Molecular mechanics modeling of oligonucleotide adducts of the antitumor drug cis-diamminedichloroplatinum(II)

A pyrazolato-bridged dinuclear platinum(II) complex induces only minor distortions upon DNA-binding

The cytotoxic, pyrazolato-bridged dinuclear platinum(II) complex [(cis-{Pt(NH3)2})2(mu-OH)(mu-pz)]2+ (pz=pyrazolate) has been found to cross-link two adjacent guanines of a double-stranded DNA decamer without destabilizing the duplex and without changing the directionality of the helix axis. A 1H NMR study of the oligonucleotide d(CTCTG*G*TCTC)-d(GAGACCAGAG), cross-linked at the two G* guanines by [(cis-{Pt(NH3)2})2(mu-pz)]3+, and molecular dynamics simulations of the explicitly solvated duplex were performed to characterize the structural details of the adduct. The dinuclear platinum cross-link unwinds the helix by approximately 15 degrees , that is, to a similar extent as the widely used antitumor drug cisplatin, but, in contrast to the latter, induces no significant bend in the helix axis. The Watson-Crick base-pairing remains intact, and the melting temperature of the duplex is unaffected by the cross-link. The helical twist is considerably reduced between the two platinated bases, as becomes manifest in an unusually short sequential H1'-H1' distance. This unwinding also affects the sugar ring of the guanosine in the 3'-position to the cross-link, which presents an N<-->S equilibrium. This is the first cytotoxic platinum complex that has been successfully designed by envisioning the structural consequences of its binding to DNA.

A tris(2,2′-bipyridine)ruthenium(ii) derivative tethered to a cis-PtCl2(amine)2moiety: syntheses, spectroscopic properties, and visible-light-induced scission of DNA

A tris(2,2'-bipyridine)ruthenium(II) derivative having two N-(3-ammoniopropyl)carbamoyl pendant units has been prepared and reacted with cis-PtCl2(DMSO)2 (DMSO = dimethyl sulfoxide) to give a heteronuclear Ru(II)Pt(II) dimer having a cis-Pt(II)Cl2(aliphatic amine)2 unit, [Ru(bpy)2(mu-bridge)PtCl2](PF6)2 (bpy = 2,2'-bipyridine, bridge = 4,4'-bis(N-(3-aminopropyl)carbamoyl)-2,2'-bipyridine). The ESI-TOF mass spectrum of the Ru(II)Pt(II) dimer shows a set of signals corresponding to {[Ru(bpy)2(mu-bridge)PtCl2](PF6)}(+) (m/z 1181.1). The MLCT (metal-to-ligand charge transfer) luminescence intensity is enhanced upon the platination of two amine units, presumably due to the formation of a relatively rigid metallocycle. More interestingly, the luminescence intensity is further enhanced by the complexation of the Ru(II)Pt(II) dimer with either 5'-GMP (guanosine 5'-monophosphate disodium salt) or calf thymus DNA. Visible-light-induced scission of supercoiled pBR322 DNA is found to be efficiently enhanced in the presence of the title Ru(II)Pt(II) dimer.

Biophysical characterization and molecular modeling of the coordinative-intercalative DNA monoadduct of a platinum-acridinylthiourea agent in a site-specifically modified dodecamer

The guanine- N7 monoadduct of [Pt(en)Cl(ACRAMTU)](NO(3))(2) (PT-ACRAMTU; en=ethane-1,2-diamine, ACRAMTU=1-[2-(acridin-9-ylamino)ethyl]-1,3-dimethylthiourea), a dual metalating/intercalating cytotoxic agent, was generated in a double-stranded dodecamer, d(CCTCTCG*TCTCC/GGAGACGAGAGG) (III*), and isolated by preparative reverse-phase high-performance liquid chromatography (HPLC). The adduct was characterized using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), circular-dichroism spectropolarimetry (CD), UV-melting curves, and NMR spectroscopy. In addition, a molecular mechanics/restrained molecular dynamics (MM/rMD) study was performed for this adduct using the AMBER force field. Monoadduction of the sequence leads to a pronounced increase in melting temperature, Delta T(m)= T(m)(III*)- T(m)(III)=9.7 degrees C. Because there is complete enthalpy-entropy compensation, binding occurs without noticeable thermodynamic destabilization. This feature and the CD (induced-ligand circular dichroism) and NMR (upfield shifts of aromatic acridine proton signals) data are indicative of a unique, nondenaturing dual-binding mode that involves partial intercalation of the acridine chromophore. An energy-minimized AMBER model ofIII* demonstrates that platination of G7- N7 of guanine in the major groove and partial insertion of the acridine moiety into the C6G19/G7C18 base step on the 5' face of the modified purine base is feasible and supportive of the experimental results. Differences in the biophysical properties betweenIII* and duplexes containing adducts of the clinical-drug cisplatin are outlined, and possible biological consequences are discussed.

