Recent highlights in modified oligonucleotide chemistry

The synthesis of modified nucleic acids has been the subject of much study ever since the structure of DNA was elucidated by Watson and Crick at Cambridge and Wilkins and Franklin at King's College over half a century ago. This review describes recent developments in the synthesis and application of these artificial nucleic acids, predominantly the phosphoramidites which allow for easy inclusion into oligonucleotides, and is divided into three separate sections. Firstly, modi. cations to the base portion will be discussed followed secondly by modi. cations to the sugar portion. Finally, changes in the type of nucleic acid linker will be discussed in the third section. Peptide Nucleic Acids ( PNAs) are not discussed in this review as they represent a separate and large area of nucleic acid mimics.

Buffering of recovery from acidification by organic acids

In the United Kingdom, as in other regions of Europe and North America, recent decreases in surface water sulphate concentrations, due to reduced sulphur emissions, have coincided with marked increases in dissolved organic carbon (DOC) concentrations. Since many of the compounds comprising DOC are acidic, the resulting increases in organic acidity may have the potential to offset the benefits of a decrease in mineral (sulphate) acidity. To test this, we used a triprotic model of organic acid dissociation to estimate the proportional organic acid buffering of reduced mineral acidity as measured in the 22 lakes and streams monitored by the UK Acid Waters Monitoring Network. For an average non-marine sulphate decrease of 30 μeq l− 1 over 15 years from 1988–2003, we estimate that around 28% was counterbalanced by rising strong organic acids, 20% by rising alkalinity (partly attributable to an increase in weak organic acids), 11% by falling inorganic aluminium and 41% by falling non-marine base cations. The situation is complicated by a concurrent decrease in marine ion concentrations, and the impact this may have had on both DOC and acidity, but results clearly demonstrate that organic acid increases have substantially limited the amount of recovery from acidification (in terms of rising alkalinity and falling aluminium) that have resulted from reducing sulphur emissions. The consistency and magnitude of sulphate and organic acid changes are consistent with a causal link between the two, possibly due to the effects of changing acidity, ionic strength and aluminium concentrations on organic matter solubility. If this is the case, then organic acids can be considered effective but partial buffers to acidity change in organic soils, and this mechanism needs to be considered in assessing and modelling recovery from acidification, and in defining realistic reference conditions. However, large spatial variations in the relative magnitude of organic acid and sulphate changes, notably for low-deposition sites in northwestern areas where organic acid increases apparently exceed non-marine sulphate decreases, suggest that additional factors, such as changes in sea-salt deposition and climatic factors, may be required to explain the full magnitude of DOC increases in UK surface waters.

Interaction of 6,6′′-bis(5,5,8,8-tetramethyl-5,6,7,8-tetrahydro-1,2,4-benzotriazin-3-yl)-2,2′:6′,2′′-terpyridine (CyMe4-BTTP) with some trivalent ions such as lanthanide(iii) ions and americium(iii)

The new ligand 6,6 ''-bis(5,5,8,8-tetramethyl-5,6,7,8-tetrahydro-1,2,4-benzotriazin-3-yl)2,2':6 ',2 ''-terpyridine (CyMe4-BTTP) has been synthesized in 4 steps from 2,2':6',2 ''-terpyridine. Detailed NMR and mass spectrometry studies indicate that the ligand forms 1 : 2 complexes with lanthanide(III) perchlorates where the aliphatic rings are conformationally constrained whereas 1 : 1 complexes are formed with lanthanide(III) nitrates where the rings are conformationally mobile. An optimized structure of the 1 : 2 solution complex with Yb(III) was obtained from the relative magnitude of the induced paramagnetic shifts. X-Ray crystallographic structures of the ligand and of its 1 : 1 complex with Y(III) were also obtained. The NMR and mass spectra of [Pd(CyMe4-BTTP)](n)(2n+) are consistent with a dinuclear double helical structure (n = 2). In the absence of a phase-modifier, CyMe4-BTTP in n-octanol showed a maximum distribution coefficient of Am(III) of 0.039 (+/-20%) and a maximum separation factor of Am(III) over Eu(III) of 12.0 from nitric acid. The metal(III) cations are extracted as the 1 : 1 complex from nitric acid. The generally low distribution coefficients observed compared with the BTBPs arise because the 1 : 1 complex of CyMe4-BTTP is considerably less hydrophobic than the 1 : 2 complexes formed by the BTBPs. In M(BTTP)(3+) complexes, there is a competition between the nitrate ions and the ligand for the complexation of the metal.

