Uridine-Conjugated Ferrocene DNA Oligonucleotides: Unexpected Cyclization Reaction of the Uridine Base

Synthesis and Determination of Anticancer Activity of Dicobalt Hexacarbonyl 2'-Deoxy-5-alkynylfuropyrimidines

Dicobalt hexacarbonyl 5-alkynyl furopyrimidine nucleoside analogs, with 4-methylphenyl (p-tolyl) and 4-pentylphenyl substituents attached at the C-6 base position, designed in the form of ribose acetyl esters, were synthesized (42-96%). Attached at the C-5 position were propargyl alcohol, its methyl ether and acetate derivatives, butynol, and the 4-methylphenyl- (p-tolyl) and 4-pentylphenyl-substituted alkynyl groups, which were coordinated to a dicobalt hexacarbonyl unit. The structure of 5-(3-acetoxyprop-1-yn-1-yl)-6-p-tolyl-2'-deoxyribofuranosyl-furo[2,3-d]pyrimidin-2-one was determined by X-ray crystallography. Density functional theory calculations performed on the corresponding derivative yielded geometric parameters for the dicobalt hexacarbonyl adduct of this ligand. The cytotoxic activity of each of dicobalt modified nucleosides on cancer cells of different phenotypes was determined in vitro. The investigated compounds showed antiproliferative effects with median inhibitory concentration (IC50) values in the ranges of 14-90 and 9-50 μM for HeLa and K562 cells, respectively. The formation of reactive oxygen species in the presence of modified nucleosides was determined in K562 cells. The results indicate that the mechanism of action for the studied compounds may be related to the induction of oxidative stress.

Caging of a Strongly Pairing Fluorescent Thymidine Analog with Soft Nucleophiles

Controlling the pairing strength of nucleobases in DNA through reactions with compounds found inside the cell is a formidable challenge. Here we report how a thiazolyl substituent turns a strongly pairing ethynylpyridone C-nucleoside into a reactive residue in oligonucleotides. The thiazolyl-bearing pyridone reacts with soft nucleophiles, such as glutathione, but not with hard nucleophiles like hydroxide or carbonate. The addition products pair much more weakly with adenine in a complementary strand than the starting material, and also change their fluorescence. This makes oligonucleotides containing the new deoxynucleoside interesting for controlled release. Due to its reactivity toward N, P, S, and Se-nucleophiles, and the visual signal accompanying chemical conversion, the fluorescent nucleotide reported here may also have applications in chemical biology, sensing and diagnostics.

Carborane- or Metallacarborane-Linked Nucleotides for Redox Labeling. Orthogonal Multipotential Coding of all Four DNA Bases for Electrochemical Analysis and Sequencing

We report a series of 2'-deoxyribonucleoside triphosphates bearing dicarba-nido-undecaborate ([C₂B₉H₁₁]^1-), [3,3'-iron-bis(1,2-dicarbollide)]^- (FESAN, [Fe(C₂B₉H₁₁)₂]^2-) or [3,3'-cobalt-bis(1,2-dicarbollide)]^- (COSAN, [Co(C₂B₉H₁₁)₂]^2-) groups prepared either through the Sonogashira cross-coupling or the CuAAC click reaction. The modified dN^XTPs were substrates for KOD XL DNA polymerase in enzymatic synthesis of modified DNA through primer extension (PEX). The nido-carborane- and FESAN-modified nucleotides gave analytically useful oxidation signals in square-wave voltammetry and were used for redox labeling of DNA. The redox-modified DNA probes were prepared by PEX using tailed primers and were hybridized to electrode (gold or glassy carbon) containing capture oligonucleotides. The combination of nido-carborane- and FESAN-linked nucleotides with 7-ferrocenylethynyl-7-deaza-dATP and 7-deaza-dGTP allowed polymerase synthesis of DNA fully modified at all four nucleobases, and each of the redox labels gave four differentiable and ratiometric signals in voltammetry. Thus, the combination of these four redox labels constitutes the first fully orthogonal redox coding of all four canonical nucleobases, which can be used for determination of nucleobase composition of short DNA stretches in one simple PEX experiment with electrochemical readout.

