The influence of Ni2+ and other ions on the trigonal structure of DNA

We present a new structure of a DNA dodecamer obtained in the presence of Ni2+ ions. The DNA forms Ni-guanine cross-links between neighboring molecules. Our results show that an adequate dosage of Ni2+ may help to form well-defined DNA nanostructures. We also compare our structure with other dodecamers which present unique features and also crystallize in trigonal unit cells, strongly influenced by the counterions associated with DNA. In all cases, the DNA duplexes form parallel pseudo-helical columns in the crystal, similar to DNA-protamine and native DNA fibers.Peer ReviewedPostprint (author's final draft

Crystal Structure of a Complex of DNA with One AT-Hook of HMGA1

We present here for the first time the crystal structure of an AT-hook domain. We show the structure of an AT-hook of the ubiquitous nuclear protein HMGA1, combined with the oligonucleotide d(CGAATTAATTCG)2, which has two potential AATT interacting groups. Interaction with only one of them is found. The structure presents analogies and significant differences with previous NMR studies: the AT-hook forms hydrogen bonds between main-chain NH groups and thymines in the minor groove, DNA is bent and the minor groove is widened

In this figure the DNA duplex is shown as space filling atoms with their van der Waals radii.

<p>The strong association of the inner PRGRP sequence with the duplex is clearly visible. The terminal basic amino acids (34, 40 and 41) interact with phosphates in the same duplex, with the exception of Arg33 which does not show any apparent interactions.</p

A model of the effect of methylation on Arg38 in the DBD3 AT-hook.

<p>Only the guanidinium group of Arg38 (in blue) is visible in this orientation. DNA is shown in grey. In this model the hydrogen bonds between the arginine guanidinium group and the minor groove of DNA are maintained, whereas the methyl group (in red) has an external position. In the side facing DNA there is no room for the methyl group, without disturbing the guanidinium-DNA hydrogen bonds.</p

Crystal data and refinement statistics.

<p>Values in parentheses are for the last shell.</p>a<p>.</p>b<p><i>R</i> factor of reflections used for cross validation in the refinement.</p

Electron density map (2F_o-F_c at 1σ level) of a segment of the AT-hook in the minor groove of DNA.

<p>Hydrogen bonds between main chain peptide NH atoms (Gly37 and Arg38) and thymine oxygen atoms are indicated as red dashed lines.</p

Comparison of the structures of the central PRGRP sequence of the AT-hook obtained by either X-ray diffraction (in grey, this work) or NMR [<b>10</b>].

<p>The overall conformation is similar, but the X-ray structure has significant changes in the position of the main chain NH groups, which allow the formation of hydrogen bonds with minor groove thymine oxygen atoms of DNA. This figure has been prepared with Cerius2.</p