Helix-coil transition of the dG-dC-dG-dC self-complementary duplex and complex formation with daunomycin in solution.

The duplex-to-strand transition of the self-complementary sequence dG-dC-dG-dC has been probed at the exchangeable and nonexchangeable protons and backbone phosphates by high-resolution nmr spectroscopy. The Watson-Crick imino and amino hydrogen-bonded protons, as well as the exposed amino protons, could be followed through the duplex-to-strand transition and provide information on base-pair stability at the tetranucleotide duplex level. The magnitudes of the experimental upfield nonexchangeable base-proton chemical shifts on duplex formation are consistent with calculations based on base-pair overlap geometries of the B-DNA type. The variation of the ³¹P chemical shifts in dG-dC-dG-dC with temperature appear to monitor changes in the ω,ω′ rotation angles about the O? P bonds in the postmelting transition temperature region. The complex formed between the antitumor anthracycline antibiotic daunomycin and the dG-dC-dG-dC duplex was probed at the nucleic acid and the antibiotic resonances as a function of temperature. The experimental complexation shifts of the observable daunomycin resonances have put constraints on possible overlap geometries between the intercalating anthracycline ring and adjacent base pairs.     

Proton NMR studies of manganese ion binding to tRNA-derived acceptor arm duplexes.

Several RNA duplexes corresponding to the acceptor arms of different tRNAs have been analyzed with respect to their divalent metal ion binding capability by means of proton NMR spectroscopy using paramagnetic Mn2+ ions as probes. In particular, the role of GU wobble base pairs has been analyzed with reference to their potential for creating metal ion binding sites. It is shown that both the structural modifications induced by GU pairs in the A-RNA geometry and the sequence context seem to affect the metal ion binding capabilities.     

Insertion of d(pCpG)n.d(pCpG)n into the lacZ gene of Escherichia coli inhibits expression of beta-galactosidase in vivo

Plasmids that contain a d(pCpG)13.d(pCpG)13 insert instead of a lac operator show a 34-fold decrease of beta-galactosidase synthesis. The same sequence causes a 24-fold decrease when inserted between codons 5 and 6 of the lacZ gene. In such constructs with d(pCpG)n.d(pCpG)n inserts, beta-galactosidase activity decreases approximately 1.6-fold per d(pCpG).d(pCpG) unit when n ranges from 5 to 16.     

NMR studies of L-dopa melanin-manganese(II) complex in water solution

The study of water relaxation rates of solutions of melanins with paramagnetic metal ions provides a powerful tool for investigating the binding sites and for obtaining useful structural and dynamic information. The measure of 1H- and 2H-longitudinal and transverse relaxation rates at a single, high-magnetic field for H2O/D2O (80:20) solutions allows the determination of tau c, tau R, tau e, tau M, r, q, and Z (the outer sphere contribution to the overall relaxation rate) for Mn(II)-L-Dopa melanin system.     

Helix-coil transition in copolypeptides. I. Poly (gamma-benzyl-co-gamma-methyl L-glutamate)

The helix–coil transition in poly(γ-benzyl L -glutamate-co-γ-methyl L -glutamate) copolypeptides was studied experimentally in nonaqueous solvents and the results compared with theory. It is found that the transition can be described by the same theory as for the homopolypeptides, but the corresponding parameters are not related in the expected way to those of the homopolymers, due to the effect of the side chains on the stability of the helix, which is not taken into account explicitly by the theory.     

Helix-coil transition of Poly(L-glutamic acid) in N-methylacetamide

The folding of randomly coiled poly(L -glutamic acid) to the helical state has been studied in N-methylacetamide by titration methods. Since this solvent would be expected to form amide-peptide group hydrogen bonds with the unfolded form of the polymer, to a first approximation no helix stabilization could come from intrapolymer hydrogen bonds. The titration data, collected from 30 to 70°C yield the following values per residue for the thermodynamic parameters governing the coil-helix reaction for the uncharged polymer: ΔG_30°C°, ?1. 9 ± 0.1 kcal; Δ H°, 0 ± 0.1 kcal; ΔS_30°C°, 6.3 ± 0.6 eu. In N-methyl acetamide, the helix is an order of magnitude more stable than in water, and this stabilization appears to be entirely the result of the entropy gained by solvent molecules which are released from the polymer upon folding.     

