NMR and UV studies of 3'-S-phosphorothiolate modified DNA in a DNA : RNA hybrid dodecamer duplex; implications for antisense drug design

High-resolution NMR spectroscopy has been used to establish the conformational consequences of the introduction of a single 3[prime or minute]-S-phosphorothiolate link in the DNA strand of a DNA : RNA hybrid. These systems are of interest as potential antisense therapeutic agents. Previous studies on similarly modified dinucleotides have shown that the conformation of the sugar to which the sulfur is attached shifts to the north (C(3[prime or minute])-endo/C(2[prime or minute])-exo). Comparisons made between NOESY cross-peak intensities, and coupling constants from PE-COSY spectra, for both non-modified and modified duplexes confirm that this conformational shift is also present in the double helical oligonucleotide system. In addition it is noted that in both the dinucleotides and the modified duplex, the conformation of the sugar ring 3[prime or minute] to the site of modification is also shifted to the north. That this pattern is observed in the small monomeric system as well as the larger double helix is suggestive of some pre-ordering of the sequences. The conclusion is supported by consideration of the (1)H chemical shifts of the heterocyclic bases near the site of the modification. The enhanced stability that these conformational changes should bring was confirmed by UV thermal melting studies. Subsequently a series of singly and doubly 3[prime or minute]-S-phosphorothiolate-modified duplexes were investigated by UV. The results are indicative of an additive effect of the modification with thermodynamic benefit being derived from alternate spacing of two modified linkers.     

{5′‐O‐[Bis(4‐methoxyphenyl)(phenyl)methyl]‐2′‐deoxy‐β‐D‐threopentofuranosyl}thymine ethyl acetate 0.25‐solvate

The title compound, C₃₁H₃₂N₂O₇·0.25C₄H₈O₂, is a key intermediate in the synthesis of [¹⁸F]fluorine‐labelled thymidine (¹⁸F‐FLT), which is the most widely used molecular imaging probe for positron emission tomography (PET). The crystallographic asymmetric unit contains two independent thymine molecules plus one partially occupied site for an ethyl acetate molecule. The two independent thymine molecules show similar geometrical features, except that the dimethoxytrityl groups adopt different orientations with respect to the remainder of the molecule. Each thymine base adopts an anti conformation with respect to the attached deoxyribose ring, and the deoxyribose rings show C3‐endo puckering. The conformation of the side chain at the C1 position of the deoxyribose ring is gauche+. Intermolecular N—H...O and O—H...O hydrogen bonds link the molecules into one‐dimensional chains.     

Regioselective Formation of Enediynes via Intramolecular Trapping of Allylic Cations

Enediynes are a novel class of naturally occurring antitumor antibiotics capable of causing DNA strand cleavage by hydrogen atom abstraction from the deoxyribose backbone. During the past decade, numerous synthetic methods have been developed to synthesize the naturally occurring and the "designed" enediynes for biomedical studies. Recently, we have succeeded in assembling the cis-enediynes 2 by a novel and high-yielding allylic rearrangement under mild reaction conditions (Eq 1).^1-3 This methodology has been used to synthesize a 10-membered ring enediyne³ which exhibits DNA cleavage activity.     

NMR, mass spectrometry and chemical evidence reveal a different chemical structure for methanobactin that contains oxazolone rings

Methanobactin (mb) is a small copper-binding peptide produced by methanotrophic bacteria and is intimately involved in both their copper metabolism and their role in the global carbon cycle. The structure for methanobactin comprises seven amino acids plus two chromophoric residues that appear unique to methanobactin. In a previously published structure, both chromophoric residues contain a thiocarbonyl attached to a hydroxyimidazolate ring. In addition, one is attached to a pyrrolidine ring, while the other is attached to an isopropyl ester. A published X-ray determined structure for methanobactin shows these two chromophoric groups forming an N2S2 binding site for a single Cu(I) ion with a distorted tetrahedral geometry. In this report we show that NMR, mass spectrometry, and chemical data reveal a chemical structure that is significantly different than the previously published one. Specifically, the 1H and 13C NMR assignments are inconsistent with an N-terminal isopropyl ester and point instead to a 3-methylbutanoyl group. Our data also indicate that oxazolone rings instead of hydroxyimidazolate rings form the core of the two chromophoric residues. Because these rings are directly involved in the binding of Cu(I) and other metals by methanobactin and are likely involved in the many chemical activities displayed by methanobactin, their correct identity is central to developing an accurate and detailed understanding of methanobactin's many chemical and biological roles. For example, the oxazolone rings make methanobactin structurally more similar to other bacterially produced bactins and siderophores and suggest pathways for its biosynthesis.     

