2.4 A crystal structure of an oxaliplatin 1,2-d(GpG) intrastrand cross-link in a DNA dodecamer duplex

(1R,2R-Diaminocyclohexane)oxalatoplatinum(II) (oxaliplatin) is a third-generation platinum anticancer compound that produces the same type of inter- and intrastrand DNA cross-links as cisplatin. In combination with 5-fluorouracil, oxaliplatin has been recently approved in Europe, Asia, and Latin America for the treatment of metastatic colorectal cancer. We present here the crystal structure of an oxaliplatin adduct of a DNA dodecanucleotide duplex having the same sequence as that previously reported for cisplatin (Takahara, P. M.; Rosenzweig, A. C.; Frederick, C. A.; Lippard, S. J. Nature 1995, 377, 649-652). Pt-MAD data were used to solve this first X-ray structure of a platinated DNA duplex derived from an active platinum anticancer drug other than cisplatin. The overall geometry and crystal packing of the complex, refined to 2.4 A resolution, are similar to those of the cisplatin structure, despite the fact that the two molecules crystallize in different space groups. The platinum atom of the [Pt(R,R-DACH)](2+) moiety forms a 1,2-intrastrand cross-link between two adjacent guanosine residues in the sequence 5'-d(CCTCTGGTCTCC), bending the double helix by approximately 30 degrees toward the major groove. Both end-to-end and end-to-groove packing interactions occur in the crystal lattice. The latter is positioned in the minor groove opposite the platinum cross-link. A novel feature of the present structure is the presence of a hydrogen bond between the pseudoequatorial NH hydrogen atom of the (R,R)-DACH ligand and the O6 atom of the 3'-G of the platinated d(GpG) lesion. This finding provides structural evidence for the importance of chirality in mediating the interaction between oxaliplatin and duplex DNA, calibrating previously published models used to explain the reactivity of enantiomerically pure vicinal diamine platinum complexes with DNA in solution. It also provides a new kind of chiral recognition between an enantiomerically pure metal complex and the DNA double helix.     

Relationship of solution and protein-bound structures of DNA duplexes with the major intrastrand cross-link lesions formed on cisplatin binding to DNA.

DNA bases in the three-base-pair (3bp) region of duplexes with the two major lesions of cisplatin (cis-PtCl(2)(NH(3))(2)) with DNA, namely d(XGG) and d(XAG) ( = N7-platinated base), differ in their relative positions by as much as approximately 3.5 A in structures in the literature. Such large differences impede drug design and assessments of the effects of protein binding on DNA structure. One recent and several past structures based on NMR-restrained molecular dynamics (RMD) differ significantly from the reported X-ray structure of an HMG-bound XGG 16-mer DNA duplex (Ohndorf, U.-M.; Rould, M. A.; He, Q.; Pabo, C. O.; Lippard, S. J. Nature 1999, 399, 708). This 16-mer structure has several significant novel and unique features (e.g., a bp step with large positive shift and slide). Hypothesizing that novel structural features in the XGG or XAG region of duplexes elude discovery by NMR methods (especially because of the flexible nature of the 3bp region), we studied an oligomer with only G.C bp's in the XGGY site by NMR methods for the first time. This 9-mer gave a 5'-G N1H signal with a normal shift and intensity and showed clear NOE cross-peaks to C NHb and NHe. We assigned for the first time (13)C NMR signals of a duplex with a GG lesion. These data, by adding NMR-based criteria to those inherent in NOESY and COSY data, have more specifically defined the structural features that should be present in an acceptable model. In particular, our data indicated that the sugar of the X residue has an N pucker and that the GG cross-link should have a structure similar to the original X-ray structure of cis-Pt(NH(3))(2)(d(pGpG)) (Sherman S. E.; Gibson, D.; Wang, A. H.-J.; Lippard, S. J. J. Am. Chem. Soc. 1988, 110, 7368). With these restrictions added to NOE restraints, an acceptable model was obtained only when we started our modeling with the 16-mer structural features. The new X-ray/NMR-based model accounted for the NOESY data better than NOE-based models, was very similar in structure to the 16-mer, and differed from solely NOE-based models. We conclude that all XGG and XAG (X = C or T) duplexes undoubtedly have structures similar to those of the 16-mer and our model. Thus, protein binding does not change greatly the structure of the 3bp region. The structure of this region can now be used in understanding structure-activity relationships needed in the design of new carrier ligands for improving Pt anticancer drug activity.     