Unprecedented head-to-head conformers of d(GpG) bound to the antitumor active compound tetrakis (mu-carboxylato)dirhodium(II,II)

The N7/O6 equatorial binding interactions of the antitumor active complex Rh(2)(OAc)(4)(H(2)O)(2) (OAc(-) = CH(3)CO(2)(-)) with the DNA fragment d(GpG) have been unambiguously determined by NMR spectroscopy. Previous X-ray crystallographic determinations of the head-to-head (HH) and head-to-tail (HT) adducts of dirhodium tetraacetate with 9-ethylguanine (9-EtGH) revealed unprecedented bridging N7/O6 guanine nucleobases that span the Rh-Rh bond. The absence of N7 protonation at low pH and the notable increase in the acidity of N1-H (pK(a) approximately 5.7 as compared to 8.5 for N7 only bound platinum adducts), suggested by the pH dependence titrations of the purine H8 (1)H NMR resonances for Rh(2)(OAc)(2)(9-EtG)(2) and Rh(2)(OAc)(2-)[d(GpG)],are consistent with bidentate N7/O6 binding of the guanine nucleobases. The pK(a) values estimated for N1-H (de)protonation, from the pH dependence studies of the C6 and C2 (13)C NMR resonances for the Rh(2)(OAc)(2)(9-EtG)(2) isomers, concur with those derived from the H8 (1)H NMR resonance titrations. Comparison of the (13)C NMR resonances of C6 and C2 for the dirhodium adducts Rh(2)(OAc)(2)(9-EtG)(2) and Rh(2)(OAc)(2)[d(GpG)] with the corresponding resonances of the unbound ligands [at pH 7.0 for 9-EtGH and pH 8.0 for d(GpG)], shows substantial downfield shifts of Deltadelta approximately 11.0 and 6.0 ppm for C6 and C2, respectively; the latter shifts reflect the effect of O6 binding to the dirhodium centers and the ensuing enhancement in the acidity of N1-H. Intense H8/H8 ROE cross-peaks in the 2D ROESY NMR spectrum of Rh(2)(OAc)(2)[d(GpG)] indicate head-to-head arrangement of the guanine bases. The Rh(2)(OAc)(2)[d(GpG)] adduct exhibits two major right-handed conformers, HH1 R and HH2 R, with HH1 R being three times more abundant than the unusual HH2 R. Complete characterization of both adducts revealed repuckering of the 5'-G sugar rings to C3'-endo (N-type), retention of C2'-endo (S-type) conformation for the 3'-G sugar rings, and anti orientation with respect to the glycosyl bonds. The structural features obtained for Rh(2)(OAc)(2))[d(GpG)] by means of NMR spectroscopy are very similar to those for cis-[Pt(NH(3))(2))[d(GpG)]] and corroborate molecular modeling studies.

A study of the interaction of Cr(III) complexes and their selective binding with B-DNA: a molecular modeling approach

Molecular modeling and energy minimisation calculations have been used to investigate the interaction of chromium(III) complexes in different ligand environments with various sequences of B-DNA. The complexes are [Cr(salen)(H(2)O)(2)](+); salen denotes 1, 2 bis-salicylideneaminoethane, [Cr(salprn)(H(2)O)(2)](+); salprn denotes 1, 3 bis- salicylideneaminopropane, [Cr(phen)(3)](3+); phen denotes 1, 10 phenanthroline and [Cr(en)(3)](3+); en denotes ethylenediamine. All the chromium(III) complexes are interacted with the minor groove and major groove of d(AT)(12), d(CGCGAATTCGCG)(2) and d(GC)(12) sequences of DNA. The binding energy and hydrogen bond parameters of DNA-Cr complex adduct in both the groove have been determined using molecular mechanics approach. The binding energy and formation of hydrogen bonds between chromium(III) complex and DNA has shown that all complexes of chromium(III) prefer minor groove interaction as the favourable binding mode.