Proton NMR studies of angiotensin II and its analogs in aqueous solution

The¹H nuclear magnetic resonance (NMR) spectra of angiotensin II (Asp-Arg-Val-Tyr-Ile-His-Pro-Phe) and five of its octapeptide analogs as well as angiotensin I (Asp-Arg-Val-Tyr-Ile-His-Pro-Phe-His-Leu) and angiotensin III (Arg-Val-Tyr-Ile-His-Pro-Phe) in aqueous solutions (90% H₂O/10% D₂O) were completely assigned by two-dimensional COSY and ROESY experiments. All of the peptides give rise to two distinct sets of signals. The minor set accounts for about 5% of the total population belowpH 5.5 and increases to 12–20% aroundpH 7.0. The two sets of signals result from acis-trans isomerization of the His-Pro peptide bond with the major resonances arising from thetrans isomer. One analog in which the Pro is replaced with a D-Pro displays a very different isomerization behavior. The measured coupling constants J_NH-CH, the temperature dependence of the amide proton shifts and the relative intensities of the intraresidue and sequential NH-CH ROEs, are all indicative of an extended backbone conformation for ANGII. However, some evidence for the existence of conformers with local structure involving preferred sidechain positions for the Tyr, His, Phe, and the carboxyl group of the Phe was found, particularly in the ROESY andpH-titration experiments. Moreover,pH effects and the unusual amide exchange behavior of the Arg NH suggests the presence of interactions between the Asp and Arg sidechains of ANGII. At low temperatures the Arg guanidinium NH₂ protons were detected as two broad peaks which are related by sizeable exchange peaks in ROESY experiments. This behavior could be useful as a general probe for the study of Arg sidechain mobility and accessibility in other peptides and proteinsPreliminary results of this work have been presented at the XIIth International Conference on Magnetic Resonance in Biological Systems in abstract form (1988).     

Helix-coil transition of poly(gamma-benzyl-l-glutamate) in the dioxane-dichloracetic acid mixture.

The thermal helix–coil transition of four samples of poly(γ-benzyl-L -glutamate) in the dioxane–dichloroacetic acid (DCA) mixture was studied by optical rotatory dispersion method. The transition occurred at very high DCA content (97.5% by weight) in this system. The transition parameters have been evaluated by two methods based on the theories of Zimm and Bragg and of Nagai. The values of the helix initiation parameter and of the enthalpy of transition were found to be (4.4 ± 0.4) × 10^?5 and 340 cal/mole, respectively. The range of validity and equivalence of the two methods is discussed.     

Conformation and reactivity of DNA in the complex with proteins. III. Helix-coil transition and conformational studies of model complexes of DNA''s with poly-L-histidine.

Differences in the interaction of poly-L-histidine with DNA of various base composition have been demonstrated using melting and CD measurements. The two types of complexes formed with DNA at pH values below the pK of 5.9 and in the region of pH 6.5 are very different in their CD spectral properties. The binding effects with highly protonated poly-L-histidine are AT-dependent as reflected by large negative CD spectra indicating the formation of psi-DNA as a condensed state of the double helix. GC-rich DNA may, however, also form psi-DNA structures with poly-L-histidine under certain conditions. At pH 6.5 complex formation with the weakly protonated polypeptide is GC-dependent. From the results it is concluded that protonated poly-L-histidine interacts more specifically at AT base pairs, prabably along the small groove while the weakly protonated poly-L-histidine tends to interact preferentially with GC regions which seems to occur rather in the large groove.     

NMR structural studies of intramolecular (Y+)n.(R+)n(Y-)nDNA triplexes in solution: imino and amino proton and nitrogen markers of G.TA base triple formation.

We reported previously on NMR studies of (Y+)n.(R+)n(Y-)n DNA triple helices containing one oligopurine strand (R)n and two oligopyrimidine strands (Y)n stabilized by T.AT and C+.GC base triples [de los Santos, C., Rosen, M., & Patel, D. J. (1989) Biochemistry 28, 7282-7289]. Recently, it has been established that guanosine can recognize a thymidine.adenosine base pair to form a G.TA triple in an otherwise (Y+)n.(R+)n(Y-)n triple-helix motif. [Griffin, L. C., & Dervan, P. B. (1989) Science 245, 967-971]. The present study extends the NMR research to the characterization of structural features of a 31-mer deoxyoligonucleotide that folds intramolecularly into a 7-mer (Y+)n.(R+)n(Y-)n triplex with the strands linked through two T5 loops and that contains a central G.TA triple flanked by T.AT triples. The G.TA triplex exhibits an unusually well resolved and narrow imino and amino exchangeable proton and nonexchangeable proton spectrum in H2O solution, pH 4.85, at 5 degrees C. We have assigned the imino protons of thymidine and amino protons of adenosine involved in Watson-Crick and Hoogsteen pairing in T.AT triples, as well as the guanosine imino and cytidine amino protons involved in Watson-Crick pairing and the protonated cytidine imino and amino protons involved in Hoogsteen pairing in C+.GC triples in the NOESY spectrum of the G.TA triplex. The NMR data are consistent with the proposed pairing alignment for the G.TA triple where the guanosine in an anti orientation pairs through a single hydrogen bond from one of its 2-amino protons to the 4-carbonyl group of thymidine in the Watson-Crick TA pair.(ABSTRACT TRUNCATED AT 250 WORDS)     

