DNA hairpin formation in adducts with platinum anticancer drugs: gel electrophoresis provides new information and a caveat

"Head-to-head" double-hamburger-like structure of di-ruthenated d(GpG) adducts of mono-functional Ru-arene anticancer complexes

Guanine bases in DNA are targets for some Ru-arene anticancer complexes. We have investigated the structure of the novel di-ruthenated d(GpG) adduct Ru₂-GpG (where Ru = {(η⁶-biphenyl)-Ru(en)}²⁺ (1')) in aqueous solution. 2D NMR results indicate that there are two conformers, supported by modeling studies. The major conformer I is a novel double-hamburger-like structure with a "head-to-head" (HH) base arrangement involving hydrophobic interactions between neighboring arene rings, the first example of a HH d(GpG) adduct constructed by weak interactions. Hence there are significant differences compared to Pt-d(GpG) adducts formed by cisplatin. There is no obviously rigid bending for the major conformer I. The minor conformer II of Ru₂-GpG has a back-to-back structure, with two ruthenated guanine bases flipped away from each other. 19-23 base-pair oligodeoxyribonucleotides containing central TGGT sequences di-ruthenated by 1 show no directional bending, only slightly distorted di-ruthenated duplexes, consistent with the NMR data for conformer I. The structural differences and similarities of d(GpG) residues which are di-ruthenated or cross-linked by platination are discussed in the context of the biological activity of these metal complexes.

Differentiation and distributions of DNA/cisplatin crosslinks by liquid chromatography-electrospray ionization-infrared multiphoton dissociation mass spectrometry

Liquid chromatography-electrospray ionization-infrared multiphoton dissociation (IRMPD) mass spectrometry was developed to investigate the distributions of intrastrand crosslinks formed between cisplatin and two oligodeoxynucleotides (ODNs), d(A1T2G3G4G5T6A7C8C9C10A11T12) (G3-D) and its analog d(A1T2G3G4G5T6T7C8C9C10A11T12) (G3-H), which have been reported to adopt different secondary structures in solution. Based on the formation of site-specific fragment ions upon IRMPD, two isobaric crosslink products were differentiated for each ODN. The preferential formation of G3G4 and G4G5 crosslinks was determined as a function of reaction conditions, including incubation temperature and presence of metal ions. G3-D consistently exhibited a greater preference for formation of the G4G5 crosslink compared with the G3-H ODN. The ratio of G3G4:G4G5 crosslinks increased for both G3-D and G3-H at higher incubation temperatures or when metal salts were added. Comparison of the IRMPD fragmentation patterns of the unmodified ODNs and the intramolecular platinated crosslinks indicated that backbone cleavage was significantly suppressed near the crosslink.

Marked dependence on carrier-ligand bulk but not on carrier-ligand chirality of the duplex versus single-strand forms of a DNA oligonucleotide with a series of G-Pt(II)-G intrastrand cross-links modeling cisplatin-DNA adducts

The N7-Pt-N7 adjacent G,G intrastrand DNA cross-link responsible for cisplatin anticancer activity is dynamic, promotes local "melting" in long DNA, and converts many oligomer duplexes to single strands. For 5'-d(A1T2G3G4G5T6A7C8C9C10A11T12)-3' (G3), treatment of the (G3)2 duplex with five pairs of [LPt(H2O)2]2+ enantiomers (L = an asymmetric diamine) formed mixtures of LPt-G3 products (1 Pt per strand) cross-linked at G3,G4 or at G4,G5 in all cases. L chirality exerted little influence. For primary diamines L with bulk on chelate ring carbons (e.g., 1,2-diaminocyclohexane), the duplex was converted completely into single strands (G3,G4 coils and G4,G5 hairpins), exactly mirroring results for cisplatin, which lacks bulk. In sharp contrast, for secondary diamines L with bulk on chelate ring nitrogens (e.g., 2,2'-bipiperidine, Bip), unexpectedly stable duplexes having two platinated strands (even a unique G3,G4/G4,G5 heteroduplex) were formed. After enzymatic digestion of BipPt-G3 duplexes, the conformation of the relatively nondynamic G,G units was shown to be head-to-head (HH) by HPLC/mass spectrometric characterization. Because the HH conformation dominates at the G,G lesion in duplex DNA and in the BipPt-G3 duplexes, the stabilization of the duplex form only when the L nitrogen adducts possess bulk suggests that H-bonding interactions of the Pt-NH groups with the flanking DNA lead to local melting and to destabilization of oligomer duplexes. The marked dependence of adduct properties on L bulk and the minimal dependence on L chirality underscore the need for future exploration of the roles of the L periphery in affecting anticancer activity.