TATA binding protein discriminates between different lesions on DNA, resulting in a transcription decrease

DNA damage recognition by basal transcription factors follows different mechanisms. Using transcription-competition, nitrocellulose filter binding, and DNase I footprinting assays, we show that, although the general transcription factor TFIIH is able to target any kind of lesion which can be repaired by the nucleotide excision repair pathway, TATA binding protein (TBP)-TFIID is more selective in damage recognition. Only genotoxic agents which are able to induce kinked DNA structures similar to the one for the TATA box in its TBP complex are recognized. Indeed, DNase I footprinting patterns reveal that TBP protects equally 4 nucleotides upstream and 6 nucleotides downstream from the A-T (at position -29 of the noncoding strand) of the adenovirus major late promoter and from the G-G of a cisplatin-induced 1,2-d(GpG) cross-link. Together, our results may partially explain differences in transcription inhibition rates following DNA damage.

Factors Influencing the Configuration and Conformation of Diamine Chelate Rings in Platinum(II) Compounds: 2,4-Bis(methylamino)pentane Complexes

Complexes of the type [PtX(2)(Me(2)DAP)] (Me(2)DAP = 2,4-bis(methylamino)pentane) have been prepared and studied by (1)H NMR spectroscopy, molecular mechanics/dynamics (MMD) calculations, and X-ray crystallography. The coordinated Me(2)DAP ligand has four asymmetric centers. Complexes with an enantiomeric form of the ligand (e.g., RR-Me(2)DAP, RR being the configurations of the two asymmetric carbons) have three possible configurations, namely, SRRR, RRRR, and SRRS at N, C, C, and N, respectively. Indeed these three isomers were obtained in respective ratios of 9:1: approximately 0 for X = I(-) and of 7:3:1 for X = Cl(-). Complexes with the meso ligand (RS-Me(2)DAP) have four possible configurations, i.e., SRSR, RRSS, RRSR, and SRSS at N, C, C, and N, respectively (the latter two constitute an enantiomeric pair). Only the two symmetrical isomers were obtained in the ratios of 9:1 for X = I(-) and 1:1 for X = Cl(-). In addition, the preferred chelate ring conformations in solution (CDCl(3)) were determined to be the following: delta-chair (SRRR), lambda-skew (RRRR), fluxional chair (SRRS), fluxional skew (SRSR), and lambda-chair (RRSS). This information was used to assess the contributions of intra- and interligand interactions to determine the conformational stability. MMD calculations employing the AMBER force field [as modified by Yao et al. (Yao, S.; Plastaras, J. P.; Marzilli, L. G. Inorg. Chem. 1994, 33, 6061) and extended to include parameters for the Cl(-) ligands] provided minimum-energy structures for all five X = Cl(-) complexes. These structures agreed well with the experimentally determined solution conformations except for SRSR, which had a lowest energy delta-chair instead of skew conformation. X-ray structural studies of the SRSR species (X = Cl(-) and X = I(-)) confirmed the delta-chair conformation. The results suggest that an equatorial N-methyl group has nonbonded clashes with the cis chloride ligand; therefore, axial N-methyl groups are favored. However, in solution, the solvent and entropy (connected with fluxionality of conformers) are factors which, to some degree, can overcome the interligand steric interaction.

Modulation of Nucleotide Binding of trans Platinum(II) Complexes by Planar Ligands. A Combined Proton NMR and Molecular Mechanics Study

