Intermolecular Nuclear Overhauser Effects Research Articles

Studies on the interaction of adriamycin with d-(TGATCA) 2 by proton nuclear magnetic resonance spectroscopy, time-resolved fluorescence measurement, diffusion ordered spectroscopy followed by structural refinement using restrained molecular dynamics approach

Adriamycin is one of the most potent anticancer anthracycline drug having aromatic chromophore and an amino sugar moiety. We report here the solution structure of 2:1 adriamycin–d-(TGATCA) 2 complex which has been determined using restrained molecular dynamics. Sequential NOE (nuclear Overhauser effect) connectivities between T1pG2 and C5pA6 steps are not observed on the intercalation of the drug chromophore at these base pair steps. Presence of several other intermolecular NOEs, that is, T1CH 3 7H, T1CH 3 10eqH and C5H6 4OCH 3 corroborate the same. The specificity of interaction arises from the O-glycosidic dihedral bond C7 O7 C1′ C2′ (133°), positioning of NH 3 + moiety in minor groove, conformation of ring A and daunosamine sugar. Besides this, diffusion ordered spectroscopy (DOSY) studies prove the formation of complex and time-resolved fluorescence measurement studies provide evidence for shortening of decay time on complex formation. The nonspecific interactions as well as those essential for molecular basis of drug action are discussed along with the specificity of interactions in the drug–DNA complex, which is responsible for the anticancer action of the drug.

Probing Systems in Solution by NMR Using Sulfur Hexafluoride as a Spy Molecule

The use of SF6 as a spy molecule in solution-state NMR is investigated as an alternative to 129Xe NMR. 19F chemical shift, longitudinal relaxation time, and integral measurements, as well as intermolecular nuclear Overhauser effects, are reported for SF6 dissolved in simple deuterated solvents and/or in various solutions among which are aqueous solutions of cucurbit[6]uril (CB) and alpha-cyclodextrin (alphaCD). Both CB and alphaCD form a 1:1 inclusion complex with SF6. In a 0.2 M D2SO4-D2O solution, the affinity of CB for SF6 is 2.9x10(5) L mol(-1) at 298 K; it is the largest value ever found for the inclusion of a neutral guest into the CB cavity. It is one order of magnitude larger than in a 0.2 M Na2SO4-D2O solution, and the role of the cation is evidenced. In D2O, the affinity of alphaCD for SF6 is about 25 L mol(-1). With CB, the kinetics is slow on both the 1H and 19F chemical shift time scales, while with alphaCD fast exchange is observed. The 19F chemical shift of SF6 is much less sensitive to medium effects than the chemical shift of 129Xe. This might be a limitation if minute structural changes are to be investigated but, in the present study, turned out to be an advantage for determining the affinity of alphaCD for SF6. With CB, the 19F chemical shift of included SF6 is found to be sensitive to the nature of the cation bound at the portals. The 19F relaxation time of SF6 dissolved in deuterated solvents is dominated by the spin-rotation mechanism and is orders of magnitude shorter that the 129Xe relaxation time. It is found to be rather sensitive to the environment and was used to determine the affinity of alphaCD for SF6. The detection limit of SF6 by 19F NMR is lower than the NMR detection limit of thermally polarized 129Xe by more than three orders of magnitude. It lies in the micromolar range, and SF6 concentrations of the order of 10 microM were determined by 19F NMR signal integral measurements and used to quantify the affinity of CB for SF6. Integrals, which are usually not reliable for quantitative measurements in 129Xe NMR, were proven to be highly valuable for determining the affinity of alphaCD for SF6 as well. Most interestingly, heteronuclear Overhauser effect measurements allow to selectively highlight the 1H of a SF6 binding site according to the 19F-1H proximity and were used to characterize the inclusion complex formed with alphaCD.