Translesion synthesis past platinum DNA adducts by human DNA polymerase mu

DNA polymerase mu (pol mu) is a member of the pol X family of DNA polymerases, and it shares a number of characteristics of both DNA polymerase beta (pol beta) and terminal deoxynucleotidyl transferase (TdT). Because pol beta has been shown to perform translesion DNA synthesis past cisplatin (CP)- and oxaliplatin (OX)-GG adducts, we determined the ability of pol mu to bypass these lesions. Pol mu bypassed CP and OX adducts with an efficiency of 14-35% compared to chain elongation on undamaged DNA, which is second only to pol eta in terms of bypass efficiency. The relative ability of pol mu to bypass CP and OX adducts was dependent on both template structure and sequence context. Since pol mu has been shown to be more efficient on gapped DNA templates than on primed single-stranded DNA templates, we determined the ability of pol mu to bypass Pt-DNA adducts on both primed single-stranded and gapped templates. The bypass of Pt-DNA adducts by pol mu was highly error-prone on all templates, resulting in 2, 3, and 4 nt deletions. We postulate that bypass of Pt-DNA adducts by pol mu may involve looping out the Pt-GG adduct to allow chain elongation downstream of the adduct. This reaction appears to be facilitated by the presence of a downstream "acceptor" and a gap large enough to provide undamaged template DNA for elongation past the adduct, although gapped DNA is clearly not required for bypass.

Frameshifts and deletions during in vitro translesion synthesis past Pt-DNA adducts by DNA polymerases beta and eta

DNA polymerases beta (pol beta ) and eta (pol eta ) are the only two eukaryotic polymerases known to efficiently bypass cisplatin and oxaliplatin adducts in vitro. Frameshift errors are an important aspect of mutagenesis. We have compared the types of frameshifts that occur during translesion synthesis past cisplatin and oxaliplatin adducts in vitro by pol beta and pol eta on a template containing multiple runs of nucleotides flanking a single platinum-GG adduct. Translesion synthesis past platinum adducts by pol beta resulted in approximately 50% replication products containing single-base deletions. For both adducts the majority of -1 frameshifts occurred in a TTT sequence 3-5 bp upstream of the DNA lesion. For pol eta, all of the bypass products for both cisplatin and oxaliplatin adducts contained -1 frameshifts in the upstream TTT sequence and most of the products of replication on oxaliplatin-damaged templates had multiple replication errors, both frameshifts and misinsertions. In addition, on platinated templates both polymerases generated replication products 4-8 bp shorter than the full-length products. The majority of short cisplatin-induced products contained an internal deletion which included the adduct. In contrast, the majority of oxaliplatin-induced short products contained a 3' terminal deletion. The implications of these in vitro results for in vivo mutagenesis are discussed.

Cisplatin (cis-Pt(NH(3))(2)Cl(2)) and cis-[Pt(NH(3))(2)(H(2)O)(2)](2+) Intrastrand Cross-Linking Reactions at the Telomere GGGT DNA Sequence Embedded in a Duplex, a Hairpin, and a Bulged Duplex: Use of Mg(2+) and Zn(2+) to Convert a Hairpin to a Bulged Duplex

In the past, we showed that metal species have a high affinity for the central G in the GGG sequence of the duplex d(A(1)T(2)G(3)G(4)G(5)T(6)A(7)C(8)C(9)C(10)A(11)T(12))(2) (G3-D) and that cisplatin (cis-Pt(NH(3))(2)Cl(2)) and G3-D formed an N7-Pt-N7 G(4),G(5) intrastrand cross-link preferentially over the G(3),G(4) adduct ( approximately 25:1). Thus, a putative G(4) monoadduct was postulated to cross-link in the 3'- rather than the normally more favorable 5'-direction. To evaluate this hypothesis and also to explore why the G3-D G(4),G(5) adduct had an unusual hairpin structure, we have now introduced the use of N,N'-dimethylthiourea (DMTU) as a monoadduct trap and have extended the study to a G3-D analogue with a hairpin form, d(A(1)T(2)G(3)G(4)G(5)T(6)T(7)C(8)C(9)C(10)A(11)T(12)) (G3-H). Chemical shift and 2D (1)H and (13)C NMR data indicated that the G3-H hairpin has a stem region with B-form structure and a nonhelical loop region. Zn(2+) or Mg(2+) ions transformed G3-H into a bulged duplex. Downfield shifts of G(4)H8 and G(4)C8 NMR signals indicated that Zn(2+) binds preferentially to G(4)N7. Reaction of cisplatin or cis-[Pt(NH(3))(2)(H(2)O)(2)](2+) with the bulged duplex and hairpin forms of G3-H gave a similar intrastrand cross-link ratio, G(4),G(5):G(3),G(4) = 7:3. This ratio is insensitive to DNA form or Pt leaving group. For G3-D this ratio is lower in the cis-[Pt(NH(3))(2)(H(2)O)(2)](2+) reaction ( approximately 1:1) than in the cisplatin reaction (25:1), indicating that the leaving group influences the cross-linking step for G3-D. The G(4) monoadducts of the cis-Pt(NH(3))(2)Cl(2)-G3-H and -G3-D and the cis-[Pt(NH(3))(2)(H(2)O)(2)](2+)-G3-D reactions were trapped with DMTU, but no monoadduct was trapped in the cis-[Pt(NH(3))(2)(H(2)O)(2)](2+)-G3-H reaction. The results suggest that the respective monoadducts are more long-lived for G3-D. We postulate that the G(5) in the G3-D Cl-G(4) monoadduct is placed in a favorable position to form the cross-link because of a prior conformational change induced by G(4)-A(7) stacking. This accounts for the very high selectivity for 3'-cross-linking. Nevertheless, in all other cases, regardless of the form or conformation, 3'-direction cross-linking is unusually favored at GGGT sequences, suggesting that the sequence itself contributes greatly to the 3'-cross-linking preference; since telomeres have multiple repeats of this GGGT sequence, this finding may have biological relevance.