Nonclassical trans platinum complexes containing planar nitrogen bases show biological activity different from that of trans-diamminedichloroplatinum(II) (trans-DDP). In search of the mechanism of action of such compounds, a comparative study on the nucleobase chemistry of trans-DDP and trans-[PtCl(2)(NH(3))(quinoline)] (trans-QUIN) was performed using 1D and 2D NMR spectroscopy and molecular modeling techniques. The two simple monofunctional adducts trans-[PtCl(9-ethylguanine-N7)(NH(3))L]NO(3) (L = NH(3), 1; L = quinoline, 2) were synthesized by employing the AgNO(3)/DMF method. Reactions of these species with 5'-guanosine monophosphate (5'-GMP) and 5'-cytidine monophosphate (5'-CMP) were used to simulate potential second binding steps on DNA. Guanine-N7 proved to be the kinetically preferred binding site for both 1 and 2. Reactions with 2 proceeded significantly slower than those with 1 under the same conditions. These differences in reactivity are attributed to an altered hydrolytic behavior of 2 due to steric influences of quinoline upon associative substitution reactions. This is supported by interligand NOEs observed in the 2D NOESY spectrum of 2 and by AMBER-based geometries for different conformers of 2. Signal splittings observed in the (1)H NMR spectra of 2 and the bifunctional adducts trans-[Pt(9-EtGua-N7)(5'-GMP-N7)(NH(3))L] (4) andtrans-[Pt(9-EtGua-N7)(2)(NH(3))L](2+) (6) (L = quinoline) indicate hindered rotation about the Pt-N (guanine and quinoline) bonds. Temperature-dependent NMR spectra and molecular mechanics results are in agreement with frozen rotamers in solution at room temperature where unfavorable repulsive interligand interactions result in different head-to-head and head-to-tail orientations of the bases. For the different rotamers of 4, a high barrier of interconversion of 87 kJ mol(-)(1) was estimated from NMR data. The consequences of these kinetic and geometric effects with respect to target DNA are discussed.

Distortions of the DNA double helix induced by 1,3-trans-diamminedichloroplatinum(II)-intrastrand cross-link: an internal coordinate molecular modeling study

A trans-diamminedichloroplatinum(II) (trans-DDP) intrastrand adduct within the sequence d(TCTG*TG*TC).d(GACACAGA) (where G* represents a platinated guanine) is modeled on the basis of qualitative experimental data concerning global unwinding and curvature as well as information on base pairing. Modeling is performed using the internal coordinate JUMNA program, specific to nucleic acids, and modified to include the possibility of covalently bound ligands. Calibration of the energy functions representing the Pt-N7 bond with guanine is described. The platinum atom and the platinum-nitrogen bonds are parameterized for use in the Hückel Del Re method to calculate monopoles at each atom. These monopoles are consistent with the Flex force field included in Jumna. By developing an appropriate minimization protocol we are able to generate stable, distorted three-dimensional structures compatible with the experimental data and including an unusually high global unwinding. No a priori geometric assumptions are made in generating these structures.

The actual incision determines the efficiency of repair of cisplatin-damaged DNA by the Escherichia coli UvrABC endonuclease

The UvrABC endonuclease from Escherichia coli repairs a broad spectrum of DNA lesions with variable efficiencies. The effectiveness of repair is influenced by the nature of the lesion, the local DNA sequence, and/or the topology of the DNA. To get a better understanding of the aspects of this multistep repair reaction that determine the effectiveness of repair, we compared the incision efficiencies of linear DNA fragments containing either a site-specific cis-[Pt(NH3)2(d(GpG)-N7(1),-N7(2)]] or a cis- Pt(NH3)2[d(GpCpG)-N7(1),-N7(3)]] adduct. Overall the DNA with the cis-PtGG adduct was incised about 3.5 times more efficiently than the cis-Pt.GCG-containing DNA. The rate of UvrB-DNA preincision complex formation for both lesions was similar and high in relation to the incision. DNase I footprints, however, showed that the local structure of the two preincision complexes is different. An assay was developed to measure the binding of UvrC to the preincision complexes and it was found that the binding rate of UvrC to the more slowly incised cis-Pt.GCG preincision complex was higher than to the cis-Pt.GG preincision complex. This most likely reflects a qualitative difference in preincision complex structures. For both lesions the binding of UvrC to the preincision complex was fast compared to the kinetics of actual incision. Apparently, direct incision of cisplatin damage requires an additional conformational change after the binding of UvrC.

Identification of DNA--cisplatin adducts in a blind trial of in situ scanning tunneling microscopy

Scanning tunneling microscopy (STM) reveals nanometer scale details of hydrated DNA but the interpretation of the images is controversial because of substrate artifacts and the lack of a theory for image contrast. We demonstrate that we have overcome these problems by identifying five DNA samples by their STM images alone in a blinded trial. The samples were single-stranded and double-stranded DNA with and without covalent modification by the anti-tumor drug cisplatin. The cisplatin adducts were distinguished by substantial kinking at the drug binding site. The oligomers were 20 bases in length, which was too short to permit the kinking angle to be determined with precision. However, models with a 45 degree kink gave a better fit to the images of the duplex adducts than models with a 90 degrees kink. A variety of structures was observed for the single-stranded adducts.