Enzymatic synthesis of hypermodified DNA polymers for sequence-specific display of four different hydrophobic groups

A set of modified 2'-deoxyribonucleoside triphosphates (dNTPs) bearing a linear or branched alkane, indole or phenyl group linked through ethynyl or alkyl spacer were synthesized and used as substrates for polymerase synthesis of hypermodified DNA by primer extension (PEX). Using the alkyl-linked dNTPs, the polymerase synthesized up to 22-mer fully modified oligonucleotide (ON), whereas using the ethynyl-linked dNTPs, the enzyme was able to synthesize even long sequences of >100 modified nucleotides in a row. In PCR, the combinations of all four modified dNTPs showed only linear amplification. Asymmetric PCR or PEX with separation or digestion of the template strand can be used for synthesis of hypermodified single-stranded ONs, which are monodispersed polymers displaying four different substituents on DNA backbone in sequence-specific manner. The fully modified ONs hybridized with complementary strands and modified DNA duplexes were found to exist in B-type conformation (B- or C-DNA) according to CD spectral analysis. The modified DNA can be replicated with high fidelity to natural DNA through PCR and sequenced. Therefore, this approach has a promising potential in generation and selection of hypermodified aptamers and other functional polymers.

Tuning of Oxidation Potential of Ferrocene for Ratiometric Redox Labeling and Coding of Nucleotides and DNA

Three sets of 7‐deazaadenine and cytosine nucleosides and nucleoside triphosphates bearing either unsubstituted ferrocene, octamethylferrocene and ferrocenecarboxamide linked through an alkyne tether to position 7 or 5, respectively, were designed and synthesized. The modified dN^FcXTPs were good substrates for KOD XL DNA polymerase in primer extension and were used for enzymatic synthesis of redox‐labelled DNA probes. Square‐wave voltammetry showed that the octamethylferrocene oxidation potential was shifted to lower values, whilst the ferrocenecarboxamide was shifted to higher potentials, as compared to ferrocene. Tailed PEX products containing different ratios of Fc‐labelled A (dA^Fc) and FcPa‐labelled C (dC^FcPa) were synthesized and hybridized with capture oligonucleotides immobilized on gold electrodes to study the electrochemistry of the redox‐labelled DNA. Clearly distinguishable, fully orthogonal and ratiometric peaks were observed for the dA^Fc and dC^FcPa bases in DNA, demonstrating their potential for use in redox coding of nucleobases and for the direct electrochemical measurement of the relative ratio of nucleobases in an unknown sequence of DNA.

Synthesis of Base-Modified dNTPs Through Cross-Coupling Reactions and Their Polymerase Incorporation to DNA

Synthesis of base-modified dNTPs through the Suzuki or Sonogashira cross-coupling reactions of halogenated dNTPs with boronic acids or alkynes is reported, as well as the use of these modified dNTPs in polymerase incorporations to oligonucleotides or DNA by primer extension or PCR.

Engineering of Bioinspired, Size-Controllable, Self-Degradable Cancer-Targeting DNA Nanoflowers via the Incorporation of an Artificial Sandwich Base

In this article, we used an artificial DNA base to manipulate the formation of DNA nanoflowers (NFs) to easily control their sizes and functionalities. Nanoflowers have been reported as the noncanonical self-assembly of multifunctional DNA nanostructures, assembled from long DNA building blocks generated by rolling circle replication (RCR). They could be incorporated with myriad functional moieties. However, the efficacy of these DNA NFs as potential nanocarriers delivering cargo in biomedicine is limited by the bioavailability and therapeutic efficacy of their cargo. Here we report the incorporation of metal-containing artificial analogues into DNA strands to control the size and the functions of NFs. We have engineered bioinspired, size-controllable, self-degradable cancer-targeting DNA nanoflowers (Sgc8-NFs-Fc) via the incorporation of an artificial sandwich base. More specifically, the introduction of a ferrocene base not only resulted in the size controllability of Sgc8-NFs-Fc from 1000 to 50 nm but also endowed Sgc8-NFs-Fc with self-degradability in the presence of H2O2 via Fenton's reaction. In vitro experiments confirmed that Sgc8-NFs-Fc/Dox could be selectively taken up by protein tyrosine kinase 7 (PTK7)-positive cancer cells and subsequently cleaved via Fenton's reaction, resulting in rapid release kinetics, nuclear accumulation, and enhanced cytotoxicity of their cargo. In vivo experiments further confirmed that Sgc8-NFs-Fc has good tumor-targeting ability and could significantly improve the therapeutic efficacy of doxorubicin in a xenograft tumor model. On the basis of their tunable size and on-demand drug release kinetics upon H2O2 stimulation, the Sgc8-NFs-Fc nanocarriers possess promising potential in drug delivery.