Cisplatin damage overrides the predefined rotational setting of positioned nucleosomes

Cisplatin and carboplatin are used successfully to treat various types of cancer. The drugs target the nucleosomes of cancer cells and form intrastrand DNA cross-links that are located in the major groove. We constructed two site-specifically modified nucleosomes containing defined intrastrand cis-{Pt(NH3)2}(2+) 1,3-d(GpTpG) cross-links. Histones from HeLa-S3 cancer cells were transferred onto synthetic DNA duplexes having nucleosome positioning sequences. The structures of these complexes were investigated by hydroxyl radical footprinting. Employing nucleosome positioning sequences allowed us to quantify the structural deviation induced by the cisplatin adduct. Our experiments demonstrate that a platinum cross-link locally overrides the rotational setting predefined in the nucleosome positioning sequence such that the lesion faces toward the histone core. Identical results were obtained for two DNA duplexes in which the sites of platination differed by approximately half a helical turn. Additionally, we determined that cisplatin unwinds nucleosomal DNA globally by approximately 24 degree. The intrastrand cis-{Pt(NH3)2}(2+) 1,3-d(GpTpG) cross-links are located in an area of the nucleosome that contains locally overwound DNA in undamaged reference nucleosomes. Because most nucleosome positions in vivo are defined by the intrinsic DNA sequence, the ability of cisplatin to influence the structure of these positioned nucleosomes may be of physiological relevance.     

Competitive reactions of interstrand and intrastrand DNA-Pt adducts: A dinuclear-platinum complex preferentially forms a 1,4-interstrand cross-link rather than a 1,2 intrastrand cross-link on binding to a GG 14-mer duplex

A study of the kinetics and mechanism of the reaction between the dinuclear Pt complex [(trans-PtCl(NH(3))(2))(2)(mu-NH(2)(CH(2))(6)NH(2))](2+) (1) and the 14-mer duplex 5'-d(ATACATG(7)G(8)TACATA)-3'.5'-d(TATG(25)TACCATG(18)TAT)-3' is reported. [(1)H,(15)N]-HSQC NMR was used to follow the reaction at 298 K, pH 5.4. The product is primarily the 5'-5' 1,4-interstrand cross-link between G(8) and G(18) bases and exists in two conformational forms. No evidence for the possible 1,2-intrastrand G(7)G(8) adduct was seen, confirming the preferential formation of interstrand cross-links by these dinuclear complexes. An initial electrostatic association of (15)N-1 with the duplex is indicated by changes in its (1)H/(15)N chemical shifts, followed by aquation of 1 to form the monoaqua monochloro species 2, with a rate constant of 4.00+/-0.03x10(-5) s(-1). Monofunctional binding to the duplex occurs primarily at G(8), the 3' base of the nucleophilic GG grouping, with a rate constant of 1.5+/-0.7 M(-1) s(-1). Changes in the (1)H/(15)N shifts indicate there is an electrostatic interaction between the unbound (PtN(3)Cl) group of the monofunctional adduct and the duplex. No peaks for a transient aquated monofunctional species are seen and closure of 3 to form the 1,4-G(8)G(18) interstrand cross-link (5) was treated as direct, with a rate constant of 4.47+/-0.06x10(-5) s(-1). The G(8)G(18) cross-link was confirmed from analysis of the NOESY NMR spectrum of the final product. Structural perturbations for the 1,4-interstrand cross-link extend over approximately four base-pairs and are similar to those found for a 1,4-interstrand cross-link with a shorter 8-mer -GTAC- sequence. A major distortion was evident for the 5'T (T(17)) adjacent to the platinated G(18), consistent with the findings from the use of chemical probes to investigate the conformation of 1,4-interstrand cross-links.     