NMR Coupling versus NMR Chemical Shift Information in Metallobiochemistry. High-Resolution One-Bond (1)H-(13)C Coupling Constants Obtained by a Sensitive Reverse Detection Method

Imidazole rings are involved in acid/base chemistry, catalysis, H-bonding, and metal complexation throughout biochemistry; these rings are frequently targets for anticancer drugs and carcinogens. However, interpreting the changes in (13)C NMR shifts of these rings is often difficult. We explore the use of high-resolution one-bond (1)H-(13)C coupling constants ((1)J(CH)) for the identification of electronic changes within imidazole rings of samples containing (13)C in natural abundance. The reverse detection method used, called J-coupled heteronuclear multiple quantum coherence (JHMQC) spectroscopy, employs a modified HMQC pulse sequence. The method was evaluated with B(12) models of the type Me(3)BzmCo(DH)(2)(R or X), where Me(3)Bzm = 1,5,6-trimethylbenzimidazole and DH = the monoanion of dimethylglyoxime. (1)J(CH) values of Me(3)BzmCo(DH)(2)CH(3) obtained from both JHMQC and standard coupled 1D (13)C NMR spectra led to similar values, but the JHMQC method gave better resolution and much higher signal-to-noise ratios. The (1)J(CH) values for the endocyclic carbons and the N-methyl group of the Me(3)Bzm in five models fell between those of the free and protonated Me(3)Bzm ligands. Thus, donation of electron density from Me(3)Bzm to the Co center typically increases (1)J(CH) values with respect to the free ligand. Values of (1)J(CH) for several (13)C NMR signals correlated with both EP, a reported measure of electron-donating ability of R or X, and Co-N bond lengths from X-ray structures. For the assessment of electronic properties of the metal center, the (1)J(CH) values appear to be more reliable parameters than the traditionally used (13)C shifts, especially for C's close to the metal. Moreover, (1)J(CH) values for the (13)C signals for Co-(13)C were observed in several models; the (13)C signals for these carbons attached to the quadrupolar cobalt are too broad for (1)J(CH) determination by the traditional 1D method. The JHMQC method developed here is thus very versatile and can provide information on any type of molecule showing resolved CH signals.

A New Class of Supramolecular, Mixed-Metal DNA-Binding Agents: The Interaction of Ru(II),Pt(II) and Os(II),Pt(II) Bimetallic Complexes with DNA

A new type of mixed-metal, supramolecular complex has been designed that incorporates a platinum center to allow binding to DNA. The interaction of two such platinum heterobimetallic complexes of the general formula [(bpy)(2)M(dpb)PtCl(2)]Cl(2) (M = Ru(II), Os(II); bpy = 2,2'-bipyridine; dpb = 2,3-bis(2-pyridyl)benzoquinoxaline) with DNA is reported herein. The modular design of these systems allows for synthetic variation of individual components within this structural motif. In this case, the remote metal is varied from Ru(II) to Os(II). DNA binding was analyzed using non-denaturing agarose gel electrophoresis. The interaction of these complexes with DNA was studied relative to the known DNA cross-linkers, cis-[Pt(NH(3))Cl(2)] (cisplatin) and trans-{[PtCl(NH(3))(2)](2)(&mgr;-H(2)N(CH(2))(6)NH(2))}(2+) (1,1/t,t). Our mixed-metal Ru,Pt and Os,Pt compounds retard the migration of DNA through the gel in both a concentration- and time-dependent manner. Their effect on the migration of DNA is similar to, although much more dramatic than, that observed for either cisplatin or 1,1/t,t. Our evidence suggests a covalent binding of our mixed-metal complexes to DNA through the platinum site. The degree of retardation of DNA migration suggests a large change in DNA conformation is induced by binding of our mixed-metal complexes. This work establishes these inorganic systems as a new class of DNA-binding agents and lays the groundwork for future efforts to enhance binding in an effort to develop novel anticancer drugs through serial design and testing.