Artificial Sandwich Base for Monitoring Single-Nucleobase Changes and Charge-Transfer Rates in DNA

Developing a convenient method to discriminate among different types of DNA nucleotides within a target sequence of the human genome is extremely challenging. We herein report an artificial ferrocene-base (Fe-base) that was synthesized and incorporated into different loci of a DNA strand. The Fe-base replacement on a nucleobase can interact with DNA bases and efficiently discriminate among A, T, G, and C DNA bases of the complementary locus on the basis of interacting electrochemical properties. Furthermore, cyclic-voltammetry (CV) studies demonstrated the electrochemical stability of DNA strands incorporated with Fe-bases and the reversibility of the incorporation. Square-wave voltammetry (SWV) was performed to measure current changes between Fe-bases and bases of interest in the DNA duplex. The changes in the charge-transfer rates appeared to be correlated with the position of the Fe-base in the DNA strand, allowing rapid and efficient sensing of single-nucleobase changes in DNA and showing promise for the design of Fe-oligomer chip technology as a tool for DNA sequencing.

PCR Incorporation of Polyoxometalate Modified Deoxynucleotide Triphosphates and Their Application in Molecular Electrochemical Sensing of Yersinia pestis

Redox-labeled nucleotides are of increasing interest for the fabrication of next generation molecular tools and should meet requirements of being thermally stable, sensitive, and compatible with polymerase-mediated incorporation while also being electrochemically discriminable. The synthesis and characterization of Keggin and Dawson polyoxometalate-deoxynucleotide (POM-dNTP) bioconjugates linked through 7-deaza-modified purines is described. The modified POM-dNTPs were used for polymerase-based amplification of a DNA sequence specific for Yersinia pestis and the amplified DNA detected using an electrochemical DNA sensor. This highlights the potential of polyoxometalates as thermally stable, sensitive and polymerase-compatible redox labels for exploitation in bioanalytical applications.

Ferrocene conjugated oligonucleotide for electrochemical detection of DNA base mismatch

We describe the synthesis, binding, and electrochemical properties of ferrocene-conjugated oligonucleotides (Fc-oligos). The key step for the preparation of Fc-oligos contains the coupling of vinylferrocene to 5-iododeoxyuridine via Heck reaction. The Fc-conjugated deoxyuridine phosphoramidite was used in the Fc-oligonucleotide synthesis. We show that thiol-modified Fc-oligos deposited onto gold electrodes possess potential ability in electrochemical detection of DNA base mismatch.

Nucleobase modification as redox DNA labelling for electrochemical detection

Basic aspects of DNA electrochemistry with a strong focus on the use of modified nucleobases as redox probes for electrochemical bioanalysis are reviewed. Intrinsic electrochemical properties of nucleobases in combination with artificial redox-active nucleobase modifications are frequently applied in this field. Synthetic approaches (both chemical and enzymatic) to base-modified nucleic acids are briefly summarized and their applications in redox labelling are discussed. Finally, analytical applications including DNA hybridization, primer extension, PCR, SNP typing, DNA damage and DNA-protein interaction analysis are presented (critical review, 91 references).

Synthesis of acetylene linked double-nucleobase nucleos(t)ide building blocks and polymerase construction of DNA containing cytosines in the major groove

(Cytosin-5-yl)ethynyl derivatives of pyrimidine and 7-deazaadenine 2-deoxyribonucleosides and nucleoside triphosphates (dNTPs) were prepared in one step by the aqueous Sonogashira coupling of unprotected halogenated nucleos(t)ides with 5-ethynylcytosine. The modified dNTPs were good substrates for DNA polymerases suitable for primer extension or PCR construction of DNA bearing acetylene-linked cytosine(s) in the major groove mimicking the flipped-out nucleotide.