Formation of intrastrand cross-link products between cytosine and adenine from UV irradiation of d((Br)CA) and duplex DNA containing a 5-bromocytosine

Here, we showed that Pyrex-filtered UV light irradiation of d((Br)CA) gave rise to three types of intrastrand cross-link products, that is, d(C[5-N6]A), d(C[5-2]A), and d(C[5-8]A), where the C5 carbon atom of cytosine is covalently bonded to the N6 nitrogen atom, C2, and C8 carbon atoms of adenine, respectively. Furthermore, we demonstrated by LC-MS/MS that the UV irradiation of a 5-bromocytosine-containing duplex oligodeoxynucleotide (ODN) led to the formation of five cross-link products, that is, C[5-N6]A, C[5-2]A, C[5-8]A, A[2-5]C, and A[8-5]C, under both aerobic and anaerobic conditions. LC-MS/MS quantification results showed that the yields for the formation of these cross-link products are different. The presence of molecular oxygen reduces the yields for the formation of all cross-link products except A[2-5]C. To our knowledge, this is the first report about the formation of intrastrand cross-link products between cytosine and adenine in duplex DNA. The chemistry discovered here may facilitate the future preparations of oxidative cross-link lesion-bearing substrates for biochemical and biophysical studies.     

Facile formation of an intrastrand cross-link lesion between cytosine and guanine upon pyrex-filtered UV light irradiation of d((Br)CG) and duplex DNA containing 5-bromocytosine

Pyrex-filtered UV light irradiation of d(BrCG) and 5-bromocytosine-containing duplex DNA leads to facile formation of a cross-link lesion between the C5 carbon atom of cytosine and the C8 carbon atom of its adjacent guanine. A similar cross-link lesion has been previously found in the X-ray irradiation mixture of d(CGTA).     

Photofragment translational spectroscopy of 1,3-butadiene and 1,3-butadiene-1,1,4,4-d(4) at 193 nm

The photodissociation dynamics of 1,3-butadiene at 193 nm have been investigated with photofragment translational spectroscopy coupled with product photoionization using tunable VUV synchrotron radiation. Five product channels are evident from this study: C(4)H(5) + H, C(3)H(3) + CH(3), C(2)H(3) + C(2)H(3), C(4)H(4) + H(2), and C(2)H(4) + C(2)H(2). The translational energy (P(E(T))) distributions suggest that these channels result from internal conversion to the ground electronic state followed by dissociation. To investigate the dissociation dynamics in more detail, further studies were carried out using 1,3-butadiene-1,1,4,4-d(4). Branching ratios were determined for the channels listed above, as well as relative branching ratios for the isotopomeric species produced from 1,3-butadiene-1,1,4,4-d(4) dissociation. C(3)H(3) + CH(3) is found to be the dominant channel, followed by C(4)H(5) + H and C(2)H(4) + C(2)H(2), for which the yields are approximately equal. The dominance of the C(3)H(3) + CH(3) channel shows that isomerization to 1,2-butadiene followed by dissociation is facile.     

Head-to-head cross-linked adduct between the antitumor unit bis(mu-N,N'-di-p-tolylformamidinato)dirhodium(II,II) and the DNA fragment d(GpG)