Liquid crystalline analogues of curcumin

Compounds that are modifications of curcumin were synthesised and their mesogenic properties were studied. The central keto-enolic ring in curcumin was replaced by either a pyrazole or an isoxazole ring. This gives compounds that can form liquid crystalline phases. When two alkoxy chains are attached to the molecule, nematic and lamellar phases appear; in the case of six alkoxy chains, a hexagonal columnar phase is created. The columnar phase is constructed from columns that in the cross-section have two molecules. The pyrazole derivatives in the columnar phase preserve N–H–N hydrogen bonding.     

Simple ethers as models of sugar molecules in calculations of vertical excitation energies of DNA and RNA nucleosides

The ribose and deoxyribose molecules of RNA and DNA nucleosides are substituted with simple model compounds 1-methoxy-2-ethanol and 1-methoxypropane to mimic the effect of binding to sugars on the vertical excitation energies of purine and pyrimidine bases. The (R)-1-methoxy-2-ethanol, CH(3)OC*HCH(2)OH, for model ribose nucleosides and (R)-1-methoxypropane, CH(3)OC*HC(2)H(5), for model deoxyribose nucleosides have minimal structural characteristics of ribose and deoxyribose molecules when attached to nucleic acid purine and pyrimidine bases. The bases are attached to the C1 carbon atom designated by the asterisk. The vertical excitation energies of these model nucleosides are calculated with the time-dependent density functional theory method at the B3LYP level with 6-311++G(d,p) and aug-cc-pVDZ basis sets. The attachment of the ether molecules qualitatively and quantitatively modifies the excited state energy levels of the model nucleosides when compared to the free bases. These changes can affect the deexcitation mechanisms for photoexcited nucleosides.     

Gas-solid reactions of single crystals: a study of reactions of NH3 and NO2 with single crystalline organic substrates by infrared microspectroscopy

Reaction of single crystals of benzoic and trans-cinnamic acids with 200 Torr pressure of ammonia gas in a sealed glass bulb at 20 degrees C generates the corresponding ammonium salts; there is no sign of any 1:2 adduct as has been reported previously for related systems. Isotopic substitution using ND3 has been used to aid identification of the products. Adipic acid likewise reacts with NH3 gas to form a product in which ammonium salts are formed at both carboxylic acid groups. Reaction of 0.5 Torr pressure of NO2 gas with single crystals of 9-methylanthracene and 9-anthracenemethanol in a flow system generates nitrated products where the nitro group appears to be attached at the 10-position, i.e. the position trans to the methyl or methoxy substituent on the central ring. Isotopic substitution using 15NO2 has been used to confirm the identity of the bands arising from the coordinated NO2 group. The products formed when single crystals of hydantoin are reacted with NO2 gas under similar conditions depend on the temperature of the reaction. At 20 degrees C, a nitrated product is formed, but at 65 degrees C this gives way to a product containing no nitro groups. The findings show the general applicability of infrared microspectroscopy to a study of gas-solid reactions of organic single crystals.     

Duplex stability of DNA.DNA and DNA.RNA duplexes containing 3'-S-phosphorothiolate linkages

3'-S-Phosphorothiolate (3'-SP) linkages have been incorporated into the DNA strand of both a DNA.RNA duplex and a DNA.DNA duplex. Thermal melting (T(m)) studies established that this modification significantly stabilises the DNA.RNA duplex with an average increase in T(m) of about 1.4 degrees C per modification. For two or three modifications, the increase in T(m) was larger for an alternating, as compared to the contiguous, arrangement. For more than three modifications their arrangement had no effect on T(m). In contrast to the DNA.RNA duplex, the 3'-S-phosphorothiolate linkage destabilised the DNA.DNA duplex, irrespective of the arrangement of the 3'-SP linkages. The effect of ionic strength on duplex stability was similar for both the phosphorothiolate-substituted and the unmodified RNA.DNA duplexes. The results are discussed in terms of the influence that the sulfur atom has on the conformation of the furanose ring and comparisons are also drawn between the current study and those previously conducted with other modifications that have a similar conformational effect.     