Potential cross-linking transition metal complexes (M = Ni, Cu, Zn) in the ligand-modified LNA duplexes

Options for interstrand DNA duplex linkages have been studied by incorporating transition metal ions in the ligand-functionalized LNA (locked nucleic acid) duplexes. The effect of first-row transition metal ions (M = Ni(2+), Cu(2+), and Zn(2+)) on the geometries and formation energies of mono- and dimetallic model complexes was calculated by DFT methods, and the results were compared with available experimental data. The results showed a clear preference for the formation of copper complexes over the corresponding nickel and zinc complexes, in agreement with the trends observed in the denaturation temperatures of the ligand-functionalized LNA duplexes. In addition, dichloride bridged dimeric complex, [L(LNA)Cu(μ-Cl)(2)CuL(LNA)](2+), in which L(LNA) is N,N-bis(2-pyridylmethyl)-β-alanyl functionalized LNA, was found energetically very stable, providing a potential structural option for an interstrand duplex linkage. The model complex and its simpler structural analogues were synthesized and structurally characterized. Comparison of the dimeric linker introduced into duplex tetramer strands, which provided a computational model for a double helix with two closely located LNA units, with a similar model for mononuclear Cu(L(LNA))(2)(2+) linker also showed a clear preference of the dichloride-bridged option, suggesting that the [L(LNA)Cu(μ-Cl)(2)CuL(LNA)](2+) complex produced a chemically realistic model to explain duplex stabilization in the presence of Cu(2+) and excess Cl(-).

Studies on the synthesis, spectra, catalytic and antibacterial activities of binuclear ruthenium(II) complexes

A new series of stable binuclear ruthenium(II) carbonyl complexes of the general formula [{RuX(CO)(EPh(3))(2)}(2)L] (where X=H or Cl; E=P or As and L=dibasic tetradentate diacetyl resorcinol (H(2)-DAR)) have been synthesised by reacting ruthenium(II) starting complexes [RuHX(CO)(EPh(3))(3)] (where X=H or Cl; E=P or As) and 4,6-diacetylresorcinol (H(2)-DAR) ligand in benzene medium. The structure of the new binuclear ruthenium(II) carbonyl complexes was established using elemental analysis, spectra (FT-IR, UV-vis and (1)H NMR), electrochemical and thermal studies. In these reactions, the 4,6-diacetylresorcinol (H(2)-DAR) ligand behaves as a binegative tetradentate chelating ligand coordinating through O,O atoms of both the carbonyl and phenolic C-O groups by replacing a molecule of PPh(3)/AsPh(3) and a hydride ion from the starting complexes. Further, all these complexes were also employed as new catalysts for the oxidation of primary and secondary alcohols in the presence of N-methylmorpholine-N-oxide (NMO) as a more viable co-oxidant. The free ligand and their metal complexes have also been screened for their antibacterial activity against the growth of gram +ve and gram -ve bacterial cultures.

Electrochemistry of redox-active self-assembled monolayers

Redox-active self-assembled monolayers (SAMs) provide an excellent platform for investigating electron transfer kinetics. Using a well-defined bridge, a redox center can be positioned at a fixed distance from the electrode and electron transfer kinetics probed using a variety of electrochemical techniques. Cyclic voltammetry, AC voltammetry, electrochemical impedance spectroscopy, and chronoamperometry are most commonly used to determine the rate of electron transfer of redox-activated SAMs. A variety of redox species have been attached to SAMs, and include transition metal complexes (e.g., ferrocene, ruthenium pentaammine, osmium bisbipyridine, metal clusters) and organic molecules (e.g., galvinol, C(60)). SAMs offer an ideal environment to study the outer-sphere interactions of redox species. The composition and integrity of the monolayer and the electrode material influence the electron transfer kinetics and can be investigated using electrochemical methods. Theoretical models have been developed for investigating SAM structure. This review discusses methods and monolayer compositions for electrochemical measurements of redox-active SAMs.

Synthesis of nucleoside and nucleotide conjugates of bile acids, and polymerase construction of bile acid-functionalized DNA

Aqueous Sonogashira cross-coupling reactions of 5-iodopyrimidine or 7-iodo-7-deazaadenine nucleosides with bile acid-derived terminal acetylenes linked via an ester or amide tether gave the corresponding bile acid-nucleoside conjugates. Analogous reactions of halogenated nucleoside triphosphates gave directly bile acid-modified dNTPs. Enzymatic incorporation of these modified nucleotides to DNA was successfully performed using Phusion polymerase for primer extension. One of the dNTPs (dCTP bearing cholic acid) was also efficient for PCR amplification.

