Polymorphic crystal structures of an all‐AT DNA dodecamer

Abstract

In this work, we explore the influence of different solvents and ions on the crystallization behavior of an all-AT dodecamer d(AATAAATTTATT)2 In all cases, the oligonucleotides are found as continuous columns of stacked duplexes. The spatial organization of such columns is variable; consequently we have obtained seven different crystal forms. The duplexes can be made to crystallize in either parallel or crossed columns. Such versatility in the formation of a variety of crystal forms is characteristic for this sequence. It had not been previously reported for any other sequence. In all cases, the oligonucleotide duplexes have been found to crystallize in the B form. The crystallization conditions determine the organization of the crystal, although no clear local interactions have been detected. Mg(2+) and Ni(2+) can be used in order to obtain compact crossed structures. DNA-DNA interactions in the crystals of our all-AT duplexes present crossovers which are different from those previously reported for mixed sequence oligonucleotides. Our results demonstrate that changes in the ionic atmosphere and the crystallization solvent have a strong influence on the DNA-DNA interactions. Similar ionic changes will certainly influence the biological activity of DNA. Modulation of the crystal structure by ions should also be explored in DNA crystal engineering. Liquid crystals with a peculiar macroscopic shape have also been observed.

How do non-covalent complexes dissociate in droplets? A case study of the desolvation of dsDNA from a charged aqueous nanodrop

“…Over the initial 10 ns of the dsDNA desolvation, the mean separation distance of 8.3 agrees well with the X-ray data of AÁT-rich dsDNA. [54][55][56] A possible explanation to the narrowing of the minor groove is that the cation association with the backbone shields the repulsion between the negative charges on the two strands. This can be viewed as a three-site interaction between a Na + and two of the phosphodiester oxygen atoms located across the two strands: (O 1 P) 0.5À Á Á Á(Na) 1+ Á Á Á(O 1 P) 0.5À (inset in Fig.…”

Differentiation of G:C vs A:T and G:C vs G:mC Base Pairs in the Latch Zone of α-Hemolysin

“…(A) Hairpin duplex sequences studied. (B) Representative structure for α-HL and the hairpin duplex based on pdb 7AHL, 1JVE, and 4HW1 . (C) Current-blocking histograms for mixtures of analyte and standard duplexes.…”

“…(B) Representative structure for α-HL and the hairpin duplex based on pdb 7AHL, 29 1JVE, 38 4HW1. 39 (C) Current blocking histograms for mixtures of analyte and standard duplexes. The hp-1 sequence was used as an internal standard, and it was always mixed with the analyte strand in a ratio of 1:2, respectively; therefore, the smaller peak area always represents hp-1.…”

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

“…Ni 2+ ions have never been found associated with other bases in DNA. In previous studies with all-AT DNA duplexes [6] we have used Ni 2+ as a counterion, which is not detected in the crystallized structure. Given this preference for guanine, we have used a moderate amount of Ni 2+ ions in our crystallization studies of HMGA peptides associated with DNA.…”