Synthesis and photolytic evaluation of a nitroindoline-caged glycine with a side chain of high negative charge for use in neuroscience

A photolabile precursor of the neuroinhibitory amino acid glycine has been synthesised with two phosphate groups attached to the indoline nucleus at a 4-alkoxy substituent. In common with the photochemical properties of other 1-acyl-7-nitroindolines, this releases glycine on a sub-μs time scale upon irradiation with near-UV light. The synthetic route previously developed for the preparation of the GABA analogue required some modifications because of the greater hydrolytic sensitivity of the glycine compound. The phosphorylation method used here could be beneficial to the synthesis of other nitroindoline-caged amino acids, especially the related caged GABA derivative. Glycine released by laser photolysis on spinal cord neurons generated fast-rising responses and the pharmacological properties of the reagent are such that it is useful for physiological experiments.     

Synthesis and Mesophase Behavior of Phenylthiophene Based Amphiphilic Molecules

Novel amphiphilic molecules consisting of a rigid 2‐phenylthiophene core, with a polar flexible tri(oxylethylene) moiety attached to the phenyl ring and one or two alkyl chains attached to the thiophene ring at the other side have been synthesized by using Ni(II) and Pd(0) catalyzed coupling reaction as key steps. The tri(oxylethylene) moieties were terminated with hydroxyl group, sodium carboxylate group and lithium carboxylate group respectively. The thermotropic and solvent induced liquid crystalline behavior of these substances was investigated by polarized optical microscopy, differential scanning calorimetry and X‐ray diffraction. Thereby the influence of the terminal groups attached to the tri(oxylethylene) moities as well as the influence of the length and the number of the alkyl chains on the mesophase behavior were investigated. The single alkyl chain Na‐carboxylate termianted derivatives show smectic A phases, double alkyl chain Na‐carboxylate terminated derivatives show a thermo tropic hexagonal columnar mesophase, while columnar mesophases are found in both single and double alkyl chain Li‐carbonate terminated derivatives. The model for molecular organization in the hexagonal columnar mesophase is established.     

Selective site deuteration on the sugar ring as an efficient marker of conformation in nucleosides: The CD stretching mode of the (2′-R)-[2′-2H]-2′-deoxyuridine and its 3′,5′-O-(1,1,3,3-tetraisopropyldisiloxan-1,3-diyl)-derivative

A uridine specifically deuterated on the deoxyribose ring at the C2′, and the same compound in a more rigid form, due to a chemically fused ring (between C3′ and C5′), have been synthesized. By NMR, the coupling constants J_1′-2′ and J_3′-4′ have been determined and the populations of the C2′-endo and C3′-endo conformers have been deduced for the two compounds. Comparison of these results with an FTIR and Raman study of the stretching mode νCD on the C2′ site allows a specific assignment of each observed band to one of the two classes of conformers. This enables us to consider the further step: the direct recognition, by IR and Raman spectroscopies, of the local conformation at a specific site of a synthetic oligonucleotide, using the νCD signals as marker bands.     

Low-frequency near-infrared Fourier transform Raman studies of ellipticines and deoxyribose nucleic acid

Nucleotides and nucleosides have been studied in the low-frequency region through a comparison of the performance between near-infrared Fourier transform Raman techniques and Ar⁺-excitation Raman spectroscopy. This allowed us to evaluate the influence of the filter cut-off on the low-frequency bands of the Fourier transform Raman spectra. This assessment was then applied to a study of the low-frequency bands of two samples of deoxyribose nucleic acid and five ellipticines, whose interaction with deoxyribose nucleic acid could be of importance in their use as anti-cancer drugs. In order to assign the low-frequency bands of ellipticines and understand the dynamical ring deformations, a force constant calculation was performed.     