Nucleobase-containing transition metal complexes as building blocks for biological markers and supramolecular structures

The incorporation of metal complexes into nucleobases, nucleosides and nucleotides has provided a focus for the development of many novel compounds with a wide range of applications. In this perspective article the different methods to incorporate transition metal complexes into these species will be described. Applications of these compounds as biological markers, catalysts and how the hydrogen bonding properties may be employed in directing supramolecular assembly in both the solid state and solution will be discussed.

Ferrocenylethynyl derivatives of nucleoside triphosphates: synthesis, incorporation, electrochemistry, and bioanalytical applications

Modified dATP (2'-deoxyadenosine-5'-triphosphate) and dUTP (2'-deoxyuridine-5'-triphosphate) bearing ferrocene (Fc) labels linked via a conjugate acetylene spacer were prepared by single-step aqueous-phase cross-coupling reactions of 7-iodo-7-deaza-dATP or 5-iodo-dUTP with ethynylferrocene. The Fc-labeled dNTPs were good substrates for DNA polymerases and were efficiently incorporated to DNA by primer extension (PEX). Electrochemical analysis of the 2'-deoxyribonucleoside triphosphates (dNTPs) and PEX products revealed significant differences in redox potentials of the Fc label bound either to U or to 7-deazaA and between isolated dNTPs and conjugates incorporated to DNA. Prospective bioanalytical applications are outlined.

Synthesis of 2'-deoxyadenosine nucleosides bearing bipyridine-type ligands and their Ru-complexes in position 8 through cross-coupling reactions

The synthesis of the title 2'-deoxyadenosine derivatives bearing bipyridine, phenanthroline or terpyridine ligands and their corresponding RuII-complexes in position 8 linked via acetylene or phenylene tethers was accomplished through cross-coupling reactions. The Suzuki-Miyaura reactions of boronic acids or the Sonogashira reactions of terminal acetylene derivatives of oligopyridine ligands were performed either on protected 8-bromoadenosines in organic solvents or, more efficiently, directly on unprotected nucleosides in aqueous acetonitrile or DMF. Direct cross-coupling reactions of unprotected nucleosides with RuII-complexes or the oligopyridine-boronic acids or -acetylenes gave the Ru-labelled nucleosides in one step in fair to good yields. This method was also proven to be applicable for direct Ru-labelling of dATP. Terpyridine-containing 2'-deoxyadenosine exerted significant antiviral and cytostatic effects.

Transition metal vinylidene complexes as supramolecular building blocks: nucleobase-mediated self-assembly of crystals with hexagonal symmetry

Reaction of the ruthenium half sandwich compound RuCl(eta(5)-C(5)H(5))(PPh(3))(2) with the uracil (Ur) substituted alkyne HC[triple bond, length as m-dash]CUr in the presence of halide scavengers NH(4)X (X = PF(6), BF(4), OTf) results in the formation of the vinylidene complexes [Ru([double bond, length as m-dash]C[double bond, length as m-dash]CHUr)(eta(5)-C(5)H(5))(PPh(3))(2)][X] which crystallize in the hexagonal space group P6(3)/m. The hexagonal symmetry inherent to the system is due to the formation of a hydrogen bonded array mediated by the two sets of donor-acceptor units on the uracil, resulting in the formation of a cyclic "rosette" containing six ruthenium cations. In solution the (1)H and (31)P{(1)H} NMR spectra of the vinylidene complexes are both concentration and temperature dependent, in accord with the presence of monomer-dimer equilibria in which the rate of rotation of the vinylidene group is fast on the NMR timescale in the monomeric species, but slow in the dimers. The isoelectronic molybdenum-containing vinylidene complex [Mo(eta(7)-C(7)H(7))(dppe)([double bond, length as m-dash]C[double bond, length as m-dash]CHUr)][BF(4)] (dppe = 1,2-bis(diphenylphosphino)ethane) has also been prepared, but forms symmetric dimers in the solid state.

Ferrocene-modified pyrimidine nucleosides: synthesis, structure and electrochemistry

This paper reports syntheses, crystal structures and electrochemical results for two ferrocene(Fc)-modified pyrimidine nucleosides that could potentially be used for investigating electron transfer in DNA. Fc was directly attached to the 5-position of deoxyuridine and deoxycytidine via the Stille coupling reaction. Fc-modified uridine was incorporated into DNA trinucleotides with standard solid-phase synthesis. The structures of corresponding detritylated compounds were determined by single-crystal X-ray analysis. Electrochemical investigations of all compounds by cyclic voltammetry revealed reversible redox processes.