Synthesis and crystal structure of a 3-D zinc phosphate, [C5N2H14][Zn2(PO3(OH))3], containing (4.8) net sheets

A new 3-D zinc phosphate, [C5N2H14][Zn-2(PO3(OH))(3)], has been synthesised under solvothermal conditions in the presence of 1-methylpiperazine. The structure, determined by single-crystal X-ray diffraction at 293 K (RMM = 520.9, orthorhombic, space group P2(1)2(1)2(1); a = 10.0517(2) &ANGS;, b = 10.4293(2) &ANGS; and c = 14.9050(5) &ANGS;; V = 1562.52 &ANGS;(3); Z = 4; R(F) = 2.60%, wR(F) = 2.93%), consists of vertex linked ZnO4 and PO3(OH) tetrahedra assembled into (4.8) net sheets which in turn are linked through further PO3(OH) units to generate a 3-D framework. 1-Methylpiperazinium cations reside within the 3-D channel system, held in place by a strong network of hydrogen bonds. The (4.8) net sheets occur in a number of zeolite structures e.g. ABW and GIS and related zinc phosphate phases. © 2004 Academie des sciences. Published by Elsevier SAS. All rights reserved.

Spectroscopic properties and electronic structures of 17-electron half-sandwich ruthenium acetylide complexes, [Ru(CCAr)(L2)Cp′]+ (Ar=phenyl, p-tolyl, 1-naphthyl, 9-anthryl; L2=(PPh3)2, Cp′=Cp; L2=dppe; Cp′=Cp∗)

A series of half-sandwich bis(phosphine) ruthenium acetylide complexes [Ru(C CAr)(L-2)Cp'] (Ar = phenyl, p-tolyl, 1-naphthyl, 9-anthryl; L2 = (PPh3)(2), Cp' = Cp; L-2 = dppe; Cp' = Cp*) have been examined using electrochemical and spectroelectrochemical methods. One-electron oxidation of these complexes gave the corresponding radical cations [Ru(C CAr)(L2)Cp'](+). Those cations based on Ru(dppe)Cp*, or which feature a para-tolyl acetylide substituent, are more chemically robust than examples featuring the Ru(PPh3)(2)Cp moiety, permitting good quality UV-Vis-NIR and IR spectroscopic data to be obtained using spectroelectrochemical methods. On the basis of TD DFT calculations, the low energy (NIR) absorption bands in the experimental electronic spectra for most of these radical cations are assigned to transitions between the beta-HOSO and beta-LUSO, both of which have appreciable metal d and ethynyl pi character. However, the large contribution from the anthryl moiety to the frontier orbitals of [Ru(C CC14H9)(L2)CP'](+) suggests compounds containing this moiety should be described as metal-stabilised anthryl radical cations.

Isomeric olefin tetracarbonyl complexes of tungsten(I): an infrared spectroelectrochemical study at low temperatures

