Helix geometry and hydration in an A-DNA tetramer: IC-C-G-G

Conner, Benjamin N.; Yoon, Chun; Dickerson, Joyce L.; Dickerson, Richard E.

doi:10.1016/0022-2836(84)90089-5

Cited by 125 publications

(57 citation statements)

References 20 publications

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“…This is related to the unique stacking interaction at the C7pC8 (or C17pG18) step as will be described later. The strongly correlated angular pairs, as described by potential-energy calculations as well as empirically for other A-DNA structures [9,22,231 are also observed in the present structure. In addition to the cl/[ combination mentioned above, the angular pair, u/y, is consistently in the gauche-/ gauche' configuration.…”

Section: Torsion Angles Of D(accggccggt)supporting

confidence: 80%

“…In these structures it can be correlated with various adjustment mechanisms to reduce sequence-specific cross-strand steric clashes [26]. It was also observed in the d('CCGG) tetrameric A-DNA structure [9], although here the correlation with cross-chain purine repulsion was not as good as for B-DNA. Recently, it has been described as a prominant feature of tracks of adenine-thymine base pairs, where it results in a narrowing of the width of the minor groove [27,28].…”

Section: The Decamer As Part Of a Continuum Between A-and B-dnamentioning

confidence: 76%

“…-158 (9) this work -162 (10) [30] -149 (10) [7] -160 (8) [8] -161 (7) [9] -158 (10) [lo] -162 (9) [ll] -154 ~251 -158…”

Section: Torsion Angles Of D(accggccggt)unclassified

“…Despite the small root-mean-square difference (0.04 nm) mentioned above, some fine details are different. In the idealized structure the shortest distance should be from residue n on one strand to residue n + 7 on the other strand (see [9] for numbering scheme), which corresponds to the distance between P2 and PI3 in the current molecule. In the decamer structure however, this distance is not the shortest across the groove, presumably due to some residual phosphate-phosphate repulsion at the end of the chain.…”

Section: The Decamer As Part Of a Continuum Between A-and B-dnamentioning

confidence: 99%

“…Recently, the mechanism of this environmental-and sequence-dependent conformational equilibrium has been studied by a number of techniques. For example, several DNA oligomers containing two or more consecutive guanine bases, including d(GGCCGGCC) [7], d(GGTATACC) [8], d('CCGG) [9], d(GGGGCCCC) [lo], d(CCCCGGGG) [1 11,d(GTGTACAC) [12] and other related sequences [4,131, have been found to crystallize in the A-DNA conformation. The propensity of those molecules for forming A-DNA was partially attributed to the intrastrand guanine-guanine base stacking interactions stabilized by the A-DNA conformation [7, 101. The crystallographic studies of those short DNA oligonucleotides revealed that though their overall conformation resembles the idealized A-DNA derived from fiber-diffraction Correspondence to A. H.-J.…”

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confidence: 99%

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Molecular structure of an A‐DNA decamer d(ACCGGCCGGT)

Frederick¹,

Quigley²,

Teng³

et al. 1989

European Journal of Biochemistry

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The molecular structure of the DNA decamer d(ACCGGCCGGT) has been solved and refined by single-crystal X-ray-diffraction analysis at 0.20 nm to a final R-factor of 18.0%. The decamer crystallizes as an A-DNA double helical fragment with unit-cell dimensions of a = b = 3.923 nm and c = 7.80 nm in the space group P6122. The overall conformation of this A-DNA decamer is very similar to that of the fiber model for A-DNA which has a large average base-pair tilt and hence a wide and shallow minor groove. This structure is in contrast to that of several A-DNA octamers in which the molecules all have low base-pair-tilt angles (8 -12") resulting in an appearance intermediate between B-DNA and A-DNA. The average helical parameters of this decamer are typical of A-DNA with 10.9 base pairs/turn of helix, an average helical twist angle of 33.1 O, and a base-pair-tilt angle of 18.2". However, the CpG step in this molecule has a low local-twist angle of 24.5", similar to that seen in other A-DNA oligomers, and therefore appears to be an intrinsic stacking pattern for this step. The molecules pack in the crystal using a recurring binding motif, namely, the terminal base pair of one helix abuts the surface of the shallow minor groove of another helix. In addition, the GC base pairs have large propeller-twist angles, unlike those found most other A-DNA structures.A-DNA and B-DNA are the two most commonly observed stable right-handed nucleic acid conformations. While B-DNA is considered to be the predominant from in vivo, there is increasing evidence that the A-form may also play important roles in processes such as protein recognition [l, 21 and transcriptional regulation, especially with respect to the binding of potential zinc-finger-containing proteins [3, 41. As shown by DNA-fiber X-ray-diffraction analysis, these two forms of DNA are interconvertible depending on the environmental conditions. Specifically, A-form DNA is favored by conditions of low humidity and the economical organization of solvent molecules around A helices has been compared to that of the more fully hydrated B-DNA [5]. It has also been shown that A-DNA forms more readily in certain nucleotide sequences, e.g. guanine-rich regions [6], while other sequences, like oligo-dA, resist assuming the A-DNA conformation. Recently, the mechanism of this environmental-and sequence-dependent conformational equilibrium has been studied by a number of techniques. For example, several DNA oligomers containing two or more consecutive guanine bases, including d(GGCCGGCC) [7] d(GTGTACAC) [12] and other related sequences [4, 131, have been found to crystallize in the A-DNA conformation. The propensity of those molecules for forming A-DNA was partially attributed to the intrastrand guanine-guanine base stacking interactions stabilized by the A-DNA conformation [7, 101. The crystallographic studies of those short DNA oligonucleotides revealed that though their overall conformation resembles the idealized A-DNA derived from fiber-diffraction

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Section: Torsion Angles Of D(accggccggt)supporting

confidence: 80%