An investigation into the mechanisms of DNA strand breakage by direct ionization of variably hydrated plasmid DNA

The mechanisms by which ionizing radiation directly causes strand breaks in DNA were investigated by comparing the chemical yield of DNA-trapped free radicals to the chemical yield of DNA single strand break (ssb) and double strand break (dsb), as a function of hydration (Gamma). Solid-state films of plasmid pUC18, hydrated to 2.5 < Gamma < 22.5 mol, were X-irradiated at 4 K, warmed to room temperature, and dissolved in water. Free radical yields were determined by EPR at 4 K. With use of the same samples, Gel electrophoresis was used to measure the chemical yield of total strand breaks, which includes prompt plus heat labile ssb; G'total(ssb) decreased from 0.092 +/- 0.016 micromol/J at Gamma= 2.5 to 0.066 +/- 0.008 micromol/J at Gamma= 22.5. Most provocative is that at Gamma= 2.5 the yield of total ssb exceeds the yield of trapped deoxyribose radicals: G'total(ssb) - G'sugar(fr) = 0.06 +/- 0.02 micromol/J. Nearly 2/3 of the strand breaks are derived from precursors other than radicals trapped on the deoxyribose moiety. To account for these nonradical precursors, we hypothesize that strand breaks are produced by two one-electron oxidations at a single deoxyribose residue within an ionization cluster.     

Synthesis of fused indoles by sequential palladium-catalyzed Heck reaction and N-heteroannulation

A route to 3,4-fused indoles via two consecutive palladium-catalyzed reactions; an intramolecular Heck reaction followed by a reductive N-heteroannulation is described. Using this route, a number of indoles have been prepared having a variety of ring sizes anchored to the 3- and 4-position of the indole nucleus. Furthermore, a number of functional groups, both carbon and heteroatom substituents can be introduced in (and on) the additional ring without any detrimental effects on the two reactions.     

Synthesis and mesophase behaviour of rigid rod‐like phenylthiophene‐based amphiphilic diol derivatives

Novel amphiphilic block molecules consisting of a rigid 2‐phenylthiophene or 5‐phenylbithienyl core, with a polar glycerol group attached to the phenyl ring and one or two alkyl chains attached to the thiophene ring on the other side, have been synthesised by using Ni(0) and Pd(0) catalyzed coupling reactions as key steps. The thermotropic and solvent‐induced liquid crystalline behaviour of these compounds was investigated by polarising optical microscopy and X‐ray diffraction. The influence of the length, number and position of the alkyl chains, and the length of the rigid core, on their mesophase behaviour was investigated. Compounds with one alkyl chain in the terminal 5‐position on the thiophene ring form only smectic A phases, compounds with two adjacent alkyl chains attached in the 4‐ and 5‐positions of the thiophene ring exhibit thermotropic columnar mesophases, and those with two long alkyl chains attached to the 3‐ and 5‐positions form columnar LC phases only in the presence of water. Another compound containing the longer 5‐phenylbithienyl core unit and two alkyl chains attached in lateral positions to each of the thiophene rings is not mesogenic.     

Low-energy electron scattering by deoxyribose and related molecules

We apply first-principles computational methods to study elastic scattering of low-energy electrons by 2-deoxyribose and 2-deoxyribose monophosphate, which are of interest as components of the DNA backbone, and to tetrahydrofuran (THF), which has been studied as a deoxyribose analog. To investigate the dependence of the scattering process on the molecular conformation, we examine Cs and C2 conformers of THF as well as the planar C(2v) geometry imposed in earlier calculations. There is little difference between the elastic cross sections determined at the nonplanar geometries, but there are noticeable differences between those results and the cross sections computed using the planar ring. By comparing results for tetrahydrofuran obtained with and without inclusion of polarization effects, we obtain energy shifts that are applied to the computed resonance positions for deoxyribose and deoxyribose monophosphate.     