Nmr studies on complex formation of poly(L-lysine HBr) with carbonate ion in aqueous solution

Diemer formation of poly(L -lysine HBr) in carbonate buffer at pD 10.5 was reported in our previous paper [Biopolymers(1981) 20 , 345–357]. The mechanism of the dimer formation was investigated employing carbon-13 and proton nmr. pD dependence of the ¹³C-nmr spectrum of poly(L -lysine HBr) in the presence of carbonate ion clearly shows that a complex formation between the CO ion and protonated ε-amino group is involved in the stabilization of the dimer form. The lifetime of the complex is longer than 10^?2 s. A stoichiometric evaluation suggests that CO bridges two lysyl side chains. A molecular model of the dimer form designated as a single antiparallel β-ribbon was proposed and discussed in the light of hydrodynamic and ir spectroscopic properties reported earlier. Concentration change experiments indicate that CO binds not only to the dimer formation is inferred as stabilization of the single antiparallel β-ribbon as an intermediate structure in the conversion between the α-helix and β-sheet. The α-CH proton signal of the lysine residue located in the ordered structure (α-helix and β-form) was observed to be separate from that in the random-coil region.     

NMR studies of DNA (R+)n.(Y-)n.(Y+)n triple helices in solution: imino and amino proton markers of T.A.T and C.G.C+ base-triple formation

High-resolution exchangeable proton two-dimensional NMR spectra have been recorded on 11-mer DNA triple helices containing one oligopurine (R)n and two oligopyrimidine (Y)n strands at acidic pH and elevated temperatures. Our two-dimensional nuclear Overhauser effect studies have focused on an 11-mer triplex where the third oligopyrimidine strand is parallel to the oligopurine strand. The observed distance connectivities establish that the third oligopyrimidine strand resides in the major groove with the triplex stabilized through formation of T.A.T and C.G.C+ base triples. The T.A.T base triple can be monitored by imino protons of the thymidines involved in Watson-Crick (13.65-14.25 ppm) and Hoogsteen (12.9-13.55 ppm) pairing, as well as the amino protons of adenosine (7.4-7.7 ppm). The amino protons of the protonated (8.5-10.0 ppm) and unprotonated (6.5-8.3 ppm) cytidines in the C.G.C+ base triple provide distinct markers as do the imino protons of the guanosine (12.6-13.3 ppm) and the protonated cytidine (14.5-16.0 ppm). The upfield chemical shift of the adenosine H8 protons (7.1-7.3 ppm) establishes that the oligopurine strand adopts an A-helical base stacking conformation in the 11-mer triplex. These results demonstrate that oligonucleotide triple helices can be readily monitored by NMR at the individual base-triple level with distinct markers differentiating between Watson-Crick and Hoogsteen pairing. Excellent exchangeable proton spectra have also been recorded for (R+)n.(Y-)n.(Y+)n 7-mer triple helices with the shorter length permitting spectra to be recorded at ambient temperature.(ABSTRACT TRUNCATED AT 250 WORDS)     

Magnesium-dependent supercoiling-induced transition in (dG)n.(dC)n stretches and formation of a new G-structure by (dG)n strand.