Inhibitory Mechanism of Escherichia coli RelE-RelB Toxin-Antitoxin Module Involves a Helix Displacement Near an mRNA Interferase Active Site

In Escherichia coli, RelE toxin participates in growth arrest and cell death by inducing mRNA degradation at the ribosomal A-site under stress conditions. The NMR structures of a mutant of E. coli RelE toxin, RelE(R81A/R83A), with reduced toxicity and its complex with an inhibitory peptide from RelB antitoxin, RelB(C) (Lys(47)-Leu(79)), have been determined. In the free RelE(R81A/R83A) structure, helix alpha4 at the C terminus adopts a closed conformation contacting with the beta-sheet core and adjacent loops. In the RelE(R81A/R83A)-RelB(C) complex, helix alpha3(*) of RelB(C) displaces alpha4 of RelE(R81A/R83A) from the binding site on the beta-sheet core. This helix replacement results in neutralization of a conserved positively charged cluster of RelE by acidic residues from alpha3(*) of RelB. The released helix alpha4 becomes unfolded, adopting an open conformation with increased mobility. The displacement of alpha4 disrupts the geometry of critical residues, including Arg(81) and Tyr(87), in a putative active site of RelE toxin. Our structures indicate that RelB counteracts the toxic activity of RelE by displacing alpha4 helix from the catalytically competent position found in the free RelE structure.

The Structure of an Interdomain Complex That Regulates Talin Activity

Talin is a large flexible rod-shaped protein that activates the integrin family of cell adhesion molecules and couples them to cytoskeletal actin. It exists in both globular and extended conformations, and an intramolecular interaction between the N-terminal F3 FERM subdomain and the C-terminal part of the talin rod contributes to an autoinhibited form of the molecule. Here, we report the solution structure of the primary F3 binding domain within the C-terminal region of the talin rod and use intermolecular nuclear Overhauser effects to determine the structure of the complex. The rod domain (residues 1655–1822) is an amphipathic five-helix bundle; Tyr-377 of F3 docks into a hydrophobic pocket at one end of the bundle, whereas a basic loop in F3 (residues 316–326) interacts with a cluster of acidic residues in the middle of helix 4. Mutation of Glu-1770 abolishes binding. The rod domain competes with β3-integrin tails for binding to F3, and the structure of the complex suggests that the rod is also likely to sterically inhibit binding of the FERM domain to the membrane.

Interactions of Lipopolysaccharide and Polymyxin Studied by NMR Spectroscopy

In the light of occurrence of bacterial strains with multiple resistances against most antibiotics, antimicrobial peptides that interact with the outer layer of Gram-negative bacteria, such as polymyxin (PMX), have recently received increased attention. Here we present a study of the interactions of PMX-B, -E, and -M with lipopolysaccharide (LPS) from a deep rough mutant strain of Escherichia coli. A method for efficient purification of biosynthetically produced LPS using reversed-phase high-performance liquid chromatography in combination with ternary solvent mixtures was developed. LPS was incorporated into a membrane model, dodecylphosphocholine micelles, and its interaction with polymyxins was studied by heteronuclear NMR spectroscopy. Data from chemical shift mapping using isotope-labeled LPS or labeled polymyxin, as well as from isotope-filtered nuclear Overhauser effect spectroscopy experiments, reveal the mode of interaction of LPS with polymyxins. Using molecular dynamics calculations the complex of LPS with PMX-B in the presence of dodecylphosphocholine micelles was modeled using restraints derived from chemical shift mapping data and intermolecular nuclear Overhauser effects. In the modeled complex the macrocycle of PMX is centered around the phosphate group at GlcN-B, and additional contacts from polar side chains are formed to GlcN-A and Kdo-C, whereas hydrophobic side chains penetrate the acyl-chain region.

Lipophilic Diol Induced Micellization of Pluronic® F88 in Water

The presence of a lipophilic S104 (also known as C14diol) induces micellization in a highly hydrophilic ethylene oxide–propylene oxide–ethylene oxide triblock copolymer Pluronic® F88 [(EO)103(PO)39–(EO)103] in water. The dynamic light scattering (DLS) and small angle neutron scattering (SANS) reveal that F88 remains as molecularly dissolved at ambient temperature even at fairly high concentrations (5 wt% or more). However, the micellization is induced at lower concentration/temperature in the presence of S104. The scattering measurements indicated micellar growth, though no phase transition was observed. The addition of hydrophobic S104 increases the aggregation numbers of the micellar system, but does not show a considerable increase in hydrodynamic size. The micellar parameters for the copolymer in the presence of S104 are reported at 30 and 40°C. Hydrophobic S104 interacts with PPO blocks of F88, makes the decreasing CMT of F88, which may be the synergistic effect. Using intermolecular rotating-frame nuclear overhauser effect (ROE) profiles, the interactions between PPO methyl and S104 terminal methyl groups can be obviously observed.