H8 chemical shifts in oligonucleotide cross-linked at a GpG sequence by cis-Pt(NH3)2(2+): a clue to the adduct structure

The origin of the anomalous H8 chemical shifts observed in 1H-NMR spectra of oligonucleotides cross-linked at a GpG sequence with cis-[Pt(NH3)2]2+ has been investigated and clarified. The main contributions that distinguish the H8 resonances of the two platinum-ligating guanines from other GH8 signals and from each other are: (a) the inductive effect of platinum binding which we have recently quantified as a downfield shift of 0.48 +/- 0.07 ppm (M. H. Fouchet, D. Lemaire, J. Kozelka and J.-C. Chottard, unpublished results); (b) the ring-current effect of one GpG guanine on the H8 resonance of the other guanine, which is negative (shielding) for the 5'-H8 and positive (deshielding) for the 3'-H8 in single-stranded adducts, but has the opposite sign in double-stranded adducts; (c) a deshielding polarization effect of the phosphate 5' to the GpG unit. The different signs of the ring-current effects in single-stranded and double-stranded oligonucleotides originate from the orientation of the guanines in the cis-[Pt(NH3)2(Gua)2]2+ moiety (Gua, guanine), which is left-handed helicoidal in single strands and right-handed helicoidal in double strands. In the platinated dinucleotides (cis-[Pt(NH3)2(GpG)]+, cis-[Pt(NH3)2(d(GpG))]+ and cis-[Pt(NH3)2(d(GpG))]), the guanines assume either the left-handed or the right-handed arrangement, depending on the sugar moiety (ribose or deoxyribose), protonation state at N1 and, in the solid state, on crystal forces. This work shows that chemical shifts contain valuable structural information which is complementary to that extracted from correlated spectroscopy and nuclear Overhauser spectroscopy data.

Cisplatin induced alterations in oriented fibers of DNA studied by atomic force microscopy

Oriented fibers of DNA, prepared by the wet spin method, were imaged by atomic force microscopy. It was found that an oriented fiber's substructure is an array of assemblages of DNA. For native DNA, the assemblages exhibit a characteristic width of 76 nm, a thickness of 20 nm, and appear to carry a right handed twist. Treatment with the anticancer drug cisplatin prior to wet spinning induces geometric irregularities, in the form of kinks and width distortions, into the assemblages of DNA.

The reaction of platinum(II) complexes with DNA. Kinetics of intrastrand crosslink formation in vitro

The kinetics of the formation of bifunctional DNA platinum(II) adducts (DNA-crosslinks) have been investigated by endonuclease digestion and subsequent HPLC analysis of the soluble nucleotides and nucleotide platinum(II) adducts. The results indicate two waves of crosslinking [rate constants (0.2-0.3) min-1 and (0.015-0.025) min-1] that correlate with changes in ultra violet absorbance and ethidium bromide dependent fluorescence intensity, previously interpreted in terms of two consecutive, local conformational rearrangements of platinum-DNA (Schaller, W., Reisner, H., and Holler, E. (1987) Biochemistry 26, 943-950). The formation of crosslinks at sequences d(GpG) and d(GpNpG) follows identical kinetics. A minimal reaction mechanism is proposed for the binding of cis-diamminedichloroplatinum(II) to DNA under in vitro conditions. The approximately 3-fold higher rate for meso-[1,2-bis(2,6-dichloro-4- hydroxyphenyl)ethylenediamine]diaquaplatinum(II) in comparison to the rate for cis-diamminediaquaplatinum(II) indicates that crosslink formation is affected by the nature of the non-leaving platinum ligand(s).

cis-Diamminedichloroplatinum (II) modified chromatin and nucleosomal core particle probed with DNase I