In situ electrolysis within an optically transparent thin-layer electrochemical (OTTLE) cell was applied at 293-243 K in combination with FTIR spectroscopy to monitor spectral changes in the carbonyl stretching region accompanying oxidation of four tetracarbonyl olefin complexes of tungsten(0), viz., trans-[W(CO)(4)(eta(2)-ethene)(2)], trans-[W(CO)(4)(eta(2)-norbornene)(2)], [W(CO)(4)(eta(4)-cycloocta-1,5-diene)], and [W(CO)(4)(eta(4)-norbornadiene)]. In all cases, the one-electron-oxidized radical cations (17-electron complexes) have been identified by their characteristic nu(CO) patterns. For the bidentate diene ligands, the cis stereochemistry is essentially fixed in both the 18- and 17-electron complexes. The radical cation of the trans-bis(ethene) complex was observed only at 243 K, while at room temperature it isomerized rapidly to the corresponding cis-isomer. The thermal stability of the three studied radical cations in the cis configuration correlates with the relative strength of the W-CO bonds in the positions trans to the olefin ligand, which are more affected by the oxidation than the axial W-CO bonds. For the bulky norbornene ligands, their trans configuration in the bis(norbornene) complex remains preserved after the oxidation in the whole temperature range studied. The limited thermal stability of the radical cations of the trans-bis(alkene) complexes is ascribed to dissociation of the alkene ligands. The spectroelectrochemical results are in very good agreement with data obtained earlier by DFT (B3LYP) calculations.

Supramolecular assemblies of metal ions in complex bimetallic and trimetallic salts based on hexacyanoferrate(III) ion

Two complex heterometallic salts with formulae Tl-6[Fe(CN)(6)](1) (33)(NO3)(OH) (1) and [Co(bpy)(2)(CN)(2)](2){[Ag(CN)(2)](0) (5)[Fe(CN)(6)](0) (5)} 8H(2)O (2) have been synthesized and fully characterized Single crystal X-ray analyses reveal that compound 1 is comprised of discrete Tl+ cations and [Fe(CN)(6)](3-) anions together with OH- and NO3- anions Compound 2 contains [Co(bpy)(2)(CN)(2)](+) cations and {[Ag(CN)(2)][Fe(CN)(6)]}(-) anions together with eight molecules of water of crystallization Both structures form unprecedented three-dimensional supramolecular networks via non covalent interactions Another important observation is that the stereochemically active inert (lone) pair present on Tl+ plays little role in controlling the structure of 1 The water molecules in 2 play important roles in providing stability organizing a supramolecular network through hydrogen bonding In the syntheses of 1 and 2 Fe(II) is oxidized to Fe(III) and Co(II) to Co(III) respectively facilitating the formation of the salts that are obtained Both compounds exhibit photoluminescence emission in solution near the visible region.

Hydrogen-bond assisted stabilization of the less favored conformation of a tridentate Schiff base ligand in dinuclear nickel(II) complex: an experimental and theoretical study

The Schiff base ligand, HL (2-[1-(3-methylamino-propylimino)-ethyl]-phenol), the 1:1 condensation product of 2-hydroxy acetophenone and N-methyl-1,3-diaminopropane, has been synthesized and characterized by X-ray crystallography as the perchlorate salt [H2L]ClO4 (1). The structure consists of discrete [H2L](+) cations and perchlorate anions. Two dinuclear Ni-II complexes, [Ni2L2(NO2)(2)] (2), [Ni2L2(NO3)(2)] (3) have been synthesized using this ligand and characterized by single crystal X-ray analyses. Complexes 2 and 3 are centrosymmetric dimers in which the Ni-II ions are in distorted fac- and mer-octahedral environments, respectively, bridged by two mu(2)-phenolate ions of deprotonated ligand, L. The plane of the phenyl rings and the Ni2O2 basal plane are nearly coplanar in 2 but almost perpendicular in 3. We have studied and explained this different behavior using high level DFT calculations (RI-BP86/def2-TZVP level of theory). The conformation observed in 3, which is energetically less favorable, is stabilized via intermolecular non-covalent interactions. Under the excitation of ultraviolet light, characteristic fluorescence of compound 1 was observed; by comparison fluorescence intensity decreases in case of compound 3 and completely quenched in compound 2.