Bilayer in Small Bicelles Revealed by Lipid−Protein Interactions Using NMR Spectroscopy

Intermolecular nuclear Overhauser effects (NOEs) between the integral outer membrane protein OmpX from Escherichia coli and small bicelles of dihexanoyl phosphatidylcholine (DHPC) and dimyristoyl phosphatidylcholine (DMPC) give insights into protein-lipid interactions. Intermolecular NOEs between hydrophobic tails of lipid and protein in the bicelles cover the surface area of OmpX forming a continuous cylindric jacket of approximately 2.7 nm in height. These NOEs originate only from DMPC molecules, and no NOEs from DHPC are observed. Further, these NOEs are mainly from methylene groups of the hydrophobic tails of DMPC, and only a handful of NOEs arise from methyl groups of the hydrophobic tails. The observed contacts indicate that the hydrophobic tails of DMPC are oriented parallel to the surface of OmpX and thus DMPC molecules form a bilayer in the vicinity of the protein. Thus, a bilayer exists in the small bicelles not only in the absence of but also in the presence of a membrane protein. In addition, the number of NOEs between the polar head groups of lipid molecules and protein is increased in the bicelles compared with those in micelles. This observation may be due to the closely packed head groups of the bilayer. Moreover, irregularity of hydrophobic interactions in the middle of the bilayer environment was observed. This observation together with the interactions between polar head groups and proteins gives a possible rationale for structural and functional differences of membrane proteins solubilized in micelles and in bilayer systems and hints at structural differences between protein-free and protein-loaded bilayers.

Solution Structure of the cGMP Binding GAF Domain from Phosphodiesterase 5: INSIGHTS INTO NUCLEOTIDE SPECIFICITY, DIMERIZATION, AND cGMP-DEPENDENT CONFORMATIONAL CHANGE

Phosphodiesterase 5 (PDE5) controls intracellular levels of cGMP through its regulation of cGMP hydrolysis. Hydrolytic activity of the C-terminal catalytic domain is increased by cGMP binding to the N-terminal GAF A domain. We present the NMR solution structure of the cGMP-bound PDE5A GAF A domain. The cGMP orientation in the buried binding pocket was defined through 37 intermolecular nuclear Overhauser effects. Comparison with GAF domains from PDE2A and adenylyl cyclase cyaB2 reveals a conserved overall domain fold of a six-stranded beta-sheet and four alpha-helices that form a well defined cGMP binding pocket. However, the nucleotide coordination is distinct with a series of altered binding contacts. The structure suggests that nucleotide binding specificity is provided by Asp-196, which is positioned to form two hydrogen bonds to the guanine ring of cGMP. An alanine mutation of Asp-196 disrupts cGMP binding and increases cAMP affinity in constructs containing only GAF A causing an altered cAMP-bound structural conformation. NMR studies on the tandem GAF domains reveal a flexible GAF A domain in the absence of cGMP, and indicate a large conformational change upon ligand binding. Furthermore, we identify a region of approximately 20 residues directly N-terminal of GAF A as critical for tight dimerization of the tandem GAF domains. The features of the PDE5 regulatory domain revealed here provide an initial structural basis for future investigations of the regulatory mechanism of PDE5 and the design of GAF-specific regulators of PDE5 function.

Cholesterol Location and Orientation in Aqueous Suspension of Large Unilamellar Vesicles of Phospholipid Revealed by Intermolecular Nuclear Overhauser Effect

The locational and orientational structure and the dynamics of cholesterol in the bilayer membrane were studied by using the solution-state NMR. The intermolecular nuclear Overhauser effect (NOE) was analyzed for large unilamellar vesicles (100 nm in diameter) composed of dimyristoylphosphatidylcholine (DMPC) and cholesterol at cholesterol concentrations of 9-33 mol %. The DMPC headgroups show (1)H-{(1)H}-NOEs with the methyl groups at the hydrophobic terminals of both cholesterol and DMPC, illustrating the significant fluctuation of the bilayer membrane in the vertical (bilayer normal) direction. Cholesterol was found to keep the hydroxyl (OH) group toward the outer water pool on the basis of the following observations: (1) the cross correlation between the DMPC headgroup and the cholesterol terminal methyl group is weaker than those between the DMPC headgroups and (2) the methyl group at the hydrophobic terminal of cholesterol shows strong correlation with the terminal group of the DMPC chain portion. The OH group plays a crucial role in orienting cholesterol with its OH group outward, since cholestane, which has a molecular structure similar to that of cholesterol except for the absence of the OH group, was found to have no orientational preference in the bilayer membrane. The dynamic slowdown at high cholesterol concentrations is demonstrated on the basis of the correlation times for NOE as well as the broadening of the proton linewidths.