Chromatin and nucleosomal core particles were modified with cis-diamminedichloroplatinum (II) and the nucleoprotein complexes then digested with DNase I. Limited digestion of the modified chromatin containing cis-Pt(NH3)2Cl2 mediated cross-links involving the non-histone chromosomal proteins (Scovell et al. (1987) Biochem. Biophys. Res. Commun. 142, 826-835) does not release the low mobility proteins and excises only about 20% of the high mobility proteins 1, 2, and E. This supports previous findings that the low mobility proteins are involved primarily in protein-protein cross-links. In addition, the covalent cross-links between DNA and the high mobility proteins 1, 2, and E are relatively inaccessible to DNase I, in marked contrast to their accessibility to micrococcal nuclease. Furthermore, gels of the denatured DNA fragments obtained from digestion of both modified chromatin and nucleosomal core particle reveal virtually no difference in the 10n base repeat pattern, indicating no detectable change in the DNA-protein interactions upon DNA modification. This suggests that the predominant modification produced on core particle DNA, whether contained within higher order chromatin structure or in the core particle itself, is one which does not significantly alter the helical twist of the DNA within these nucleoprotein assemblies.

Characterization of cisplatin adducts of oligonucleotides by fast atom bombardment mass spectrometry

The products of the reaction of the antitumor drug cisplatin (cis-diamminedichloroplatinum(II)) with four oligonucleotide tetramers, d(GpCpGpC), d(GpGpCpC), d(TpGpApT), and d(TpGpCpT), were separated by gel permeation chromatography and characterized by negative- and positive-ion fast atom bombardment (FAB) mass spectrometry. Fragment ions indicating the oligonucleotide sequence and the position of cisplatin binding were observed in MS/MS spectra following collisional activation and B/E-linked scanning. Positive-ion FAB MS/MS spectra were characterized by platinum-containing product ions. Nonplatinated sequence ions and internal fragment ions were present primarily in the negative-ion spectra. The most prominent fragment ions containing platinum were [HB2.Pt.B3H]+ and [HB1.Pt.B2H]+, where B1, B2, and B3 were bases in the oligonucleotide tetramer, one of which was usually guanine. Both singly and doubly charged platinum complexes were observed, probably indicating reduction of Pt(II) during the FAB ionization process. The location of the platinum complex bound to each oligonucleotide sequence could be determined, and the binding sites observed by mass spectrometry were similar to those previously determined by other methods. FAB ionization with collisional activation and MS/MS analysis could serve as a new method for structural analysis of platinated oligonucleotides.

A d(GpG)-platinated decanucleotide duplex is kinked. An extended NMR and molecular mechanics study

A conformational study of the double-stranded decanucleotide d(GCCG*G*ATCGC).d(GCGATCCGGC), with the G* guanines chelating a cis-Pt(NH3)2 moiety, has been accomplished using 1H and 31P NMR, and molecular mechanics. Correlation of the NMR data with molecular models has disclosed an equilibrium between several kinked conformations and has ruled out an unkinked structure. The deformation is localized at the CG*G*.CCG trinucleotide where the helix is kinked by approximately 60 degrees towards the major groove and unwound by 12-19 degrees. The models revealed an unexpected mobility of the cytosine complementary to the 5'-G*. This cytosine can stack on either branch of the kinked complementary strand. The energy barrier between the two positions has been calculated to be less than or equal to 12 kJ/mol. The NMR data are in support of rapid flip-flopping of this cytosine. An explanation for the strong downfield shift observed in the 31P resonance of the G*pG* phosphate is given.

Interaction of deoxyguanylic acid with alkaline earth metal ions. Evidence for the deoxyribose C3'-endo/anti, O4'-endo/anti and C2'-endo/anti conformational transitions

The interaction of 2'-deoxyguanosine-5'-monophosphoric acid (H2-dGMP) with the alkaline earth metal ions has been investigated in aqueous solution at neutral pH. The solid salts of the type Mg-dGMP.5H2O Ca-dGMP.6H2O, Sr-dGMP.7H2O and Ba-dGMP.7H2O were isolated and characterized by FT-IR, proton-NMR and X-ray powder diffraction measurements. Two types of metal-nucleotide interactions have been identified: (a) the indirect metal-base and the direct metal-phosphate bindings (outer- and inner-sphere interaction), for the Mg(II) and Sr(II) ions and (b) the direct metal-base and direct metal-phosphate bindings (inner-sphere interaction), for the Ca(II) and Ba(II) ions. In aqueous solution, a dynamic equilibrium of the type base-metal-H2O. . .PO3 in equilibrium base. . .H2O-metal-PO3 is present. The deoxyribose moiety exhibits C3'-endo/anti conformation, in the Mg(II)-, Ca(II)-, Sr(II)- and Ba(II)-dGMP salts.

