2؉ form obtained in our laboratory are used for that purpose. The central GAATTC has a very stable hydration spine identical in all cases, independent of duplex length and crystallization conditions (counterions, space group). However, the organization of the water molecules (tertiary and quaternary layers) associated with the central spine vary in each case.When the first dodecamer structure in the B-form was established, a "spine of hydration" was found in the minor groove (1). Recent high resolution data on the same dodecamer (2-5) have shown that a series of water hexagons may build up on the spine of hydration. However, some of the water-water distances are too long to be considered hydrogen bonds, and they correspond rather to Van der Waals contacts. An additional result of the studies mentioned above is that either K ϩ (3) or Rb ϩ (5) may partially occupy the water sites. It has also been suggested (2) that Na ϩ may also occupy the water sites, but this suggestion has been challenged (4, 6).The use of flash cooling and synchrotron radiation allows a much higher resolution in the x-ray diffraction data of oligonucleotides than was possible a few years ago. As a result, a much greater detail on water and ion distribution can be obtained.The detailed study of water and ions around DNA is interesting in itself, but it is also relevant to understand protein-DNA interactions. It has been suggested (7, 8) that water-mediated polar contacts may contribute to the specificity of protein-DNA recognition. A better understanding of water structure around DNA is essential to ascertain the eventual role of ions and hydration waters in DNA interactions. The data obtained from high resolution oligonucleotide structures will be of great value in this sense.Here we report the arrangement of water and divalent cations in the related structures of d(GCGAATTCG) in the presence of Mg 2ϩ (resolution ϭ 0.89 Å) and the calcium form of d(CGCGAATTCGCG) (resolution ϭ 1.45 Å). The high resolution achieved with these structures allows us to position with certainty many of the water and ions in the crystal. Thus, the influence of either monovalent (Na ϩ ) or divalent (Mg 2ϩ , Ca 2ϩ ) cations can be ascertained. The structure of the water spine is very clear and allows us to determine which water molecules occupy fixed positions. Hydrogen bonds and Van der Waals contacts can be clearly distinguished.The nonamer was crystallized, using a batch method, in sitting drops containing 0.5 mM DNA duplex, 1 mM acridine (Arg 4 ) drug-peptide adduct, 20 mM sodium cacodylate buff...

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Section: The Atomic Coordinates For Both Crystal Structures Are Availsupporting

confidence: 65%

Section: The Atomic Coordinates For Both Crystal Structures Are Availmentioning

confidence: 99%

Water and Ions in a High Resolution Structure of B-DNA

Soler-López¹,

Malinina²,

Liu³

et al. 1999

Journal of Biological Chemistry

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“…8 and 9, and has a very low B factor (6.5). It was also found with a low B factor in the room temperature structure (4). The precise interactions shown in Fig.…”

Section: Organization Of Counterions: An Ionic Crystal Around the Trimentioning

confidence: 64%

“…Related data from the 2.05-Å resolution structure (4) are also shown. The results presented here differ from our previous refinement (Nucleic Acid Database code: BD0016) in several features, which have already been discussed.…”

Section: Methodsmentioning

confidence: 99%

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Solvent Organization in an Oligonucleotide Crystal

Soler-López¹,

Malinina²,

Subirana³

2000

Journal of Biological Chemistry

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We describe the crystal structure of d(GCGAATTCG) determined by x-ray diffraction at atomic resolution level (0.89 Å). The duplex structure is practically identical to that described at 2.05 Å resolution (Van Meervelt, L., Vlieghe, D., Dautant, A., Gallois, B., Pré cigoux, G., and Kennard, O. (1995) Nature 374, 742-744), however about half of the phosphate groups show multiple conformations. The crystal has three regions with different solvent structure. One of them contains several ordered Mg ؉2 ions and can be considered as an ionic crystal. A second region is formed by a network of ordered water molecules with a polygonal organization that binds three duplexes. The third region is formed by channels of solvent in which very few ordered solvent molecules are visible. The less ordered phosphates are found facing this channel. The latter region provides a view of DNA with highly movable charges, both negative phosphates and counterions, without a precise location.Two periods could be distinguished in the x-ray diffraction studies of DNA: the era of fiber diffraction of polymeric DNA/ polynucleotides and the time of single crystal x-ray structures of short fragments. The data available from fiber diffraction were limited and allowed no detailed analysis. The goal of DNA crystallography is, therefore, the study of detailed DNA structures. However, crystallographic data are also limited in some important aspects of DNA structure. For example, it is well known (1) that the solvent environment plays an important role in the conformational behavior and interactions of DNA. To study this feature in detail, it is necessary to work with x-ray data at atomic resolution level. Until recently, such data were available only for Z-DNA fragments. This situation is now changing. Synchrotron radiation of increasing power, together with better detectors and cryotechniques, make possible a third period of DNA crystallography: the epoch of high resolution DNA structures.We recently presented (2) a preliminary account of the structure of the B-DNA fragment (GCGAATTCG) solved at atomic resolution (0.89 Å). This structure had already been solved at 2.05-Å resolution (3, 4). In our previous analysis we described the water spine in the minor groove and compared it with related structures. Here we present a detailed analysis of the same oligonucleotide, which has multiple conformations in several parts of the phosphodiester backbone. We also describe the organization of the solvent, which in some regions shows well resolved water molecules, whereas in other regions it remains disordered, despite the fact that our crystals have been studied at 120 K. Thus, a frozen sample at atomic resolution, instead of showing a highly ordered duplex, demonstrates multiple conformations and regions of disordered solvent. MATERIALS AND METHODSCrystallization-The d(GCGAATTCG) nonamer was crystallized, using a batch method, in sitting drops containing 0.5 mM DNA duplex, 1 mM acridine-(Arg 4 ) drug-peptide aduct, 20 mM sodium cacodylate buffer, pH 7, 100 mM...

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Nucleic Acid-Metal Ion Interactions in the Solid State

Aoki

Murayama

2011

Metal Ions in Life Sciences

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Metal ions play a key role in nucleic acid structure and activity. Elucidation of the rules that govern the binding of metal ions is therefore an essential step for better understanding of the nucleic acid functions. This review is as an update to a preceding one (Metal Ions Biol. Syst., 1996, 32, 91-134), in which we offered a general view of metal ion interactions with mono-, di-, tri-, and oligonucleotides in the solid state, based on their crystal structures reported before 1994. In this chapter, we survey all the crystal structures of metal ion complexes with nucleotides involving oligonucleotides reported after 1994 and we have tried to uncover new characteristic metal bonding patterns for mononucleotides and oligonucleotides with A-RNA and A/B/Z-DNA fragments that form duplexes. We do not cover quadruplexes, duplexes with metal-mediated base-pairs, tRNAs, rRNAs in ribosome, ribozymes, and nucleic acid-drug and -protein complexes. Factors that affect metal binding to mononucleotides and oligonucleotide duplexes are also dealt with.

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Formation of (C.G)*G Triplets in a B-DNA Duplex with Overhanging Bases

Cited by 14 publications

References 33 publications

Water and Ions in a High Resolution Structure of B-DNA

Water and Ions in a High Resolution Structure of B-DNA

Solvent Organization in an Oligonucleotide Crystal

Nucleic Acid-Metal Ion Interactions in the Solid State

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