The Crystal Structure of d(CCCCGGGG): A New A-Form Variant with an Extended Backbone Conformation

Haran, Tali E.; Shakked, Zippora; Wang, A. H.-J.; Rich, Alexander

doi:10.1080/07391102.1987.10506390

Cited by 105 publications

(54 citation statements)

References 25 publications

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“…This kind of intercalation or stacking is characteristic of all the tetragonal octamers and is independent of the sequence. View perpendicular to the base pair G(l).C (8). These symmetric interaction about the dyad axis in the minor groove will have the effect of pushing the top and the bottom half of the duplex towards the major groove and will result in unwinding the central pyrimidine-purine step, commonly found in all the tetragonal octamers.…”

Section: The Base Pair Rollmentioning

confidence: 97%

Crystal Packing Effects on A-DNA Helix Parameters: A Comparative Study of the Isoforms of the Tetragonal & Hexagonal Family of Octamers with Differing Base Sequences

Ramakrishnan¹,

Sundaralingam²

1993

Journal of Biomolecular Structure and Dynamics

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The helix and base pair parameters of A-DNA octamers have been compared having different base sequences both in the tetragonal and hexagonal crystal systems. For the eight structures in the tetragonal family, the twist, rise, slide, inclination and tilt are essentially the same, influenced by the similarity in crystal packing. The propeller twist and the base pair buckle display small sequence dependent variations. But the base pair roll appears to be changed by the specific intermolecular hydrogen bonding interactions. For four of the five octamer structures in the hexagonal family, the base pair rise, slide, inclination, tilt, as well as the propeller twist and buckle are all very similar, while the twist angle and the base pair roll are not. The intermolecular hydrogen bonding interactions seem to be primarily responsible for the differences in the roll angle in the tetragonal structures but for both the roll and twist angles in the hexagonal structures. These results demonstrate that the majority of the observed helix base pair parameters for A-DNA octamers in crystals are affected by the crystal packing environment, while a few parameters, like propeller twist and base pair buckle display some base sequence dependence.

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Section: The Base Pair Rollmentioning

confidence: 97%

Crystal Packing Effects on A-DNA Helix Parameters: A Comparative Study of the Isoforms of the Tetragonal & Hexagonal Family of Octamers with Differing Base Sequences

Ramakrishnan¹,

Sundaralingam²

1993

Journal of Biomolecular Structure and Dynamics

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“…12 ). To our knowledge, only one DNA crystal containing exclusively GC base pairs [ d ( C,G,)] studied both by x-ray diffraction (8) and Raman spectroscopy l3 has been described as formed mainly by nucleotides in A conformation. However, both A and B backbone characteristics and both C2'-endo and C3'-& d o nucleoside puckers were detected.…”

Section: Introductionmentioning

confidence: 99%

A and Z canonical conformations in d(C_nGCG_n) crystals characterized by microFTIR and microRaman spectroscopies

et al. 1993

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Two crystals d(C2GCG2) and d(C5GCG5) have been studied under microscope by Fourier transform ir spectroscopy and Raman spectroscopy. The x-ray diffraction study of the latter crystal had shown that the d(C5GCG5) sequence is the first DNA dodecamer known to adopt a canonical A conformation [N. Verdaguer, J. Aymami, D. Fernandez-Forner, I. Fita, M. Coll, T. Huynh-Dinh, J. Igolen, and J. A. Subirana (1991) Journal of Molecular Biology, Vol. 221, pp. 623-635]. Characteristic ir marker bands and Raman marker peaks of the A conformation have thus been obtained and are compared with previously proposed assignments correlated to fiber diffraction x-ray results obtained on polymers. The d(C2GCG2) sequence crystal had previously been studied in an intermediate form between B and Z [L. Urpi, J. P. Ridoux, J. Liquier, N. Verdagner, I. Fita, J. A. Subirana, F. Iglesias, T. Huynh-Dinh, J. Igolen, and E. Taillandier (1989) Nucleic Acids Research, Vol. 17, pp. 6669-6679]. In this paper we present results obtained from a crystal with this oligonucleotide in Z conformation. The effect of the crystallization conditions on the geometry of the obtained oligomer helix is discussed. The influence of the addition, to the central tetramer CGCG, of dCn stretches (at the 5' end) and dGn stretches (at the 3' end) of different lengths, on the conformational flexibility of the nucleic acid, is considered.