DNA bending induced by covalently bound drugs. Gel electrophoresis and chemical probe studies

Modification of nucleotide residues arising from the covalent binding of a drug or as a result of irradiation with ultraviolet light can induce distortion of the DNA double helix. The purpose of this review is to show that, from investigation of the electrophoretic mobility of the modified DNA fragments, one can deduce whether the distortions behave more as the centers of directed bends or as hinge joints. It is also demonstrated that chemical probes are a complementary tool for the analysis of distortions at the nucleotide level.

How does cisplatin alter DNA structure? A molecular mechanics study on double-stranded oligonucleotides

Molecular models for two double-stranded decanucleotides, d(GCCG*G*ATCGC)-d(GCGATCCGGC) (1) and d(GCTG*G*ATCGC)-d(GCGATCCAGC) (2), with the G* guanines cross-linked by a cis-Pt(NH3)2 moiety, were calculated using molecular mechanics. Nine models for 1 and eight models for 2 are reported; in all of them, the double helix is kinked by approx. 60 degrees towards the major groove and slightly unwound. The model building has been guided by comparison with the NMR data available for duplex 1. The influence of the base at the 5'-side of the coordinated G*G* dinucleotide is discussed.

Bending studies of DNA site-specifically modified by cisplatin, trans-diamminedichloroplatinum(II) and cis-[Pt(NH3)2(N3-cytosine)Cl]+

Duplex oligonucleotides containing a single intrastrand [Pt(NH3)2]2+ cross-link or monofunctional adduct and either 15 or 22 bp in length were synthesized and chemically characterized. The platinum-modified and unmodified control DNAs were polymerized in the presence of DNA ligase and the products studied on 8% native polyacrylamide gels. The extent of DNA bending caused by the various platinum-DNA adducts was revealed by their gel mobility shifts relative to unplatinated controls. The bifunctional adducts cis-[Pt(NH3)2[d(GpG)]]+, cis-[Pt(NH3)2[d(ApG)]]+, and cis-[Pt(NH3)2[d(G*pTpG*)]], where the asterisks denote the sites of platinum binding, all bend the double helix, whereas the adduct trans-[Pt(NH3)2[d(G*pTpG*)]] imparts a degree of flexibility to the duplex. When modified by the monofunctional adduct cis-[Pt(NH3)2(N3-cytosine)(dG)]Cl the helix remains rod-like. These results reveal important structural differences in DNAs modified by the antitumor drug cisplatin and its analogs that could be important in the biological processing of the various adducts in vivo.

Theoretical studies of cis-Pt(II)-diammine binding to duplex DNA

The binding of cis-Pt(II) diammine (cis-DP) to double-stranded DNA was studied with several kinked conformations that can accommodate the formation of a square planar complex. Molecular mechanics (MM) calculations were performed to optimize the molecular fit. These results were combined with quantum mechanical (QM) calculations to ascertain the relative energetics of ligand binding through water vs direct binding of the phosphate to the ammine and platinum, and to guide the selection of DNA conformations to model complex formation. Based on QM and MM calculations, models are proposed that may be characterized by several general features. A structure involving hydrogen bonding between each ammine and distinct adjacent phosphate groups, referred to as closed conformation (CC), has already been reported. This is also found in the crystal structure of small dimers. We report alternative conformations that may be important in platination of duplex DNA. They are characterized by an intermediate conformation (IC), involving hydrogen bonding between one ammine and phosphate group, and an open conformation (OC), without ammine phosphate hydrogen bonding. The IC and OC can be stabilized by water bridges in the space between the ammine and the phosphate groups. Sugar puckers alternate from the type C(2')-endo or C(1')-exo (S), to the type C(3')-endo or C(2')-exo (N), with intermediate types near O(1')-endo (O). In general, the sugar puckers alternate from S to N to S through the platinated region (3'-TpG*pG*p-5'), with the complexed strand exhibiting, (3')-S*-N*-S-(5') alternation, while the complementary strand shows either (3')-S*-N*-S-(5') or (3')-S*-N*-O-(5') alternation. In both the OC and IC, a hydrogen bond is found between the ammine and O4(T) on thymine (T) at the (3') end, adjacent to the complex site. There is a continuous range of backbone conformations through the platinated region which relate the OC to the IC. The models presented suggest that the dynamics of the binding of the cis-Pt(II)-diammines to adjacent N7(G) in double-stranded DNA may encompass several conformational possibilities, and that water bridges may play a roll in supporting open and intermediate conformations. Proton-proton distances are reported to assist in the experimental determination of conformations.