Production and dissolution rates of earthworm-secreted calcium carbonate

Earthworms secrete granules of calcium carbonate. These are potentially important in soil biogeochemical cycles and are routinely recorded in archaeological studies of Quaternary soils. Production rates of calcium carbonate granules by the earthworm Lumbricus terrestris L. were determined over 27 days in a range of soils with differing chemical properties (pH, organic matter content, water holding capacity, bulk composition, cation exchange capacity and exchangeable cations). Production rate varied between soils, lay in the range 0–0.043 mmolCaCO3 (0–4.3 mg) earthworm−1 d−1 with an average rate of 8 × 10−3 mmolCaCO3 (0.8 mg) earthworm−1 d−1 and was significantly correlated (r = 0.68, P ≤ 0.01) with soil pH. In a second experiment lasting 315 days earthworms repeatedly (over periods of 39–57 days) produced comparable masses of granules. Converting individual earthworm granule production rates into fluxes expressed on per hectare of land per year basis depends heavily on estimates of earthworm numbers. Using values of 10–20 L. terrestris m−2 suggests a rate of 18– 3139 molCaCO3 ha−1 yr−1. Data obtained from flow-through dissolution experiments suggest that at near neutral pH, granule geometric surface areanormalised dissolution rates are similar to those for other biogenic and inorganic calcium carbonate. Fits of the data to the dissolution relationship r = k(1 − ˝)n where r = dissolution rate, k = a rate constant, ˝ = relative saturation and n = the reaction order gave values of k = 1.72 × 10−10 mol cm−2 s−1 and n = 1.8 for the geometric surface area-normalised rates and k = 3.51 × 10−13 mol cm−2 s−1 and n = 1.8 for the BET surface area-normalised rates. In 196 day leaching column experiments trends in granule dissolution rate referenced to soil chemistry corresponded to predictions made by the SLIM model for dissolution of limestone in soil. If soil solution approaches saturation with respect to calcium carbonate granule dissolution will slow or even stop and granules be preserved indefinitely. Granules have the potential to be a small but significant component of the biogeochemical cycling of C and Ca in soil.

Structural characterization of a new crystal form of the four-way Holliday junction formed by the DNA sequence d(CCGGTACCGG)2: sequence versus lattice?

DNA-strand exchange is a vital step in the recombination process, of which a key intermediate is the four-way DNA Holliday junction formed transiently in most living organisms. Here, the single-crystal structure at a resolution of 2.35 Å of such a DNA junction formed by d(CCGGTACCGG)2, which has crystallized in a more highly symmetrical packing mode to that previously observed for the same sequence, is presented. In this case, the structure is isomorphous to the mismatch sequence d(CCGGGACCGG)2, which reveals the roles of both lattice and DNA sequence in determining the junction geometry. The helices cross at the larger angle of 43.0° (the previously observed angle for this sequence was 41.4°) as a right-handed X. No metal cations were observed; the crystals were grown in the presence of only group I counter-cations.

The anions [(ZrOH(CO3)3)2]6− and [(ZrOH(C2O4)3)2]6−: single crystal X-ray diffraction studies of the complexes guanidinium zirconium carbonate [(C(NH2)3)3ZrOH(CO3)3·H2O]2 and sodium zirconium oxalate Na6(ZrOH(C2O4)3)2·7H2O

The complex [(C(NH2)3)3ZrOH(CO3)3·H2O]2 (A) has been shown by means of a single crystal X-ray diffraction study to contain [C(NH2)3]+ cations and dimeric anions of formulation [(ZrOH(CO3)3)2]6−. The anion is centrosymmetric with each metal being bonded to two bridging OH groups and three chelating CO2−3 ions. The Zr atoms are thus eight coordinate with a dodecahedral environments. The ZrO distances formed by the bridgng OH groups are shorter than those formed through zirconiu carbonate interactions. The non-bonded Zr…Zr distance is 3.47(2) Å. An infrared spectroscopic investigation of A provides data which support the findings of the crystallographic study. Likewise the complex Na6(ZrOH(CO2O4)3)2·7H2O (B) contains the anion [(ZrOH(C2O4)3)2]6−. This anion is structurally related to the anion in A as each Zr atom has an eight-coordinate dodecahedral environment being bonded to two bridging OH groups and three chelating oxalate ligands, but has no imposed crysallographic symmetry. The Zr…Zr non-bonded distance is 3.50(1) Å. The OZrO bridge angles are 69.7(4)° and A and 67.4(3)° in B.

