Crystal structure of double-stranded DNA containing the major adduct of the anticancer drug cisplatin

Takahara, Patricia M.; Rosenzweig, Amy C.; Frederick, Christin; Lippard, Stephen J.

doi:10.1038/377649a0

Cited by 753 publications

(625 citation statements)

References 25 publications

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“…We assembled Pol II-nucleic acid scaffold complexes by incubating pure core Pol II with two molar equivalents of nucleic acid scaffold in transcription buffer (20 mM HEPES (pH 7.6), 60 mM (NH 4 ) 2 SO 4 , 8 mM MgSO 4 , 10 mM ZnCl 2 , 10% (v/v) glycerol, 10 mM DTT) at 20 1C for 30 min as described 8 . DNA strands containing the 1,2-d(GpG) and 1,2-(IpG) cisplatin intrastrand cross-links were synthesized as described 11 .…”

Section: Methodsmentioning

confidence: 99%

“…The change in the downstream DNA position results from the presence of the cisplatin lesion rather than from the scaffold design or the nucleic acid sequences, which were highly similar to those used previously 8 . Structures of free DNA containing a cisplatin lesion 10,11 reveal that the lesion at the center of the duplex leads to DNA bending. In our structure, the lesion is located at the end of the duplex and induces a slight repositioning of the downstream DNA, without substantial changes in its internal structure.…”

Section: Structure Of a Cisplatin-damaged Pol II Elongation Complexmentioning

confidence: 99%

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Mechanism of transcriptional stalling at cisplatin-damaged DNA

Damsma

Alt

Brueckner

et al. 2007

Nat Struct Mol Biol

160

133

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The anticancer drug cisplatin forms 1,2-d(GpG) DNA intrastrand cross-links (cisplatin lesions) that stall RNA polymerase II (Pol II) and trigger transcription-coupled DNA repair. Here we present a structure-function analysis of Pol II stalling at a cisplatin lesion in the DNA template. Pol II stalling results from a translocation barrier that prevents delivery of the lesion to the active site. AMP misincorporation occurs at the barrier and also at an abasic site, suggesting that it arises from nontemplated synthesis according to an 'A-rule' known for DNA polymerases. Pol II can bypass a cisplatin lesion that is artificially placed beyond the translocation barrier, even in the presence of a G . A mismatch. Thus, the barrier prevents transcriptional mutagenesis. The stalling mechanism differs from that of Pol II stalling at a photolesion, which involves delivery of the lesion to the active site and lesion-templated misincorporation that blocks transcription.Cisplatin (cis-diamminedichloroplatinum(II)) is a widely used anticancer drug that forms DNA adducts that interfere with replication and transcription 1 . The most frequent cisplatin DNA adducts are 1,2-d(GpG) intrastrand cross-links, or cisplatin lesions, in which platinum coordinates the N7 atoms of adjacent guanosines in a DNA strand 2 (Fig. 1a). A cisplatin lesion in the DNA template strand blocks transcription elongation by the single-subunit RNA polymerase from phage T7 (ref.3) and by Pol II 4-6 , and leads to stable polymerase stalling 7 . The stalled Pol II elongation complex can be bound by the elongation factor TFIIS, which stimulates polymerase back-tracking and 3¢ RNA cleavage 6 . A small fraction of polymerases can apparently read through a cisplatin lesion 6 .The detailed molecular mechanisms of cisplatin DNA adduct processing by nucleic acid polymerases are not understood. Here we have used a combination of X-ray crystallography and RNA-extension assays to derive the molecular mechanism of Saccharomyces cerevisiae Pol II stalling at a cisplatin lesion. Comparison of the results with our previous analysis of Pol II stalling at a DNA photolesion, a TT cyclobutane pyrimidine dimer 8 (CPD, Fig. 1a), reveals that the two types of dinucleotide lesions trigger transcriptional stalling by different mechanisms. RESULTS Structure of a cisplatin-damaged Pol II elongation complexTo elucidate recognition of cisplatin-induced DNA damage by transcribing Pol II, we carried out a structure-function analysis of elongation complexes containing a cisplatin lesion in the template DNA strand. Elongation complexes were reconstituted from the 12-subunit S. cerevisiae Pol II and nucleic acid scaffolds as described 8,9 .A cisplatin lesion was first incorporated at registers +2/+3 of the template strand, directly downstream of the NTP-binding site at register +1 (scaffold A, Fig. 1b). The crystal structure of the resulting cisplatin-damaged elongation complex (complex A) was determined at 3.8-Å resolution (Fig. 1c,d and Methods). A very strong peak in the anomalous differe...

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Section: Methodsmentioning

confidence: 99%

Section: Structure Of a Cisplatin-damaged Pol II Elongation Complexmentioning

confidence: 99%

Mechanism of transcriptional stalling at cisplatin-damaged DNA

Damsma

Alt

Brueckner

et al. 2007

Nat Struct Mol Biol

160

133

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“…Additionally, the products of reaction 1, corresponding to electrontransfer, may also arise via charge-transfer at a crossing point without proceeding through a long-lived complex. Previous ion/ion reaction studies involving multiply charged ions have suggested that charge-transfer at crossing points without long-lived complex formation can contribute significantly, in at least some cases, to electron-transfer [13][14][15]. Reactions 2 and 3, on the other hand, are expected to proceed via a long-lived complex.…”

Section: Computational Chemistrymentioning

confidence: 99%

“…Ruthenium(II) complexes have been extensively examined as spectroscopic probes of local DNA structure [11,12]. The mechanism of action of the chemotherapeutic agent cisplatin involves binding to DNA to prevent replication [13][14][15]. Mass spectrometry has been used as a tool for the examination of ODN complexes with metal ions [16].…”

mentioning

confidence: 99%

Gas-phase ion/ion reactions of transition metal complex cations with multiply charged oligodeoxynucleotide anions