A2E‐Mediated Photochemical Modification to Fibronectin and its Implications to Age‐Related Changes in Bruch's Membrane

Lipofuscin accumulates normally with age and is more pronounced in retinal dystrophies such as age‐related macular degeneration. The major bis‐retinoid component of lipofuscin is A2E. In addition to cell damage effects by A2E, we have previously demonstrated that blue‐light–mediated A2E leads to modifications in the basement membrane protein laminin. Therefore, the purpose of this study was to advance the understanding of A2E photooxidation effects on fibronectin, the major glycoprotein of Bruch's membrane. In this study, A2E was irradiated with blue light in the presence of a fibronectin peptide consisting of amino acids from the integrin binding region. The modification sites were identified via LC/MS. Our research indicated that blue light irradiation caused cleavage throughout the A2E molecule closest to the pyridinium ring, and attached to the fibronectin peptide preferentially at lysine and arginine residues. All of these reactions are similar to the Maillard reaction. Altogether this study suggests that blue‐light–irradiated A2E modifies peptides and forms advance glycation endproducts. Furthermore, these results can be used to identify modifications that occur in Bruch's membrane in vivo.     

Investigation of the regio- and stereo-selectivity of deoxyguanosine linkage to deuterated 2-hydroxyestradiol by using liquid chromatography/ESI-ion trap mass spectrometry

From previous studies on the reactivity of estradiol 2,3-quinone towards deoxyribonucleosides, it was demonstrated that several isomeric adducts were formed. Although adduction on steroid ring A or B has been evidenced using sequential MS(n) experiments, in some cases attachment positions are difficult to identify unambiguously. In this work, 2-hydroxyestradiol labeled with deuterium at various positions [6beta (1); 6alpha-7alpha (2); 6alpha-6beta-7alpha (3)] have been used. Isomeric adduct differentiation could be achieved using LC-ESI-MS(n). The m/z shift of the quasi-molecular ions as well as the fragmentation pathways suggested that adduction could occur on both C6 and C9 sites of the steroid B ring: Nucleophilic attack of the base on the C6 position of the steroid led to major adducts and addition of the base on the activated C9 site gave minor adducts that were found to be unstable. LC-MS(n) experiments carried out under deuterated medium provided information about some fragmentation processes by studying the m/z shift of fragment ions: (1) the loss of deoxyribose from the quasi-molecular ions took place according to a process involving a deuterium transfer from the deoxyribose alcohol function; (2) the cleavage of the steroid-base linkage involved a deuterium transfer from the hydroxy group of the catechol and likely occurred via the formation of an ion-dipole complex. The model studies conducted in this work provide new information on the fragmentation mechanisms of covalent adducts formed from estrogen quinones and deoxyguanosine, the most reactive DNA base. Besides, the first unequivocal characterization of adducts involving the steroid C9 position is shown by using deuterium labeled estrogen quinones.     

Chemical shifts for the unusual DNA structure in Pf1 bacteriophage from dynamic-nuclear-polarization-enhanced solid-state NMR spectroscopy

Solid-state NMR spectra, including dynamic nuclear polarization enhanced 400 MHz spectra acquired at 100 K, as well as non-DNP spectra at a variety of field strengths and at temperatures in the range 213-243 K, have allowed the assignment of the (13)C and (15)N resonances of the unusual DNA structure in the Pf1 virion. The (13)C chemical shifts of C3' and C5', considered to be key reporters of deoxyribose conformation, fall near or beyond the edges of their respective ranges in available databases. The (13)C and (15)N chemical shifts of the DNA bases have above-average values for AC4, AC5, CC5, TC2, and TC5, and below average values for AC8, GC8, and GN2, pointing to an absence of Watson-Crick hydrogen bonding, yet the presence of some type of aromatic ring interaction. Crosspeaks between Tyr40 of the coat protein and several DNA atoms suggest that Tyr40 is involved in this ring interaction. In addition, these crosspeak resonances and several deoxyribose resonances are multiply split, presumably through the effects of ordered but differing interactions between capsid protein subunits and each type of nucleotide in each of the two DNA strands. Overall, these observations characterize and support the DNA model proposed by Liu and Day and refined by Tsuboi et al., which calls for the most highly stretched and twisted naturally occurring DNA yet encountered.     

Die Strukturen der mittleren Ringverbindungen. X. 1, 6-trans-Diaminocyclodecan-dihydrochlorid,monokline Modifikation

The structure of the monoclinic modification of 1,6-trans-diaminocyclodecanedihydrochloride has been determined, and refined by full-matrix least-squares analysis of three-dimensional X-ray data. The cyclodecane skeleton is very similar to that found previously in the triclinic modification, but the substituents are attached to different types of carbon atoms. The two crystal modifications thus correspond to different conformational isomers.