Salt-induced hydrogelation of functionalised-dipeptides at high pH

Addition of divalent cations to a solution of a naphthalene-diphenylalanine that forms worm-like micelles at high pH results in the formation of a rigid, self-supporting hydrogel

Substituent and counterion effects on the formation of p-dimer dications of end-capped heptathienoacenes

We have investigated the impact of the functionalization and the chemical nature of counterions on the p-dimer dications formation in two end-capped heptathienoacenes. Radical cations of an a-substituted heptathienoacene with triisopropylsilyl groups do not p-dimerize, while those of an a,b-substituted heptathienoacene with four n-decyl side chains show a high propensity toward p-dimerization, increased by PF6 ÿ counterions.

Synthesis and evaluation of lipophilic BTBP ligands for An/Ln separation in nuclear waste treatment: the effect of alkyl substitution on extraction properties and implications for ligand design

Four new 6,6′-bis(1,2,4-triazin-3-yl)-2,2′-bipyridine (BTBP) ligands, which contain either additional alkyl groups on the pyridine rings or seven-membered aliphatic rings attached to the triazine rings, have been synthesized, and the effects of the additional alkyl substitution in the 4- and 4′-positions of the pyridine rings on their extraction properties with LnIII and AnIII cations in simulated nuclear waste solutions have been studied. The speciation of ligand 13 with some trivalent lanthanide nitrates was elucidated by 1H NMR spectroscopic titrations and ESI-MS. Although 13 formed both 1:1 and 1:2 complexes with LaIII and YIII, only 1:2 complexes were observed with EuIII and CeIII. Quite unexpectedly, both alkyl-substituted ligands 12 and 13 showed lower solubilities in certain diluents than the unsubstituted ligand CyMe4-BTBP. Compared to CyMe4-BTBP, alkyl-substitution was found to decrease the rates of metal-ion extraction of the ligands in both 1-octanol and cyclohexanone. A highly efficient (DAm > 10) and selective (SFAm/Eu > 90) extraction was observed for 12 and 13 in cyclohexanone and for 13 in 1-octanol in the presence of a phase-transfer agent. The implications of these results for the design of improved extractants for radioactive waste treatment are discussed.

The effects of a changing pollution climate on throughfall deposition and cycling in a forested area in southern England

This study compares two sets of measurements of the composition of bulk precipitation and throughfall at a site in southern England with a 20-year gap between them. During this time, SO2 emissions from the UK fell by 82%, NOx emissions by 35% and NH3 emissions by 7%. These reductions were partly reflected in bulk precipitation, with deposition reductions of 56% in SO4,38% in NO3, 32% in NH4, and 73% in H+. In throughfall under Scots pine, the effects were more dramatic, with an 89% reduction in SO4 deposition and a 98% reduction in H+ deposition. The mean pH under these trees increased from 2.85 to 4.30. Nitrate and ammonium deposition in throughfall increased slightly, however. In the earlier period, the Scots pines were unable to neutralise the high flux of acidity associated with sulphur deposition, even though this was not a highly polluted part of the UK, and deciduous trees (oak and birch) were only able to neutralise it in summer when the leaves were present. In the later period, the sulphur flux had reduced to the point where the acidity could be neutralised by all species — the neutralisation mechanism is thus likely to be largely leaching of base cations and buffering substances from the foliage. The high fluxes are partly due to the fact that these are 60–80 year old trees growing in an open forest structure. The increase in NO3 and NH4 in throughfall in spite of decreased deposition seems likely due to a decrease in foliar uptake, perhaps due to the increasing nitrogen saturation of the catchment soils. These changes may increase the rate of soil microbial activity as nitrogen increases and acidity declines, with consequent effects on water quality of the catchment drainage stream.