Barlow

Hodges

Xia

et al. 2008

J. Am. Soc. Mass Spectrom.

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Multiply deprotonated hexadeoxyadenylate anions, (A 6 ϪnH) nϪ , where n ϭ 3-5, have been subjected to reaction with a range of divalent transition-metal complex cations in the gas phase. The cations studied included the bis-and tris-1,10-phenanthroline complexes of Cu II , Fe II , and Co II , as well as the tris-1,10-phenanthroline complex of Ru II . In addition, the hexadeoxyadenylate anions were subjected to reaction with the singly charged Fe III and Co III N,N=-ethylenebis(salicylideneiminato) complexes. The major competing reaction channels are electron-transfer from the oligodeoxynucleotide anion to the cation, the formation of a complex between the anion and cation, and the incorporation of the transition-metal into the oligodeoxynucleotide. The latter process proceeds via the anion/cation complex and involves displacement of the ligand(s) in the transition-metal complex by the oligodeoxynucleotide. Competition between the various reaction channels is governed by the identity of the transition-metal cation, the coordination environment of the metal complex, and the oligodeoxynucleotide charge state. In the case of the divalent metal phenanthroline complexes, competition between electron-transfer and metal ion incorporation is particularly sensitive to the coordination number of the reagent metal complexes. Both electron-transfer and metal ion incorporation occur to significant extents with the bis-phenanthroline ions, whereas the trisphenanthroline ions react predominantly by metal ion incorporation. To our knowledge this work reports the first observations of the gas-phase incorporation of multivalent transition-metal cations into oligodeoxynucleotide anions and represents a means for the selective incorporation of transition-metal counter-ions into gaseous oligodeoxynucleotides. [6 -8] have allowed the formation of gas-phase ions of biopolymers, including oligodeoxynucleotides (ODNs), making these ions amenable to study by mass spectrometry. Like peptides and proteins, ODNs are amphoteric, [9] allowing formation of either positively or negatively charged ions. Formation of negatively charged oligonucleotides is quite facile using ESI and, as a result, negatively charged ODN ions have been the most widely studied [9]. Oligodeoxynucleotide ions with bound metals formed by MALDI or ESI, especially those containing transition metals, have shown fragmentation behavior, which is distinct and complementary to that of ions devoid of metals [6 -8].The study of the interaction of transition metals with DNA is of critical importance, given the variety of roles such interactions fulfill. Transition-metal complexes display nuclease activity and consequently complexes such as (methidium-propyl-EDTA)iron(II) have been utilized as footprinting agents [10]. Ruthenium(II) complexes have been extensively examined as spectroscopic probes of local DNA structure [11,12]. The mechanism of action of the chemotherapeutic agent cisplatin involves binding to DNA to prevent replication [13][14][15]. Mass spectrometry has been u...

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“…Similar to bifunctional alkylating agents, CIS interferes with DNA function by forming cross-links within DNA and between DNA and DNA-associated proteins (e.g., DNA polymerases, DNA topoisomerases, and histones) (3,4). Cellular studies have shown that the most frequent bivalent DNA adducts produced by CIS cross-link adjacent purines within one DNA strand, with a preference for guanines (5,6). Intramolecular links involving guanine (N7) are also formed, as are less frequent intermolecular links, representing an obstacle for DNA replication and transcription; the intramolecular links are relevant to drug cytotoxicity (7).…”

Section: Introductionmentioning

confidence: 99%

Platinum-Based Drugs and DNA Interactions Studied by Single-Molecule and Bulk Measurements

Salerno

Beretta

Zanchetta

et al. 2016

Biophysical Journal

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Platinum-containing molecules are widely used as anticancer drugs. These molecules exert cytotoxic effects by binding to DNA through various mechanisms. The binding between DNA and platinum-based drugs hinders the opening of DNA, and therefore, DNA duplication and transcription are severely hampered. Overall, impeding the above-mentioned important DNA mechanisms results in irreversible DNA damage and the induction of apoptosis. Several molecules, including multinuclear platinum compounds, belong to the family of platinum drugs, and there is a body of research devoted to developing more efficient and less toxic versions of these compounds. In this study, we combined different biophysical methods, including single-molecule assays (magnetic tweezers) and bulk experiments (ultraviolet absorption for thermal denaturation) to analyze the differential stability of double-stranded DNA in complex with either cisplatin or multinuclear platinum agents. Specifically, we analyzed how the binding of BBR3005 and BBR3464, two representative multinuclear platinum-based compounds, to DNA affects its stability as compared with cisplatin binding. Our results suggest that single-molecule approaches can provide insights into the drug-DNA interactions that underlie drug potency and provide information that is complementary to that generated from bulk analysis; thus, single-molecule approaches have the potential to facilitate the selection and design of optimized drug compounds. In particular, relevant differences in DNA stability at the single-molecule level are demonstrated by analyzing nanomechanically induced DNA denaturation. On the basis of the comparison between the single-molecule and bulk analyses, we suggest that transplatinated drugs are able to locally destabilize small portions of the DNA chain, whereas other regions are stabilized.

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Crystal structure of double-stranded DNA containing the major adduct of the anticancer drug cisplatin

Cited by 753 publications

References 25 publications

Mechanism of transcriptional stalling at cisplatin-damaged DNA

Mechanism of transcriptional stalling at cisplatin-damaged DNA

Gas-phase ion/ion reactions of transition metal complex cations with multiply charged oligodeoxynucleotide anions

Platinum-Based Drugs and DNA Interactions Studied by Single-Molecule and Bulk Measurements

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