Ferrocenyl-modified DNA: synthesis, characterization and integration with semiconductor electrodes

The ferrocenyl-nucleoside, 5-ethynylferrocenyl-2'-deoxycytidine (1) has been prepared by Pd-catalyzed cross-coupling between ethynylferrocene and 5-iodo-2'-deoxycytidine and incorporated into oligonucleotides by using automated solid-phase synthesis at both silica supports (CPG) and modified single-crystal silicon electrodes. Analysis of DNA oligonucleotides prepared and cleaved from conventional solid supports confirms that the ferrocenyl-nucleoside remains intact during synthesis and deprotection and that the resulting strands may be oxidised and reduced in a chemically reversible manner. Melting curve data show that the ferrocenyl-modified oligonucleotides form duplex structures with native complementary strands. The redox potential of fully solvated ferrocenyl 12-mers, 350 mV versus SCE, was shifted by +40 mV to a more positive potential upon treatment with the complement contrary to the anticipated negative shift based on a simple electrostatic basis. Automated solid-phase methods were also used to synthesise 12-mer ferrocenyl-containing oligonucleotides directly at chemically modified silicon <111> electrodes. Hybridisation to the surface-bound ferrocenyl-DNA caused a shift in the reduction potential of +34 mV to more positive values, indicating that, even when a ferrocenyl nucleoside is contained in a film, the increased density of anions from the phosphate backbone of the complement is still dominated by other factors, for example, the hydrophobic environment of the ferrocene moiety in the duplex or changes in the ferrocene-phosphate distances. The reduction potential is shifted >100 mV after hybridisation when the aqueous electrolyte is replaced by THF/LiClO(4), a solvent of much lower dielectric constant; this is consistent with an explanation based on conformation-induced changes in ferrocene-phosphate distances.

NMR conformational analysis of p-tolyl furanopyrimidine 2'-deoxyribonucleoside and crystal structure of its 3',5'-di-O-acetyl derivative

The conformation of a representative molecule of a new, potent class of antiviral-active modified nucleosides is determined. A bicyclic nucleoside, 3-(2'-deoxy-beta-D-ribofuranosyl)-6-(4-methylphenyl)-2,3-dihydrofuro[2,3-d]pyrimidin-2-one, shows C2'-endo and C3'-endo ribose conformations in solution (63:37, 37 degrees C; DMSO-d6), as determined by 1H NMR studies. The crystal structure of a 3',5'-di-O-acetyl-protected derivative (monoclinic, P21, a/b/c= 6.666(1)/12.225(1)/24.676(2) A, beta=90.24(1) degrees , Z=4) shows exclusively C2'-endo deoxyribose puckering. The base is found in the anti position both in solution and in crystalline form.

Recognition of CG inversions in DNA triple helices by methylated 3H-pyrrolo[2,3-d]pyrimidin-2(7H)-one nucleoside analogues

Substituted 3H-pyrrolo[2,3-d]pyrimidin-2(7H)-one nucleoside analogues have been synthesised from 5-alkynyl-uridine derivatives, incorporated into triplex forming oligonucleotides (TFOs) and found to selectively bind CG inversions with enhanced affinity compared to T.

An electrochemical study of enzymatic oligonucleotide digestion

This paper describes the synthesis and application of a novel ferrocene (Fc) label that can be efficiently attached to oligonucleotides. We demonstrate how pulse electrochemical methods can be used to measure very low concentrations of ferrocene label and, importantly, show good electroanalytical discrimination between a labelled oligonucleotide and an enzyme digested labelled oligonucleotide, in which the ferrocene label nucleotide conjugate has been released. Real time in situ analysis gives a much greater understanding of the process. Potential applications include the detection of specific nucleic acid sequences and measurement of nuclease activity.