Kinetic analysis of the cis-diamminedichloroplatinum(II)--cysteine reaction: implications to the extent of platinum--DNA binding

The reaction between cis-diamminedichloroplatinum(II) (cis-DDP) and L-cysteine was examined at neutral pH at 37 degrees C. The reaction proceeds through a Pt(NH3)2 (cys)Cl intermediate which undergoes parallel reactions with a second molecule of cysteine to form a bis(cysteine) complex, Pt(NH3)2(cys)2 and with the starting platinum complex to form a cysteine-bridged dinuclear complex. In the presence of excess cysteine, the product is predominantly the bis(cysteine) complex. The intermediate is formed by the direct reaction of the platinum complex with cysteine with a bimolecular rate constant 2.2 +/- 0.2 x 10(-2) M-1.s-1 at 37 degrees C as well as through a rapid reaction with the mono aqua-platinum complex. The rate constant for the formation of the dimer was evaluated to be 0.24 +/- 0.4 M-1.s-1, an order of magnitude higher than that for the mononuclear complex formation. The intermediate reacts with a second cysteine molecule with a bimolecular rate constant, 5.6 +/- 0.4 x 10(-2) M-1.s-1. The rate constant for the equation of Pt(NH3)2(cys)Cl was evaluated to be 1.8 +/- 0.2 10(-4) s-1. The Pt-195 chemical shifts for the mono(cysteine), bis(cysteine), and cysteine bridged dimer were found to be -3308, -3705, and -3104 ppm. The bis(cysteine) complex at neutral pH undergoes slow reaction (t1/2 approximately equal to four days) to form a secondary product, presumably Pt(NH3)(cys)2, in which one cysteine acts a bidentate chelating agent. In acidic solution, with equimolar concentrations of cysteine and diaqua-platinum complex, the reaction predominantly yielded a cysteine bridged dimeric complex. When cysteine concentration was increased fourfold over the platinum complex, the bis(cysteine) chelate with complete removal of coordinated ammonia appeared as the dominant product. The platinum-195 chemical shift for this chelate was found to be -3290 ppm. Considering the abundance of thiols in amino acids/peptides and replication enzymes in the cellular milieu, it remains to be seen how platinum complexes react with DNA. Direct platination to replication enzymes as a possible mechanism for antineoplactic activity is yet to be ruled out.

Structural effect of intra-strand cisplatin-crosslink on palindromic DNA sequences

Three self-complementary DNA oligonucleotides, each having a single GpG site, have been reacted with the anticancer platinum compound cis-Pt(NH3)2Cl2 (cisplatin). Their covalent intra-strand didentate adducts have been purified and studied by NMR. In d(GAC-CATATG*G*TC), the two G*G* sites (G*G* denoting the cisplatin crosslinked lesion site) are separated by four base pairs and capped by two base pairs at the ends of the helix and the dodecamer forms a doubly-kinked duplex structure. Multi-stranded aggregate of the dodecamer was formed over time in the presence of chloride. This is due to the meta-stable property of the intra-strand Pt-G*pG* crosslink in dsDNA, similar to that first seen recently in another duplex (Yang et al., Biochemistry (1995) 34, 12912-12920). In d([c7A]CC[c7G][c7G]CCG*G*T), the CG*G*T segment of the decamer is essentially single-stranded with the G*8 in the syn conformation. In d([c7G]CC[c7G]CG*G*C), two possible structures, a full duplex and a staggered partial duplex, were formed. Therefore, the structural consequence of the incorporation of the G*G* lesion site into palindromic sequences is dependent on the location of the lesion sites in the sequence. The destabilizing effect of G*G* in dsDNA may facilitate the formation of a hairpin structure as shown recently (Iwamoto et al., J. Amer. Chem. Soc. (1994) 116, 6238-6244). Such alternative structural distortions may be relevant in understanding the protein recognition of the lesions induced by cisplatin.

A novel DNA structure induced by the anticancer bisplatinum compound crosslinked to a GpC site in DNA

The bifunctional platinum compound, [(trans-PtCI(NH)3)2)2(H2N(CH2)4NH2)]2+, forms a stable adduct with the self-complementary DNA oligomer CATGCATG, with the two platinum atoms coordinated at the N7 positions of the two symmetrical G4 nucleotides. The NMR-derived structure shows that the DNA octamer forms a novel hairpin structure with the platinated G4 residue adopting a syn conformation and the guanine base in the minor groove. Two such hairpins stack end-over-end and are linked together by the butanediamine tether to form a dumbbell structure. Such unusual structural distortion is different from that of the anticancer drug cisplatin-DNA adduct and may provide clues to explain the distinct biological activities of the two compounds.