Fine-Tuning Ligand−Receptor Design for Selective Molecular Recognition of Dicarboxylic Acids

The host-guest interaction between the hexaaza macrocyclic ligand 3,7,11,18,22,26-hexaazatricyclo[26.2.2.2]tetratriaconta-1(31),13(34),14,16(33),28(32),29-hexaene (P3) and three rigid dicarboxylic acids (isophthalic acid, H2is; phthtalic acid, H2ph; and terephthalic acid, H2te) has been investigated using potentiometric equilibrium methods and NMR spectroscopy including the measurement of intermolecular nuclear Overhauser effects (NOEs) and self-diffusion coefficients (D). Ternary complexes are formed in aqueous solution as a result of hydrogen bond formation and Coulombic interactions between the host and the guest. In the [(H6P3)(is)]4+ complex, those bonding interactions reach a maximum yielding a log K6R of 4.74. Competitive distribution diagrams and total species distribution diagrams are used to illustrate the main features of these systems. In particular, a selectivity of over 89% at p[H] = 5.0 is obtained for the complexation of the is versus the te substrates. The recognition capacity of P3 over dicarboxylic acids (da) is compared to the related hexaaza macrocycle Me2P3 (7,22-dimethyl-3,7,11,18,22,26-hexaazatricyclo[26.2.2.2]tetratriaconta-1(30),13,15,28,31,33-hexaene) that binds da with a lesser strength, and it is not selective. Theoretical calculations performed at molecular dynamics level have also been carried out and point out that the origin of selectivity is mainly due to the capacity of the P3 ligand receptor to adapt to the geometry of the dicarboxylic acid to form relatively strong hydrogen bonds.

Solution-State Molecular Structure of Apo and Oleate-Liganded Liver Fatty Acid-Binding Protein

Rat liver fatty acid-binding protein (LFABP) is distinctive among intracellular lipid-binding proteins (iLBPs): more than one molecule of long-chain fatty acid and a variety of diverse ligands can be bound within its large cavity, and in vitro lipid transfer to model membranes follows a mechanism that is diffusion-controlled rather than mediated by protein-membrane collisions. Because the apoprotein has proven resistant to crystallization, nuclear magnetic resonance spectroscopy offers a unique route to functionally informative comparisons of molecular structure and dynamics for LFABP in free (apo) and liganded (holo) forms. We report herein the solution-state structures determined for apo-LFABP at pH 6.0 and for holoprotein liganded to two oleates at pH 7.0, as well as the structure of the complex including locations of the ligands. 1H, 13C, and 15N resonance assignments revealed very similar types and locations of secondary structural elements for apo- and holo-LFABP as judged from chemical shift indices. The solution-state tertiary structures of the proteins were derived with the CNS/ARIA computational protocol, using distance and angular restraints based on 1H-1H nuclear Overhauser effects (NOEs), hydrogen-bonding networks, 3J(HNHA) coupling constants, intermolecular NOEs, and residual dipolar (NH) couplings. The holo-LFABP solution-state conformation is in substantial agreement with a previously reported X-ray structure [Thompson, J., Winter, N., Terwey, D., Bratt, J., and Banaszak, L. (1997) The crystal structure of the liver fatty acid-binding protein. A complex with two bound oleates, J. Biol. Chem. 272, 7140-7150], including the typical beta-barrel capped by a helix-turn-helix portal. In the solution state, the internally bound oleate has the expected U-shaped conformation and is tethered electrostatically, but the extended portal ligand can adopt a range of conformations based on the computationally refined structures, in contrast to the single conformation observed in the crystal structure. The apo-LFABP also has a well-defined beta-barrel structural motif typical of other members of the iLBP protein family, but the portal region that is thought to facilitate ligand entry and exit exhibits conformational variability and an unusual "open cap" orientation with respect to the barrel. These structural results allow us to propose a model in which ligand binding to LFABP occurs through conformational fluctuations that adjust the helix-turn-helix motif to open or close the top of the beta-barrel, and solvent accessibility to the protein cavity favors diffusion-controlled ligand transport.