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“…For example, d(CCGG) crystallizes in the A form (26,27). The oligomers d(GGCCGG-CC) (30,40), d(CCCCGGGG) (28), and d(GGGGCCCC) (29) crystallize in the A form due to the presence of sequential CC and GG sequences. Poly(dG)-poly(dC) (21) goes into the A genus in saturated salt solution.…”

Section: Effect Of Nearest-neighbor Interactions In Directing Dna Conmentioning

confidence: 99%

Some rules for predicting the base-sequence dependence of DNA conformation.

Peticolas

Wang

Thomas

1988

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

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Two tables have been constructed showing the crystal and solution conformations of short sequences of DNA. Each of these DNAs has been found to be in one of three different conformations-the A, B, or Z form-depending upon the base sequence and the environmental conditions. A set of rules is presented showing the tendency of certain base pairs to direct the DNA conformation into the A, B, or Z genus in saturated salt solutions and in crystals. These rules are based on a consideration of nearest-neighbor interactions that are interpreted in terms of 10 different two-letter code words made from the letters denoting the bases guanine (G), cytosine (C), adenine (A), and thymine (T). One table discusses the effect on DNA conformation of 3 strong words that tend to direct a DNA oligomer into either the A, B, or Z genus in crystals or in aqueous solutions containing a high salt concentration (6 M). The second table discusses the remaining 7 code words that appear to have a much weaker effect on conformation. The sequences that are most likely to lead to A-Z, B-Z, and A-B junctions are discussed, as is the possible biological significance of these rules.The biological activity of DNA is carried out in association with numerous proteins in order to perform various cellular functions. Protein-nucleic acid interactions are often discussed in terms of two main characteristics-the overall topology of the two partners and the interactions between the nucleotides and the main chain or side chains of the protein (1). The primary specificity of the DNA-protein interaction is undoubtedly governed by the base-sequencedependent array of hydrogen-bonding donor and acceptor patterns that occur along the major and minor grooves of the DNA double helix (2-4). However, it is reasonable to assume that variations in the conformation of DNA may occur along the double-helical axis as it performs its functions in the cell and that these variations in conformation may play a role in the regulation of its biological function. Although the usual conformation of DNA is the canonical B form, it may be that, through interaction with other components in the cell, particularly proteins, partial or total change from this form may occur in regions of DNA. Even a partial change from the canonical B conformation toward the A genus or Z genus would result in a deformation of the hydrogen-bonding donor and acceptor patterns along the major and minor grooves. This effect could be used to aid DNA-binding proteins in locating base-sequence-specific binding sites. As we will show, the possible conformational variations of DNA appear to be determined by specific base sequences as well as the environment.

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The Crystal Structure of d(CCCCGGGG): A New A-Form Variant with an Extended Backbone Conformation

Cited by 105 publications

References 25 publications

Crystal Packing Effects on A-DNA Helix Parameters: A Comparative Study of the Isoforms of the Tetragonal & Hexagonal Family of Octamers with Differing Base Sequences

Crystal Packing Effects on A-DNA Helix Parameters: A Comparative Study of the Isoforms of the Tetragonal & Hexagonal Family of Octamers with Differing Base Sequences

A and Z canonical conformations in d(C_nGCG_n) crystals characterized by microFTIR and microRaman spectroscopies

Some rules for predicting the base-sequence dependence of DNA conformation.

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The Crystal Structure of d(CCCCGGGG): A New A-Form Variant with an Extended Backbone Conformation

Cited by 105 publications

References 25 publications

Crystal Packing Effects on A-DNA Helix Parameters: A Comparative Study of the Isoforms of the Tetragonal & Hexagonal Family of Octamers with Differing Base Sequences

Crystal Packing Effects on A-DNA Helix Parameters: A Comparative Study of the Isoforms of the Tetragonal & Hexagonal Family of Octamers with Differing Base Sequences

A and Z canonical conformations in d(CnGCGn) crystals characterized by microFTIR and microRaman spectroscopies

Some rules for predicting the base-sequence dependence of DNA conformation.

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A and Z canonical conformations in d(C_nGCG_n) crystals characterized by microFTIR and microRaman spectroscopies