Plasmids containing (dG)27.(dC)27 inserts (pPG27), (dG)37.(dC)37 inserts (pPG37), and (dG)24C(dG)21.(dC)24G(dC)21 inserts (pPG46C) were constructed for the study of structural transitions within (dG)n.(dC)n stretches. Two-dimensional gel electrophoresis has shown that a Mg2+-dependent supercoiling-induced structural transition takes place at pH 8 in plasmid pPG46C. The transition occurs at -0=0.06 and involves a supercoiling release corresponding to 5 superhelical turns. After denaturation of the restriction fragments containing (dG)n.(dC)n inserts, the strands do not renature completely and (dG)n-containing strand migrates in PAGE much faster than the (dC)n-containing one. Chemical modification experiments with the (dG)n-strand have revealed the periodic nature of the protection of guanines against dimethyl sulfate methylation. The (dG)n strand in the presence of Mg2+ forms complexes with the complementary (dC)n strand, which differ from the native duplex in mobility. We believe these effects to be due to the formation of an intrastrand structure within the (dG)n strand stabilized by G.G interactions (we called it G-structure), which in the presence of Mg2+ forms an interstrand complex. with the (dC)n strand.     

Antimony(V) complex formation with adenine nucleosides in aqueous solution

Despite the clinical use of pentavalent antimonial drugs for over half a century, their mode of action against leishmaniasis remains poorly understood. In this paper, we investigated the ability of Sb(V) to form in aqueous solution complexes with adenine nucleosides and deoxynucleosides, using circular dichroism (CD) and (1)H and (13)C NMR spectroscopies. We report that the ribonucleosides, adenosine (A) and adenosine monophosphate (AMP), form in water complexes with Sb(V), as evidenced by the changes induced in their CD spectra. On the other hand, 2'-deoxyadenosine (dA) did not show such a change. CD titration of the ribonucleosides with Sb(V) suggests the formation of 1:2 Sb(V)-nucleoside complexes. NMR analysis indicates that Sb(V) binds to the sugar moiety at the 2' position. Furthermore, the incubation of the antimonial drug, meglumine antimonate, with adenosine at 37 degrees C led to the transfer of Sb(V) from its original ligand to the nucleoside molecule, at acidic pH (pH 5), but not at neutral pH (7.2). Our data therefore suggests that the formation of such complexes may take place in vivo within the acidic cell compartments, including the phagolysosome of macrophage in which Leishmania resides.     

Mercury(II) complex formation with glutathione in alkaline aqueous solution

The structure and speciation of the complexes formed between mercury(II) ions and glutathione (GSH = L-glutamyl-L-cysteinyl-glycine) have been studied for a series of alkaline aqueous solutions (\( C_{{{\text{Hg}}^{{2 + }}}}\,{\sim18\,{\rm{mmol}}\,{\rm{{dm^{-3}}}}}\) and C _GSH = 40–200 mmol dm^?3 at pH ～10.5) by means of extended X-ray absorption fine structure (EXAFS) and ¹⁹⁹Hg NMR spectroscopy at ambient temperature. The dominant complexes are [Hg(GS)₂]^4? and [Hg(GS)₃]^7?, with mean Hg–S bond distances of 2.32(1) and 2.42(2) Å observed in digonal and trigonal Hg–S coordination, respectively. The proportions of the Hg²⁺–glutathione complexes were evaluated by fitting linear combinations of model EXAFS oscillations representing each species to the experimental EXAFS spectra. The [Hg(GS)₄]^10? complex, with four sulfur atoms coordinated at a mean Hg–S bond distance of 2.52(2) Å, is present in minor amounts (<30%) in solutions containing a large excess of glutathione (C _GSH ≥ 160 mmol dm^?3). Comparable alkaline mercury(II) cysteine (H₂Cys) solutions were also investigated and a reduced tendency to form higher complexes was observed, because the deprotonated amino group of Cys^2? allows the stable [Hg(S,N-Cys)₂]^2? chelate to form. The effect of temperature on the distribution of the Hg²⁺–glutathione complexes was studied by comparing the EXAFS spectra at ambient temperature and at 25 K of a series of glycerol/water (33/67, v/v) frozen glasses with \( C_{{{\text{Hg}}^{{2 + }} }} \,{\sim7\,{\rm{mmol}}\,{\rm{{dm^{-3}}}}} \) and C _GSH = 16–81 mmol dm^?3. Complexes with high Hg–S coordination numbers, [Hg(GS)₃]^7? and [Hg(GS)₄]^10?, became strongly favored when just a moderate excess of glutathione (C _GSH ≥28 mmol dm^?3) was used in the glassy samples, as expected for a stepwise exothermic bond formation. Addition of glycerol had no effect on the Hg(II)–glutathione speciation, as shown by the similarity of the EXAFS spectra obtained at room temperature for two parallel series of Hg(II)-glutathione solutions with \( C_{{{\text{Hg}}^{{2 + }} }} \,{\sim7\,{\rm{mmol}}\,{\rm{{dm^{-3}}}}},\) with and without 33% glycerol. Also, the ¹⁹⁹Hg NMR chemical shifts of a series of ～18 mmol dm^?3 mercury(II) glutathione solutions with 33% glycerol were not significantly different from those of the corresponding series in aqueous solution.     

