NMR Solution Structure of a DNA Dodecamer Duplex Containing a <i>cis</i>-Diammineplatinum(II) d(GpG) Intrastrand Cross-Link, the Major Adduct of the Anticancer Drug Cisplatin

Gelasco, Andrew; Lippard, Stephen J.

doi:10.1021/bi973176v

Cited by 282 publications

(326 citation statements)

References 30 publications

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“…The Pt complex preparation was achieved with a usual protocol. 28,43 All solutions were prepared in a buffer containing 40 mM cacodylate and 60 mM NaCl, pD ) 6.25. Complete deuterium exchange was achieved by lyophilizing and resolving all solutions 3 times in D 2 O.…”

Section: Methodsmentioning

confidence: 99%

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DNA Oligonucleotide−cis-Platin Binding: Ab Initio Interpretation of the Vibrational Spectra

2007

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The cis-platin binding to the d(CCTGGTCC)*d(GGACCAGG) model DNA octamer was monitored with infrared absorption (IR) and vibrational circular dichroism (VCD) spectroscopies. The spectra were modeled with the aid of density functional computations and a Cartesian coordinate-based transfer of molecular property tensors from smaller DNA fragments. Because of the fragmentation, the tensors could be calculated with a higher precision. Environmental effects, such as the presence of the solvent or the cis-platin ligand, could be included in the modeling. The solvent was modeled by an explicit inclusion of hydrogen-bound water molecules, positions of which were estimated from a molecular dynamics simulation, or by the polarized continuum COSMO model. The B3LYP and BPW91 functionals used for the calculations of the spectral parameters were combined with the relativistic LANL2DZ platinum pseudo-potentials. The simulations reproduced the main IR and VCD DNA spectral features and explained most of the changes observed experimentally upon metal binding. The results confirmed that the influence of the ligand on DNA vibrational properties is quite complex; it originates in the geometry deformation and normal mode coupling pattern changes of the platinated octamer, as well as in local perturbations of the electronic structure and force field of the GC base pairs to which the platinum is bound. Many of the local effects could be accounted for by a point charge used in place of the metal in the GC complex.

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Section: Methodsmentioning

confidence: 99%

“…25,26 NMR studies of a metalated DNA duplex suggest that the platinum binds to the N7 site of two neighboring guanines in the GG sequence. 27,28 The binding significantly perturbs the regular DNA geometry. The parallel stacking of the guanine bases is destroyed, and the double helix bends toward the major groove at the platination site.…”

Section: Introductionmentioning

confidence: 99%

DNA Oligonucleotide−cis-Platin Binding: Ab Initio Interpretation of the Vibrational Spectra

2007

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“…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%

Mechanism of transcriptional stalling at cisplatin-damaged DNA

Damsma

Alt

Brueckner

et al. 2007

Nat Struct Mol Biol

155

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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“…An exhaustive analysis of DNA fragments containing modified nucleotides shows that some of these chemical modifications produce only minor changes in the local structure of the DNA (70 -74), whereas in other cases the structure of the double helix is highly distorted (75,76). Several DNA adducts with bulky modifications have been studied.…”

Section: Molecular Recognition Properties Of the Damaged Dnas-mentioning

confidence: 99%

Effect of Bulky Lesions on DNA

Gómez‐Pinto

Cubero

Kalko

et al. 2004

Journal of Biological Chemistry

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The three-dimensional solution structure of two DNA decamers of sequence d(CCACXGGAAC)-(GTTCCG-GTGG) with a modified nucleotide containing a cholesterol derivative (X) in its C1(chol)␣ or C1(chol)␤ diastereoisomer form has been determined by using NMR and restrained molecular dynamics. This DNA derivative is recognized with high efficiency by the UvrB protein, which is part of the bacterial nucleotide excision repair, and the ␣ anomer is repaired more efficiently than the ␤ one. The structures of the two decamers have been determined from accurate distance constraints obtained from a complete relaxation matrix analysis of the NOE intensities and torsion angle constraints derived from J-coupling constants. The structures have been refined with molecular dynamics methods, including explicit solvent and applying the particle mesh Ewald method to properly evaluate the long range electrostatic interactions. These calculations converge to well defined structures whose conformation is intermediate between the A-and B-DNA families as judged by the root mean square deviation but with sugar puckerings and groove shapes corresponding to a distorted B-conformation. Both duplex adducts exhibit intercalation of the cholesterol group from the major groove of the helix and displacement of the guanine base opposite the modified nucleotide. Based on these structures and molecular dynamics calculations, we propose a tentative model for the recognition of damaged DNA substrates by the UvrB protein.DNA is susceptible to a number of lesions, such as those caused by chemicals, ionizing radiation, and ultraviolet light.Failure to repair DNA damage is thought to play a significant role in cancer and aging. Nucleotide excision repair (NER) 1 is a universal DNA repair mechanism that recognizes and removes many structurally diverse DNA lesions. This system repairs the damage in the DNA by a three step mechanism: (i) recognition of the lesion, (ii) dual nicking (3Ј and 5Ј) of the damaged strand around the altered site, and (iii) DNA synthesis and ligation to fill the 12-13-base gap. The NER system in eucaryotes is very complex and involves the action of at least 16 different polypeptides (1). On the contrary, in procaryotic organisms the NER mechanism involves only four specific proteins, UvrA, UvrB, UvrC, and UvrD (in addition to DNA polymerase and ligase). Despite the fact that the general mechanism of the UvrABCD system is known, many key issues remain unclear. The most important one is the determination of the structural characteristics of DNA lesions that trigger the repair system. The wide range of lesions that are recognized by the UvrABCD system suggests that the feature that induces repair is an alteration of the structural characteristics of the damaged DNA rather than a particular chemical structure of the damaging agent (2-4). After the analysis of a large number of lesions that are substrates of the UvrABCD system, van Houten (3) classified them into six categories: (i) covalent damage, (ii) bulky substituents, (iii) localize...

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NMR Solution Structure of a DNA Dodecamer Duplex Containing a cis-Diammineplatinum(II) d(GpG) Intrastrand Cross-Link, the Major Adduct of the Anticancer Drug Cisplatin

Cited by 282 publications

References 30 publications

DNA Oligonucleotide−cis-Platin Binding: Ab Initio Interpretation of the Vibrational Spectra

DNA Oligonucleotide−cis-Platin Binding: Ab Initio Interpretation of the Vibrational Spectra

Mechanism of transcriptional stalling at cisplatin-damaged DNA

Effect of Bulky Lesions on DNA

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