Oil-Induced Aggregation of Block Copolymer in Aqueous Solution

The oil-induced aggregation behavior of PEO-PPO-PEO Pluronic P84 [(EO)19(PO)39(EO)19] in aqueous solutions has been systematically investigated by 1H NMR spectroscopy, freeze-fracture transmission electron microscopy (FF-TEM), and dynamic light scattering (DLS). The critical micellization temperature (CMT) for P84 in the presence of oils decreases with increasing oil concentration. The effectiveness of various oils in decreasing the CMT of block copolymer follows the order m-xylene (C(8)H(10)) > toluene (C(7)H(8)) > benzene (C(6)H(6)) > n-octane (C(8)H(18)) > n-hexane (C(6)H(14)) approximately cyclohexane (C(6)H(12)). It was found that the amount of anhydrous PO methyl groups increases whereas the amount of hydrated PO methyl groups decreases upon the addition of oils. At low oil concentration, the oil molecules are entrapped by the micellar core, but as the oil concentration increases above a certain value, the micellar core swells significantly as a result of the penetrated oil molecules, and much larger aggregates are formed. Intermolecular rotating-frame nuclear Overhauser effect (ROE) measurements between P84 and benzene were performed at 10 and 40 degrees C. The specific interaction between benzene and the methyl groups of PPO was determined, and it was observed that the interaction site remained unchanged as the temperature was increased.

Metal-ion binding and metal-ion induced folding of the adenine-sensing riboswitch aptamer domain

Divalent cations are important in the folding and stabilization of complex RNA structures. The adenine-sensing riboswitch controls the expression of mRNAs for proteins involved in purine metabolism by directly sensing intracellular adenine levels. Adenine binds with high affinity and specificity to the ligand binding or aptamer domain of the adenine-sensing riboswitch. The X-ray structure of this domain in complex with adenine revealed an intricate RNA-fold consisting of a three-helix junction stabilized by long-range base-pairing interactions and identified five binding sites for hexahydrated Mg2+-ions. Furthermore, a role for Mg2+-ions in the ligand-induced folding of this RNA was suggested. Here, we describe the interaction of divalent cations with the RNA–adenine complex in solution as studied by high-resolution NMR spectroscopy. Paramagnetic line broadening, chemical shift mapping and intermolecular nuclear Overhauser effects (NOEs) indicate the presence of at least three binding sites for divalent cations. Two of them are similar to those in the X-ray structure. The third site, which is important for the folding of this RNA, has not been observed previously. The ligand-free state of the RNA is conformationally heterogeneous and contains base-pairing patterns detrimental to ligand binding in the absence of Mg2+, but becomes partially pre-organized for ligand binding in the presence of Mg2+. Compared to the highly similar guanine-sensing riboswitch, the folding pathway for the adenine-sensing riboswitch aptamer domain is more complex and the influence of Mg2+ is more pronounced.

Conformational and thermodynamic changes of the repressor/DNA operator complex upon monomerization shed new light on regulation mechanisms of bacterial resistance against β-lactam antibiotics

In absence of β-lactam antibiotics, BlaI and MecI homodimeric repressors negatively control the expression of genes involved in β-lactam resistance in Bacillus licheniformis and in Staphylococcus aureus. Subsequently to β-lactam presence, BlaI/MecI is inactivated by a single-point proteolysis that separates its N-terminal DNA-binding domain to its C-terminal domain responsible for its dimerization. Concomitantly to this proteolysis, the truncated repressor acquires a low affinity for its DNA target that explains the expression of the structural gene for resistance. To understand the loss of the high DNA affinity of the truncated repressor, we have determined the different dissociation constants of the system and solved the solution structure of the B. licheniformis monomeric repressor complexed to the semi-operating sequence OP1 of blaP (1/2OP1blaP) by using a de novo docking approach based on inter-molecular nuclear Overhauser effects and chemical-shift differences measured on each macromolecular partner. Although the N-terminal domain of the repressor is not subject to internal structural rearrangements upon DNA binding, the molecules adopt a tertiary conformation different from the crystallographic operator–repressor dimer complex, leading to a 30° rotation of the monomer with respect to a central axis extended across the DNA.These results open new insights for the repression and induction mechanisms of bacterial resistance to β-lactams.