Computational analysis of the effects of site-specific phosphate alkylation in the DNA oligomer (d-[GGAATTCC])2

Alkylation of the sugar-phosphate backbone of DNA can result upon exposure to several potent carcinogens, inducing DNA misfunction. In order to assess the structural and energetic changes in DNA helices induced by such alkylation, we have performed AMBER-based analyses on phosphotriester containing analogues of (d-[GGAATTCC])2. Fourteen analogues of the nonalkylated oligomer were examined, each bearing a single alkylation of known stereochemistry. Results indicate that although there is minimal effect on the aromatic bases, the presence of a phosphotriester disturbs the sugar-phosphate backbone in complex ways. For most analogues, total minimum energies are lower for the Sp-alkylations than for the Rp-alkylations which point directly into the major groove of the helix; however, different energetic contributions follow different, or no, trends in dependence on alkylation site and/or stereochemistry. Where data is available, experimental nmr results agree with the calculations reported here.

Chemical probes of the conformation of DNA modified by cis-diamminedichloroplatinum(II)

The purpose of this work was to analyze at the nucleotide level the distortions induced by the binding of cis-diamminedichloroplatinum(II) (cis-DDP) to DNA by means of chemical probes. In order to test the chemical probes, experiments were first carried out on two platinated oligonucleotides. It has been verified by circular dichroism and gel electrophoresis that the binding of cis-DDP to an AG or to a GTG site within a double-stranded oligonucleotide distorts the double helix. The anomalously slow electrophoretic mobility of the multimers of the platinated and ligated oligomers strongly suggests that the platinated oligonucleotides are bent. The reactivity of the oligonucleotide platinated at the GTG site with chloroacetaldehyde, diethyl pyrocarbonate, and osmium tetraoxide, respectively, suggests a local denaturation of the double helix. The 5'G residue and the T residue within the adduct are no longer paired, while the 3'G residue is paired. The double helix is more distorted (but not denatured) at the 5' side of the adduct than at the 3' side. In the case of the oligonucleotide platinated at the AG site, the double helix is also more distorted at the 5' side of the adduct than at the 3' side. The G residue within the adduct is paired. The reactivities of the chemical probes with six platinated DNA restriction fragments show that even at a relatively high level of platination only a few base pairs are unpaired but the double helix is largely distorted. No local denaturation has been detected at the GG sites separated from the nearest GG or AG sites by at least three bases pairs.(ABSTRACT TRUNCATED AT 250 WORDS)

The major adduct of the antitumor drug cis-diamminedichloroplatinum(II) with DNA bends the duplex by approximately equal to 40 degrees toward the major groove

We used gel electrophoresis methods to show that reaction of DNA with cis-diamminedichloroplatinum(II) results in a substantial (approximately equal to 40 degrees) bend in the double helix at the intrastrand crosslink between the N7 atoms of adjacent guanosine nucleosides, which bond to the platinum(II) complex with loss of two chloride ions. Multimers of a 22-base-pair (bp) oligonucleotide platinated at a single site show strong anomalies in their electrophoretic mobilities as a consequence of coherent addition of in-phase platinum-induced bends. Increase of the sequence repeat of the platinated site to 27 bp yields multimers of nearly normal mobility because the bends are out of phase. The direction of Pt-induced bends relative to adenosine-tract bends was determined from the electrophoretic mobility of multimers in which repeated platination sites are interdigitated at various phasings relative to repeated adenosine tracts. Optimum bending occurs when 1.5 helical turns separate the cis-[Pt(NH3)2[d(pGpG)]](N7,N7) adducts from the center of the adenosine tracts. This phasing produces coherent addition of adenosine tract bends toward the minor groove at their centers and Pt-induced bends toward the major groove, where the platinum is located.