Medium Effects on Reactivity Profiles for Platination of Phosphorothioate-Containing Oligonucleotides

Site-specific platinum(II) cross-linking in a ribozyme active site

The function of RNA depends on its ability to adopt complex and dynamic structures, and the incorporation of site-specific cross-linking probes is a powerful method for providing distance constraints that are valuable in RNA structural biology. Here we describe a new RNA-RNA cross-linking strategy based on Pt(II) targeting of specific phosphorothioate substitutions. In this strategy cis-diammine Pt(II) complexes are kinetically recruited and anchored to a phosphorothioate substitution embedded within a structured RNA. Substitution of the remaining exchangeable Pt(II) ligand with a nucleophile supplied by a nearby RNA nucleobase results in metal-mediated cross-links that are stable during isolation. This type of cross-linking strategy was explored within the catalytic core of the Hammerhead ribozyme (HHRz). When a phosphorothioate substitution is installed at the scissile bond normally cleaved by the HHRz, Pt(II) cross-linking takes place to nucleotides G8 and G10 in the ribozyme active site. Both of these positions are predicted to be within ~8 Å of a phosphorothioate-bound Pt(II) metal center. Cross-linking depends on Mg(2+) ion concentration, reaching yields as high as 30%, with rates that indicate cation competition within the RNA three-helix junction. Cross-linking efficiency depends on accurate formation of the HHRz tertiary structure, and cross-links are not observed for RNA helices. Combined, these results show promise for using kinetically inert Pt(II) complexes as new site-specific cross-linking tools for exploring RNA structure and dynamics.

Effects of geometric isomerism and anions on the kinetics and mechanism of the stepwise formation of long-range DNA interstrand cross-links by dinuclear platinum antitumor complexes

Reported herein is a detailed study of the kinetics and mechanism of formation of a 1,4-GG interstrand cross-link by the dinuclear platinum anticancer compound [15N][{cis-PtCl(NH3)2}2{mu-NH2(CH2)6NH2}]2+ (1,1/c,c (1)). The reaction of [15N]1 with 5'-{d(ATATGTACATAT)2} (I) has been studied by [1H,15N] HSQC NMR spectroscopy in the presence of different concentrations of phosphate. In contrast with the geometric trans isomer (1,1/t,t), there was no evidence for an electrostatic preassociation of 1,1/c,c with the polyanionic DNA surface, and the pseudo-first-order rate constant for the aquation of [(15)N]1 was actually slightly higher (rather than lower) than that in the absence of DNA. When phosphate is absent, the overall rate of formation of the cross-link is quite similar for the two geometric isomers, occurring slightly faster for 1,1/t,t. A major difference in the DNA binding pathways is the observation of phosphate-bound intermediates only in the case of 1,1/c,c. 15 mM phosphate causes a dramatic slowing in the overall rate of formation of DNA interstrand cross-links due to both the slow formation and slow closure of the phosphate-bound monofunctional adduct. A comparison of the molecular models of the bifunctional adducts of the two isomers shows that helical distortion is minimal and globally the structures of the 1,4 interstrand cross-links are quite similar. The effect of carrier ligand was investigated by similar studies of the ethylenediamine derivative [15N]1-en. A pKa value of 5.43 was determined for the [15N]1,1/c,c-en diaquated species. The rate of reaction of [15N]1-en with duplex I is similar to that of 1,1/c,c and the overall conformation of the final adduct appears to be similar. The significance of these results to the development of "second-generation" polynuclear platinum clinical candidates based on the 1,1/c,c chelate (dach) series is discussed.

Platination of the siRNA sense-strand modulates both efficacy and selectivity in vitro

The use of short interfering RNAs (siRNA) for selective suppression of protein production has rapidly become a commonly used technique for transient modulation of protein levels. In the present paper, we investigate whether introduction of platinated bases in the sense strand can be used to modulate the efficacy of siRNAs. Four different siRNAs were studied, all targeting the initial AU-rich 3' UTR of Wnt-5a mRNA. The siRNAs were characterized with respect to melting properties and translational inhibitory effect in vitro using luciferase as a reporter gene. The translation inhibition studies reveal that all platinated siRNA remain efficient. For an siRNA with partial complementarity to the luciferase gene, platination was shown to reduce the off-target effects. All siRNAs were found to be active in cellular in vitro translation systems, reaching suppression levels well above 80% for the majority of siRNAs investigated.

The polyamines spermidine and spermine retard the platination rate of single-stranded DNA oligomers and plasmids

The presence of polyamines in living cells is crucial for survival. Due to their high net charge at physiological pH, polyamines effectively charge neutralize the phosphodiester backbone of DNA in an interaction that also may protect the DNA from external damage. We here present a study illustrating the influence of spermidine and spermine on the platination reactions of the model oligonucleotides d(T(6)GT(6)), d(T(12)GT(12)), and d(T(24)GT(24)), and the pUC18 DNA plasmid. The aquated forms of the anticancer active compounds cisplatin (cis-[Pt(NH(3))(2)Cl(2)]) and the major Pt(II) metabolite of JM216 (cis-[PtCl(2)(NH(3))(c-C(6)H(11)NH(2))], JM118) were used as platination reagents. The study shows that the kinetics for formation of the coordinative Pt-DNA adduct are strongly influenced by the presence of sub-millimolar polyamine concentrations. At polyamine concentrations in the muM-range, the reactions remain salt-dependent. In contrast, platination of pUC18 is effectively prevented at mM concentrations of both spermidine and spermine with the latter as the more potent inhibitor. The results suggest that variations of intracellular polyamine concentrations may have a profound influence on the efficacy by which cationically charged reagents interfere with DNA function in vivo by modulation of the preassociation conditions.