Determination of the Three-Dimensional Structure of the Mrf2−DNA Complex Using Paramagnetic Spin Labeling

Understanding the mechanism of protein-DNA interactions at the molecular level is one of the main focuses in structural and molecular biological investigations. At present, NMR spectroscopy is the only approach that can provide atomic details of protein-DNA recognition in solution. However, determining the structures of protein-DNA complexes using NMR spectroscopy has been dependent on the observation of intermolecular nuclear Overhauser effects (NOE) and their assignments, which are difficult to obtain in many cases. In this study, we have shown that intermolecular distance constraints derived from a single spin-label in combination with docking calculations have defined many specific contacts of the complex between the AT-rich interaction domain (ARID) of Mrf2 and its target DNA. Mrf2 contacts DNA mainly using the two flexible loops, L1 and L2. While the L1 loop contacts the phosphate backbone, L2 and several residues in the adjacent helices interact with AT base pairs in the major groove of DNA. Despite the structural diversity in the ARID family of DNA-binding proteins, Mrf2 maintains contacts with DNA similar to those observed in the homologous Dri-DNA complex.

NMR Structural Studies of the ItchWW3 Domain Reveal that Phosphorylation at T30 Inhibits the Interaction with PPxY-Containing Ligands

In this work, we study the role of phosphorylation as a regulatory mechanism for the interaction between the E3 ubiquitin ligase ItchWW3 domain and two PPxY motifs of one of its targets, the Epstein-Barr virus latent membrane protein 2A. Whereas ligand phosphorylation only diminishes binding, domain phosphorylation at residue T30 abrogates it. We show that two ItchWW domains can be phosphorylated at this position, using CK2 and PKA kinases and/or with stimulated T lymphocyte lysates. To better understand the regulation process, we determined the NMR structures of the ItchWW3-PPxY complex and of the phosphoT30-ItchWW3 variant. The peptide binds the domain using both XP and tyrosine grooves. A hydrogen bond from T30 to the ligand is also detected. This hydrogen-bond formation is precluded in the variant, explaining the inhibition upon phosphorylation. Our results suggest that phosphorylation at position 30 in ItchWW domains can be a mechanism to inhibit target recognition in vivo.

Solving the Structure of PTB in Complex with Pyrimidine Tracts: An NMR Study of Protein–RNA Complexes of Weak Affinities†

NMR spectroscopy has proven to be a powerful tool for the structure determination of protein/RNA complexes. However, the quality of these structures depends critically on the number of unambiguous intermolecular and intra-RNA nuclear Overhauser effect (NOE) constraints that can be derived. This number is often limited due to exchange phenomena that can cause signal line broadening and the fact that unambiguous NOE assignments are challenging in systems that exchange between different conformations in the intermediate to fast exchange limit. These exchange processes can include exchange between free and bound form, as well as exchange of the ligand between different binding sites on the protein. Furthermore, for the large class of RNA metabolizing proteins that bind repetitive low-complexity RNA sequences in multiple register, exchange of the protein between these overlapping binding sites introduces additional exchange pathways. Here, we describe the strategy we used to overcome these exchange processes and to reduce significantly the line width of the RNA resonances in complexes of the RNA recognition motifs (RRMs) of the polypyrimidine tract-binding protein (PTB) in complex with pyrimidine tracts and hence allowed a highly precise structure determination. This method could be employed to derive structures of other protein/single-stranded nucleic acid complexes by NMR spectroscopy. Furthermore, we have determined the affinities of the individual RRMs of PTB for pyrimidine tracts of different length and sequence. These measurements show that PTB binds preferentially to long pyrimidine tracts that contain cytosine and hence confirm the structure of PTB in complex with RNA. Furthermore, they provide quantitative insight into the question of which pyrimidine sequences within alternatively spliced pre-mRNAs will be preferentially bound by PTB.