Reactions of the compound cis-[Rh2(DTolF)2(CH3CN)6](BF4)2, a formamidinate derivative of the class of antitumor compounds [Rh2(O2CR)4] (R=Me, Et, Pr), with 9-ethylguanine (9-EtGuaH) or the dinucleotide d(GpG) proceed by substitution of the acetonitrile groups, with the guanine bases spanning the Rh--Rh bond, in a bridging fashion, through sites N7/O6. In the case of 9-EtGuaH, both head-to-head (HH) and head-to-tail (HT) isomers are formed, whereas with the tethered bases in d(GpG), only one right-handed conformer HH1R [Rh2(DTolF)2{d(GpG)}] is present in solution. For both cis-[Rh2(DTolF)2(9-EtGuaH)2](BF4)2 and [Rh2(DTolF)2{d(GpG)}], the absence of N7 protonation at low pH and the substantial decrease of the pKa values for N1-H deprotonation, support N7/O6 binding of the bases to the dirhodium core. The N7/O6 binding of the bases is further corroborated by the downfield shift by Deltadelta approximately 4.0 ppm of the 13C NMR resonances for the C6 nuclei as compared to the corresponding resonances of the free ligands. The HH arrangement of the guanine bases in [Rh2(DTolF)2{d(GpG)}] is indicated by the intense H8/H8 ROE cross-peaks in the 2D ROESY NMR spectrum. Complete characterization of the [Rh2(DTolF)2{d(GpG)}] conformer by 2D NMR spectroscopy supports anti-orientation and N (C3'-endo) conformation for both deoxyribose residues. The N-pucker for the 5'-G base is universal in such cross-links, but it is very unusual for platinum and unprecedented for dirhodium HH cross-linked adducts to have both deoxyribose residues in the N-type conformation. The bulk, the nonlabile character, and the electron-donating ability of the formamidinate bridging groups spanning the dirhodium core affect the nature of the preferred dirhodium DNA adducts. Molecular modeling studies performed on [Rh2(DTolF)2{d(GpG)}] corroborate the structural features obtained by NMR spectroscopy.     

Dynamics of inter- and intrastrand hole transport in DNA hairpins

The dynamics of photoinduced electron transfer has been investigated in DNA hairpins possessing a stilbenedicarboxamide (Sa) electron acceptor, a guanine (G) primary donor, and two adjacent guanines (GG) as secondary donors. Hole transport from G to GG across a single A is more rapid than across AA or T by factors of 20 +/- 7 and 40 +/- 15, respectively. Intrastrand hole transport across a single A is more rapid than interstrand transport by a factor of 7 +/- 3.     

Charge transfer between DNA and proteins in the nucleosomes

Recently X-ray diffraction provided the structure of nucleosomes. External disturbances can unwrap DNA from the histone–protein and their genetic information becomes readable. This is strongly connected with cancer initiation. Therefore, first we performed charge transfer (CT) calculations between polythymidine and a periodic model-protein chain with a lysine or arginine and three glycines. The CT calculations were repeated between the infinite chains using combined solid state physical and quantum chemical methods. We found that the CT between the unit cells of an infinite polythymidine and poly(lysine-triglycine) is 0.04 e and 0.03 e for poly(arginine-triglycine). We investigated the influence of the basis set quality on the calculated CT values using a molecular model built of a thymidine and lysine or arginine. We have calculated also the bands of polythymidine and the two protein model chains. We have found that the differences between the highest level of the valence band of single polythymidine chain and the lowest level of the conduction bands of the model protein chains (6-11 eV depending on the basis set) are too large to assume a direct CT between these two bands.     

Synthesis and characterization of DNA duplexes containing an N(4)C-ethyl-N(4)C interstrand cross-link