NMR studies of pH-dependent conformational polymorphism of alternating (C-T)n sequences.

Alternating (C-T)n sequences are involved in the H-DNA structure associated with (GA)n.(CT)n sequences. Low pH values facilitate H-DNA formation. We have undertaken a detailed analysis of the structural consequences of the (C-T)n sequence as a function of pH. The structures of three DNA oligonucleotides, d(CT)4, d(TC)4 and d(TC)15, have been studied by NMR. We found that their conformations are polymorphic and pH dependent. There are at least three major conformational species: an antiparallel-stranded (APS) duplex with entirely C:T base pairs at pH 7, an antiparallel-stranded (APS) duplex with entirely C+:T base pairs at pH 3, and a possible parallel-stranded (PS) duplex with C+:C and T:T base pairs near pH 5. In the intermediate pH range, the APS duplex may have varying numbers of C+:T and C:T base pairs, and there may be a fast exchange going on between APS duplex species involving these two kinds of base pairs. However, the transition between the APS and PS duplexes is slow. Structural refinement of the two octamers, d(TC)4 and d(CT)4, at pH = 6.9 and pH = 3 using 2D-NOE data suggests that the molecules are likely in the duplex form at 5 degrees C. We lack evidence that the structure at pH 3 is a PS structure with T nucleotides residing in the exterior of the helix. Titration of the longer oligonucleotide, d(TC)15, showed a prominent pKa of approximately 6, approaching the value of 7.0 obtained from the titration of poly-(dC).     

Oxovanadium(IV) complex formation by simple sugars in aqueous solution.

The binding of oxovanadium(IV) to simple sugars in neutral or basic aqueous solution, as studied by EPR and electronic absorption spectroscopy, is reported. The complexation is favored in basic media and involves the coordination of the metal ion to couples of adjacent deprotonated hydroxyls of the sugar molecule. However, only the ligands provided with cis couples can adopt this chelating ligand behavior. The ability of the cis hydroxyl couples to yield chelated complexes has been related to the structural rearrangement (decrease of the O-C-C-O torsion angle in the five-membered chelated ring) needed to permit the oxovanadium(IV) coordination by the sugar molecule.     

Tetraplex formation of d(GGGGGTTTTT): 1H NMR study in solution.

The oligonucleotide d(G5T5) can in principle form a fully matched duplex with G.T pairing and/or a tetraplex. Non-denaturing gel electrophoresis, circular dichroism and NMR experiments show that the tetraplex is exclusively formed by this oligomer in solution. In the presence of its complementary strand d(A5C5) at low temperature, d(G5T5) forms the tetraplex over the normally expected Watson-Crick duplex. However, when d(G5T5) and d(A5C5) are mixed together in equimolar amounts and heated for several minutes at 85 degrees C, and then allowed to cool, the product was essentially the Watson-Crick duplex. The lack of resolution in the 500 MHz 1H NMR spectra and the presence of extensive spin diffusion do not allow us to derive a quantitative structure for the tetraplex from the NMR data. However, we find good qualitative agreement between the NOESY and MINSY data and a theoretically derived stereochemically sound structure in which the G's and T's are part of a parallel tetraplex.     

Interaction of Pd(II) glycyl--L-histidine complex with cytidine and GMP. Proton and carbon-13 nmr studies

1H and 13C nmr studies on the Pd(II)Gly-His complex interaction with cytidine and GMP have shown that the nucleoside binds the palladium complex via N3 nitrogen and the nucleotide binds that complex via N7 nitrogen. The analysis of the Cyd or GMP aromatic ring influence on the chemical shift of the H2 proton or the C2 carbon of imidazole ring has supported the earlier suggestions that nucleoside or nucleotide base and Pd(II) complex plane are almost perpendicular to each other. The Pd(II)Gly-His: Cyd or GMP ternary systems are easily decomposed already in weak basic solutions, which may suggest that the polymerization of Pd(II)Gly-His binary species might be the competitive process in the interactions with nucleosides or nucleotides.