NMR analysis of duplex d(CGCGATCGCG)2 modified by Λ- and Δ-[Ru(bpy)2(m-GHK)]Cl2 and DNA photocleavage study

The interaction of the diastereomeric complexes Lambda-[Ru(bpy)2(m-GHK)]Cl2 and Delta-[Ru(bpy)2(m-GHK)]Cl2 (bpy is 2,2'-bipyridine, GHK is glycine-L-histidine-L-lysine) with the deoxynucleotide duplex d(5'-CGCGATCGCG)2 was studied by means of 1H NMR spectroscopy. At a Delta-isomer to DNA ratio of 1:1, significant shifts for the metal complex are observed, whereas there is negligible effect on the oligonucleotide protons and only one intermolecular nuclear Overhauser effect (NOE) is present at the 2D nuclear Overhauser enhancement spectroscopy spectrum. The 1Eta NMR spectrum at ratio 2:1 is characterized by a slight shift for the Delta-isomer's bpy aromatic protons as well as significant shifts for the decanucleotide G4 H1' and Eta2'', A5 H2, G10 H1', T6 NH and G2 NH protons. Furthermore, at ratio 2:1, 11 intermolecular NOEs are observed. The majority of the NOEs involve the sugar Eta2' and Eta2'' protons sited in the major groove of the decanucleotide. Increasing the Delta-isomer to d(CGCGATCGCG)2 ratio to 5:1 results in noteworthy spectral changes. The Delta-isomer's proton shifts are reduced, whereas significant shifts are observed for the decanucleotide protons, especially the sugar protons, as well as for the exchangeable protons. Interaction is characterized by the presence of only one intermolecular NOE. Furthermore, there is significant broadening of the imino proton signals as the ratio of the Delta-isomer to DNuAlpha increases, which is attributed to the opening of the two strands of the duplex. The Lambda-isomer, on the other hand, approaches the minor groove of the oligonucleotide and interacts only weakly, possibly by electrostatic interactions. Photocleavage studies were also conducted with the plasmid pUC19 and a 158-bp restriction fragment, showing that both diastereomers cleave DNA with similar efficiency, attacking mainly the guanines of the sequence probably by generating active oxygen species.

293 POSTER Phase I trial of the histone deacetylase inhibitor valproic acid with the topoisomerase I inhibitor, karenitecin in advanced melanoma

Ditercalinium (2,2′-{[4,4′-bipiperidine]-1,1′-diyldi-2,1-ethane-diyl}bis-{10-methoxy-7H pyrido[4,3-c]carbazolium} tetramethane sulfonate (NSC 366241)), a DNA bis-intercalating compound, is a potent anti-tumoral rigid dimer. Previous studies have shown that a reduced flexibility of the linking chain of such a dimer is essential for its biological activity. In order to understand, at the molecular level, the mechanism of action and the structure-activity relationships of this series of DNA intercalators, new dimers with additional methylene groups between the two piperidine rings have been synthesized. Addition of one methylene group in the chain preserved the activity, whereas addition of two methylene groups reduced the cytotoxicity, which finally disappeared when three methylene groups were inserted. Therefore, the study of the interaction of dimers bearing no (202), two (222) and three (232) methylene groups with the self-complementary hexanucleotide d(CGATCG)2 have been investigated by 1H and 31P nuclear magnetic resonance studies.The results reported here indicate that all dimers bis-intercalate into the minihelix. The intermolecular nuclear Overhauser effects (NOEs) between the dimers and the nucleotide lead to the conclusion that the three dimers intercalate with their rigid bis-ethyl bipiperidine chain fitting the major groove of the helix. Inter-residue nuclear Overhauser effects at the DNA level, as well as induced shifts, are discussed in relation to the conformational changes induced in DNA upon intercalation and to the different activity of the dimers.

Combined use of Overhauser spectroscopy and NMR diffusion experiments for mapping the hydration structure of nucleosides: structure and dynamics of uridine in water

Complementary results from 13C intermolecular nuclear Overhauser effects (NOE), 1H-13C heteronuclear Overhauser spectroscopy (HOSEY) and 1H-NMR diffusion measurements were used for probing the structure of the first solvation shell of uridine in water. It is demonstrated that a cyclic dihydrate is formed. The two water molecules produce two hydrogen bonds with the two oxygen atoms from the pyrimidine ring and accept only one hydrogen bond from the amide proton. The dihydrate has only a short lifetime as compared with the rotational correlation time of the free nucleoside. The chemical exchange constant of the amide proton with water is then estimated by diffusion experiments. The results are consistent with previous data obtained for uracil in water and provide interesting information about water accessibility in nucleic acid bases.