Short DNA duplexes containing an N(4)C-ethyl-N(4)C interstrand cross-link, C-C, were synthesized on controlled pore glass supports. Duplexes having two, three, or four A/T base pairs on either side of the C-C cross-link and terminating with a C(4) overhang at their 5'-ends were prepared. The cross-link was introduced using a convertible nucleoside approach. Thus, an oligonucleotide terminating at its 5'-end with O(4)-triazoyl-2'-deoxyuridine was first prepared on the support. The triazole group of support-bound oligomer was displaced by the aminoethyl group of 5'-dimethoxytrityl-3'-O-tert-butyldimethylsilyl-N(4)-(2-aminoethyl)deoxycytidine to give the cross-link. The dimethoxytrityl group was removed, and the upper and lower strands of the duplex were extended from two 5'-hydroxyl groups of the cross-link using protected nucleoside 3'-phosphoramidites. The tert-butyldimethylsilyl group of the resulting partial duplex was then removed, and the chain was extended in the 3'-direction from the resulting 3'-hydroxyl of the cross-link using protected nucleoside 5'-phosphoramidites. The cross-linked duplexes were purified by HPLC and characterized by enzymatic digestion and MALDI-TOF mass spectrometry. Duplexes with three or four A/T base pairs on either side of the C-C cross-link gave sigmoidal shaped A(260) profiles when heated, a behavior consistent with cooperative denaturation of the A/T base pairs. Each cross-linked duplex could be ligated to an acceptor duplex using T4 DNA ligase, a result that suggests that the C-C cross-link does not interfere with the ligation reaction, even when it is located only two base pairs from the site of ligation. The ability to synthesize duplexes with a defined interstrand cross-link and to incorporate these duplexes into longer pieces of DNA should enable preparation of substrates that can be used for a variety of biophysical and biochemical experiments, including studies of DNA repair.     

A study of the relation between translational and rotational diffusion through measurement of molecular recollision

Translational and rotational diffusion rates of perdeuterated tempone (PDT) in ethanol are determined using electron paramagnetic resonance spectroscopy. The translational motion is measured on two scales: the macroscopic, as represented by the Heisenberg spin-exchange rate, and the microscopic, which entails recollisions between the same spin-exchange particle pair. The spin-exchange and recollision rates are used together to calculate the overall translational diffusion coefficient without recourse to assumptions concerning the value of the Stokes radius or collision distance. When observed as a function of solvent isothermal compressibility, the recollision time in ethanol is displaced from the common alkane curve at low temperatures but joins that curve at higher temperatures. Rotational correlation times in ethanol are obtained and show a decreasing rotation-translation coupling with increasing temperature, revealing a pattern that is qualitatively identical with respect to both collision and recollision. In comparison, an examination of PDT diffusion in toluene reveals an increasing rotation-translation coupling with increasing temperature. The contrasting behavior of the coupling in the two solvents is attributable to the degree of anisotropy in PDT rotation.     

Separating the contribution of translational and rotational diffusion to protein association

The association of two proteins is preceded by a mutual diffusional search in solution. The role of translational and rotational diffusion in this process has been studied theoretically for many years. However, systematic experimental verification of theoretical results is still lacking. We report here measurements of association rates of the proteins beta-lactamase (TEM) and beta-lactamase inhibitor protein (BLIP) in solutions of glycerol and poly(ethylene glycol) of increasing viscosity. We also measured translational and rotational diffusion in the same solutions, using fluorescence correlation spectroscopy and fluorescence anisotropy, respectively. It is found that in glycerol both translational and rotational diffusion rates are inversely dependent on viscosity, as predicted by the classical Stokes-Einstein relations, while the association rate depends nonlinearly on viscosity. In contrast, the association rate depends only weakly on the viscosity of the polymer solutions, which results in a similar weak dependence of k(on) on viscosity. The data are modeled using the theory of diffusion-limited association. Deviations from the theory are explained by a short-range solute-induced repulsion between the proteins in glycerol solution and an attractive depletion interaction generated by the polymers. These results open the way to the creation of a unified framework for all nonspecific effects involved in the protein association process, as well as to better theoretical understanding of these effects. Further, they reflect on the complex factors controlling protein association within the crowded environment of cells and suggest that a high concentration of macromolecules does not significantly impede protein association.     