More pronounced salt dependence and higher reactivity for platination of the hairpin r(CGCGUUGUUCGCG) compared with d(CGCGTTGTTCGCG)

The DNA interference pathways exhibited by cisplatin and related anticancer active metal complexes have been extensively studied. Much less is known to what extent RNA interaction pathways may operate in parallel, and perhaps contribute to both antineoplastic activity and toxicity. The present study was designed with the aim of comparing the reactivity of two model systems comprising RNA and DNA hairpins, r(CGCGUUGUUCGCG) and d(CGCGTTGTTCGCG), towards a series of platinum(II) complexes. Three platinum complexes were used as metallation reagents; cis-[PtCl(NH3)2(OH2)]+ (1), cis-[PtCl(NH3)(c-C6H11NH2)(OH2)]+ (2), and trans-[PtCl(NH3)(quinoline)(OH2)]+ (3). The reaction kinetics were studied at pH 6.0, 25 degrees C, and 1.0 mM < or = I < or = 500 mM. For both types of nucleic acid targets, compound 3 was found to react about 1 order of magnitude more rapidly than compounds 1 and 2. Further, all platinum compounds exhibited a more pronounced salt dependence for the interaction with r(CGCGUUGUUCGCG). Chemical and enzymatic cleavage studies revealed similar interaction patterns with r(CGCGUUGUUCGCG) after long exposure times to 1 and 2. A substantial decrease of cleavage intensity was found at residues G4 and G7, indicative of bifunctional adduct formation. Circular dichroism studies showed that platinum adduct formation leads to a structural change of the ribonucleic acid. Thermal denaturation studies revealed platination to cause a decrease of the RNA melting temperatures by 5-10 degrees C. Our observations therefore suggest that RNA is a kinetically competitive target to DNA. Furthermore, platination causes destabilization of RNA structural elements, which may lead to deleterious intracellular effects on biologically relevant RNA targets.

A combination of access to preassociation sites and local accumulation tendency in the direct vicinity of G-N7 controls the rate of platination of single-stranded DNA

Adduct formation between cationic reagents and targets on DNA are facilitated by the ability of DNA to attract cations to its surface. The electrostatic interactions likely provide the basis for the documented preference exhibited by cisplatin and related compounds for nuclear DNA over other cellular constituents. As an extension of a previous communication, we here present an investigation illustrating how the rate of adduct formation with the naturally occurring base guanine (G-N7) can be modulated by i) bulk solvent conditions, ii) local nature and size of the surrounding DNA and, iii) increasing DNA concentration. A series of single-stranded DNA oligomers of the type d(TnGTm); n= 0, 2, 4, 6, 8, 10, 12, 14, 16 and m= 16 -n or n=m= 4, 6, 8, 12, 16, 24 were allowed to react with the active metabolite of a potential orally active platinumIV drug, cis-[PtCl(NH3))(c-C6H11NH2)(OH2)]+ in the presence of three different bulk cations; Na+, Mg2+, and Mn2+. For all positions along the oligomers, a change from monovalent bulk cations to divalent ones results in a decrease in reactivity, with Mn2+ as the more potent inhibitor as exemplified by the rate constants determined for interaction with d(T8GT8): 10(3) x k obs/s(-1)= 6.5 +/- 0.1 (Na+), 1.8 +/- 0.1 (Mg2+), 1.0 +/- 0.1 (Mn2+) at pH 4.2 and 25 degrees C. Further, the adduct formation rate was found to vary with the exact location of the binding site in the presence of both Na+ and Mg2+, giving rise to reactivity maxima at the middle position. Increasing the size of the DNA-fragments was found to increase the reactivity only up to a total length of ca. 20 bases. The influence from addition of further bases to the reacting DNA was found to be salt dependent. At [Na+]= 0.5 mM a retardation in reactivity was observed whereas [Na+] < or = 4.5 mM give rise to length independent kinetics. Finally, for the first time we have here been able to evaluate the influence from an increasing concentration of non-reactive DNA bases on the adduct formation process. The latter data were successfully fitted to an inhibition model suggesting that non-productive association of the platinum complex with sites distant from G-N7 competes with productive ones in the vicinity of the G-N7 target. Taken together, the kinetics support a reaction mechanism in which access to suitable association sites in the direct vicinity of the target site controls the rate of platination.

Influence of sodium ions on the dynamics and structure of single-stranded DNA oligomers: a molecular dynamics study

The effects of sodium counterion presence and chain length on the structure and dynamics of single DNA strands of polythymidylate were studied by means of molecular dynamics simulations. The importance of the base-base stacking phenomenon increases with the chain length and partially reduces the flexibility of the strand. Sodium ions directly interact with the phosphate groups and keto oxygens of the thymine bases, complexes showing lifetimes below 400 ps. Simultaneous phosphate and keto complexes were observed for one of the sodium ions with lifetimes around 1 ns. The implications of such complexes in the folding process experienced by the strand are considered. Structurally, cation inner- and outer-sphere complexes were observed in the coordination of phosphate groups. For the inner-sphere complexes, the structural information retrieved from the simulations is in very good agreement with experimental data. The diffusion properties of the sodium ions also reflect both types of coordination modes.