Structure of d(CACGCG)\cdotd(CGCGTG) in Crystals Grown in the Presence of Ruthenium^IIIHexammine Chloride

Abstract

Hexammine ions are strong inducers of the transition from the B-form to the left-handed Z-form in DNA. Here the structure of d(CACGCG)Ád(CGCGTG) obtained from crystals grown from a drop containing [Ru(NH 3 ) 6 ]Cl 3 is reported. The structure is clearly characterized as Z-DNA. When compared with the structure of d(CACGCG)Ád(CGCGTG)/MgCl 2 and that of d(CGCGCG) 2 , subtle differences are seen, most noticeably in the water structure. Since stable well diffracting crystals grow easily in the presence of [Ru(NH 3 ) 6 ]Cl 3 and since this ion is not visible in the electron density it is concluded that the ion plays a nonspeci®c role in stabilizing Z-DNA.

Structure of d(TGCGCG)·d(CGCGCA) in two crystal forms: effect of sequence and crystal packing in Z-DNA

“…These structures show that HT1, with a GÁC tract length of 5, is closely similar to the fibre model Z-helix. Taken together with previous reports, both from our laboratory (Karthe & Gautham, 1998;Sadasivan & Gautham, 1995;Thiyagarajan et al, 2002) as well as from others (Harper et al, 1998;Parkinson et al, 1995;Wang et al, 1984;Geierstanger et al, 1991;Coll et al, 1988), the observation of Wang et al (1987) that the formation of Z-DNA is dependent on the length of the alternating CÁG tract is supported. However, there are a few exceptions to this hypothesis.…”

Intercalative Stacking: A Critical Feature of DNA Charge-Transport Electrochemistry

“…Methylene blue (MB + ) binds readily to DNA-modified surfaces by intercalation with an association constant of 3.8(5) × 10 6 M -1 (5 mM phosphate, 50 mM NaCl buffer, pH 7) and undergoes a reversible reduction at -250 mV vs SCE. 52 Ru(NH 3 ) 6 3+ binds in the groove of duplex DNA, 77,78 is reduced at approximately the same potential as MB + , and associates with DNA through electrostatic and hydrogen-bonding interactions. Tarlov and co-workers have exploited these properties in the development of an electrochemical assay to quantify DNA immobilized onto an electrode surface.…”

Redox‐Induced Switching of the Viscoelasticity of DNA Layers Observed by using Electrochemical Quartz Crystal Microbalance on the Millisecond Timescale

“…Additionally, CoHex was more effective in this transition than sodium and magnesium ions. Z‐DNA, which contains a flat surface instead of the major grooves in B‐DNA, provides an environment for cobalt ions to form more hydrogen bonds and stabilize the Z‐DNA structure …”

“…Z-DNA, which contains a flat surface instead of the major grooves in B-DNA, provides an environment for cobalt ions to form more hydrogen bonds and stabilize the Z-DNA structure. [29] This integration of both RuHex and CoHex into the network of hydrogen bonds between the DNA strands is probably the main reason for the observed redox-switching of viscoelasticity. The latter depends on number and strength of hydrogen bonds between immobilized DNA strands, and the oxidation state of the central ion in both hexammine complexes is likely to influence hydrogen bonds that include the ammonia ligands.…”