Rigid, conjugated, fluoresceinated thymidine triphosphates: syntheses and polymerase mediated incorporation into DNA analogues

Syntheses of a unique set of energy transfer dye labeled nucleoside triphosphates, compounds 1-3, are described. Attempts to prepare these compounds were only successful if the triphosphorylation reaction was performed before coupling the dye to the nucleobase, and not the other way around. Compounds were prepared as both the 2'-deoxy (a) and 2',3'-dideoxy- (b) forms. They feature progressively longer rigid conjugated linkers connecting the nucleobase and the hydroxyxanthone moiety. UV spectra of the parent nucleosides 12-14 show that as the length of the linker increases so does the absorption of the donor in the 320-330 nm region, but with relatively little red-shift of the maxima. Fluorescence spectra of the same compounds show that radiation in the 320-330 nm region results in predominant emission from the fluorescein. When the linker is irradiated at 320 nm, the only significant emission observed corresponds to the hydroxyxanthone part of the molecules at 520 nm; this corresponds to an effective Stokes' shift of 200 nm. As the absorption at 320-330 nm by the linker increases with length, so does the intensity of the fluorescein emission. A gel assay was used to gauge relative incorporation efficiencies of compounds 1-3, dTTP, ddTTP, and 6-TAMRA-ddTTP. Throughout, the thermostable polymerase TaqFS was used, as it is the one most widely applied in high throughput DNA sequencing. This assay showed that only compounds 3 were incorporated efficiently; these have the longest linkers. Of these, the 2'-deoxy nucleoside 3 a was incorporated and did not prevent the polymerase from extending the chain further. The 2',3'-dideoxy nucleoside 3 b was incorporated only about 430 times less efficiently than ddTTP under the same conditions, and caused chain termination. The implications of these studies on modified sequencing protocols are discussed.

A nucleic acid base derivative tethered to a ruthenium carbene complex: hydrogen bonded dimers in both the solid state and solution?

A ruthenium carbene bearing a uracil (Ur) substituent has been prepared and has a dimeric structure in the solid state-the dimer being held together by hydrogen bonds between two uracil groups on neighbouring molecules: evidence for the persistence of this interaction in solution has been obtained.

Fluorescent Sugar and Uridine Conjugates of 1,8-Naphthalimides with Methyl and Ferrocenyl Headgroups

The first amphiphilic sugar and deoxyuridine conjugates with a 4-ethynyl-1,8-N-methylnaphthalimide linker, a 4-ethynyldeoxyuridine conjugate with a N-undecylferrocenyl headgroup, and a 1,8-naphthalimide with a 2,3,4,6-tetra-O-acetate-β-d-glucopyranoside headgroup have been synthesized. A novel acrylate monomeric precursor for sugar–ethynylnaphthalimide polymers is also reported. The ethynyl tether forms complexes with Co2(CO)8 and Co2(CO)6dppm. The single-crystal X-ray structures of 2′-propynyl-2,3,4,6-tetra-O-acetate-β-d-glucopyranoside 4 and 4-(2′-propynyl-2,3,4,6-tetra-O-acetate-β-d-glucopyranoside)-N-methyl-1,8-naphthalimide 6 are also reported. With the exception of the Co2 complexes, the sugar and deoxyuridine conjugates are strongly fluorescent. ‘On–off’ fluorescent switching is achieved in the deoxyuridine conjugate with an undecylferrocenyl headgroup.

Oligonucleotides with strongly fluorescent groups pi-conjugated to a nucleobase: syntheses, melting temperatures, and conformation

Phosphoramidite 1 was prepared, incorporated into oligonucleotides, and these were studied via thermal denaturation and circular dichroism.

Bioelectronic DNA detection of human papillomaviruses using eSensor: a model system for detection of multiple pathogens

BACKGROUND

We used human papillomaviruses (HPV) as a model system to evaluate the utility of a nucleic acid, hybridization-based bioelectronic DNA detection platform (eSensor) in identifying multiple pathogens.

METHODS

Two chips were spotted with capture probes consisting of DNA oligonucleotide sequences specific for HPV types. Electrically conductive signal probes were synthesized to be complementary to a distinct region of the amplified HPV target DNA. A portion of the HPV L1 region that was amplified by using consensus primers served as target DNA. The amplified target was mixed with a cocktail of signal probes and added to a cartridge containing a DNA chip to allow for hybridization with complementary capture probes.

RESULTS

Two bioelectric chips were designed and successfully detected 86% of the HPV types contained in clinical samples.

CONCLUSIONS

This model system demonstrates the potential of the eSensor platform for rapid and integrated detection of multiple pathogens.