Molecular dynamics study of translational and rotational diffusion in liquid ortho-terphenyl

NVT molecular dynamics simulations were performed on liquid o-terphenyl as a function of temperature in the range 320-480 K. Computed translational diffusion coefficients displayed the non-Arrhenius behavior expected of a fragile glass-forming liquid and were in good, semiquantitative agreement with experimental results. Rotational correlation functions calculated for various vectors within the molecule exhibited a very short time (0-1 ps) initial decay, followed by a reversal, which corresponds to free reorientation within the "solvent" cage prior to collision with a wall. Rotational correlation times of three orthogonal vectors fixed on the central benzene were close to equal at all temperatures, indicating nearly isotropic overall molecular reorientation. The average correlation times exhibited a non-Arrhenius temperature dependence and were in very good agreement with experimental values derived from 2D and 1H NMR relaxation times. Correlation times of vectors located on the lateral phenyl rings were used to calculate the "spinning" internal rotation diffusion coefficients, which were approximately twice as great as the overall rotational diffusion constants, indicating rapid internal rotation of the phenyl side groups over wide ranges of angle in the liquid.     

Green and Facile Synthesis of New 3-(Phenylallylideneamino)indeno[1,2-d]imidazoles

A green and facile strategy has been proposed for the synthesis of previously unknown 3a,8a-dihydroxy-3-[(3-phenylprop-2-en-1-ylidene)amino]-2-sulfanylidene-2,3,3a,8a-tetrahydro-1H-indeno[1,2-{und}]imidazol-8-one and 3a,8a-dihydroxy-3-[(3-phenylprop-2-en-1-ylidene)amino]-1,3,3a,8a-tetrahydroindeno[1,2-d]-imidazole-2,8-dione in excellent yields by condensation of cinnamaldehyde thiosemicarbazone and semicarbazone, respectively, with ninhydrin in boiling dioxane. The reaction is clean, simple, and free of work-up and column chromatography.

     

Synthesis and some transformations of 2-(2-thienyl)naphtho[1,2-d]oxazole

Condensation of 1-amino-2-hydroxynaphthalene with thenoyl chloride in 1-methyl-2-pyrrolidinone medium afforded 2-(2-thienyl)naphtho[1,2-d]oxazole. The latter was brought into electrophilic substitution reactions like nitration, bromination, sulfonation, formylation, and acylation. The reactions proceeded via electrophilic attack at the 5-position of the thiophene ring, but the nitration and bromination occurred involving both the thiophene and naphthalene fragments.     

Exploiting rotational and translational invariance of the energy in derivative calculations in quantum chemistry

It is shown how the invariance of the Born—Oppenheimer potential energy to overall translations and rotations of a molecule can be used to reduce the computational labor required for derivative evaluations at various orders.     

Nonadditive nature of nucleobases interactions in model d(GpG) dinucleotide steps

High nonadditive character of intermolecular interaction energy (IIE) has been found for many d(GpG) dinucleotide steps in B‐DNA conformations. Although three‐ and four‐body terms posses opposite signs in all cases, positive nonadditivity is observed. On the other hand, the pairwise additive simplification may still be applied because there is linear correlation between magnitude of additive and nonadditive terms of IIE. The application of the linear regression leads to a higher accuracy with values of standard deviation about 0.5 kcal/mol. The heterogeneity of intermolecular interactions in two subsequent GC pairs was identified as the main source of nonadditivity. The higher the difference between hydrogen bonding and interstrand stacking, the higher the absolute values of three‐ and four‐body terms. This trend is of linear character and may be used for both parametric correction and measure of nonadditivity in d(GpG) steps without necessity of energy calculations for the whole tetramer. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Synthesis of dioxoanthra[1,2-d]pyrazoline-1,2-amine(I)imides by the photolysis of 1-azido-2-dialkylaminomethyl-9,10-anthraquinones

The photolysis of 1-azido-2-dialkylaminomethyl-9,10-anthraquinones leads to 2,2-dialkyl-6H,11H,6,11-dioxanthra[1,2-d]pyrazoline-1,2-amide(I)imides. The same products are formed in the thermolysis of the initial compounds; however, they decompose under the reaction conditions.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 7, pp. 956–959, July, 1985.