An efficient method for the construction of functionalized DNA bearing amino acid groups through cross-coupling reactions of nucleoside triphosphates followed by primer extension or PCR

Single-step aqueous cross-coupling reactions of nucleobase-halogenated 2'-deoxynucleosides (8-bromo-2'-deoxyadenosine, 7-iodo-7-deaza-2'-deoxyadenosine, or 5-iodo-2'-deoxy-uridine) or their 5'-triphosphates with 4-boronophenylalanine or 4-ethynylphenylalanine have been developed and used for efficient synthesis of modified 2'-deoxynucleoside triphosphates (dNTPs) bearing amino acid groups. These dNTPs were then tested as substrates for DNA polymerases for construction of functionalized DNA through primer extension and PCR. While 8-substituted adenosine triphosphates were poor substrates for DNA polymerases, the corresponding 7-substituted 7-deazaadenine and 5-substituted uracil nucleotides were efficiently incorporated in place of dATP or dTTP, respectively, by Pwo (Pyrococcus woesei) DNA polymerase. Nucleotides bearing the amino acid connected through the less bulky acetylene linker were incorporated more efficiently than those directly linked through a more bulky phenylene group. In addition, combinations of modified dATPs and dTTPs were incorporated by Pwo polymerase. Novel functionalized DNA duplexes bearing amino acid moieties were prepared by this two-step approach. PCR can be used for amplification of duplexes bearing large number of modifications, while primer extension is suitable for introduction of just one or several modifications in a single DNA strand.     

Synthesis of nucleoside mono- and triphosphates bearing oligopyridine ligands, their incorporation into DNA and complexation with transition metals

Modified nucleoside mono- (dA(R)MPs and dC(R)MPs) and triphosphates (dA(R)TPs and dC(R)TPs) bearing bipyridine or terpyridine ligands attached via acetylene linker were prepared by single-step aqueous-phase Sonogashira cross-coupling of 7-iodo-7-deaza-dAMP or -dATP, and 5-iodo-dCMP or -dCTP with the corresponding bipyridine- or terpyridine-linked acetylenes. The modified dN(R)TPs were successfully incorporated into the oligonucleotides by primer extension experiment (PEX) using different DNA polymerases and the PEX products were used for post-synthetic complexation with Fe(2+).     

Anthraquinone as a redox label for DNA: synthesis, enzymatic incorporation, and electrochemistry of anthraquinone-modified nucleosides, nucleotides, and DNA

Modified 2'-deoxynucleosides and deoxynucleoside triphosphates (dNTPs) bearing anthraquinone (AQ) attached through an acetylene or propargylcarbamoyl linker at the 5-position of pyrimidine (C) or at the 7-position of 7-deazaadenine were prepared by Sonogashira cross-coupling of halogenated dNTPs with 2-ethynylanthraquinone or 2-(2-propynylcarbamoyl)anthraquinone. Polymerase incorporations of the AQ-labeled dNTPs into DNA by primer extension with KOD XL polymerase have been successfully developed. The electrochemical properties of the AQ-labeled nucleosides, nucleotides, and DNA were studied by cyclic and square-wave voltammetry, which show a distinct reversible couple of peaks around -0.4 V that make the AQ a suitable redox label for DNA.     

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.     

7‐Aryl‐7‐deazaadenine 2′‐Deoxyribonucleoside Triphosphates (dNTPs): Better Substrates for DNA Polymerases than dATP in Competitive Incorporations

A series of 7‐substituted 7‐deazaadenine and 5‐substituted cytosine 2′‐deoxyribonucleoside triphosphates (dNTPs) were tested for their competitive incorporations (in the presence of dATP and dCTP) into DNA by several DNA polymerases by using analysis based on cleavage by restriction endonucleases. 7‐Aryl‐7‐deazaadenine dNTPs were more efficient substrates than dATP because of their higher affinity for the active site of the enzyme, as proved by kinetic measurements and calculations.     

Base-Modified DNA Labeled by [Ru(bpy)3]2+ and [Os(bpy)3]2+ Complexes: Construction by Polymerase Incorporation of Modified Nucleoside Triphosphates,Electrochemical and Luminescent Properties,and Applications

Modified 2′-deoxynucleoside triphosphates (dNTPs) bearing [Ru(bpy)₃]²⁺ and [Os(bpy)₃]²⁺ complexes attached via an acetylene linker to the 5-position of pyrimidines (C and U) or to the 7-position of 7-deazapurines (7-deaza-A and 7-deaza-G) have been prepared in one step by aqueous cross-couplings of halogenated dNTPs with the corresponding terminal acetylenes. Polymerase incorporation by primer extension using Vent (exo-) or Pwo polymerases gave DNA labeled in specific positions with Ru²⁺ or Os²⁺ complexes. Square-wave voltammetry could be efficiently used to detect these labeled nucleic acids by reversible oxidations of Ru^2+/3+ or Os^2+/3+. The redox potentials of the Ru²⁺ complexes (1.1–1.25 V) are very close to that of G oxidation (1.1 V), while the potentials of Os²⁺ complexes (0.75 V) are sufficiently different to enable their independent detection. On the other hand, Ru²⁺-labeled DNA can be independently analyzed by luminescence. In combination with previously reported dNTPs bearing ferrocene, aminophenyl, and nitrophenyl tags, the Os-labeled dATP has been successfully used for “multicolor” redox labeling of DNA and for DNA minisequencing.     

Incorporation of 4'-C-aminomethyl-2'-O-methylthymidine into DNA by thermophilic DNA polymerases

The dual modified nucleotide 4'-C-aminomethyl-2'-O-methylthymidine 5'-triphosphate was synthesized and enzymatically incorporated into DNA by the thermophilic DNA polymerases Pfu and Therminator III. The dual ribose modification imparted increased exonuclease resistance to DNA compared to the well-known 2'-O-methyl modification.     

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.     

Structures of KlenTaq DNA polymerase caught while incorporating C5-modified pyrimidine and C7-modified 7-deazapurine nucleoside triphosphates

The capability of DNA polymerases to accept chemically modified nucleotides is of paramount importance for many biotechnological applications. Although these analogues are widely used, the structural basis for the acceptance of the unnatural nucleotide surrogates has been only sparsely explored. Here we present in total six crystal structures of modified 2'-deoxynucleoside-5'-O-triphosphates (dNTPs) carrying modifications at the C5 positions of pyrimidines or C7 positions of 7-deazapurines in complex with a DNA polymerase and a primer/template complex. The modified dNTPs are in positions poised for catalysis leading to incorporation. These structural data provide insight into the mechanism of incorporation and acceptance of modified dNTPs. Our results open the door for rational design of modified nucleotides, which should offer great opportunities for future applications.     

Synthesis of Polyanionic C5-Modified 2′-Deoxyuridine and 2′-Deoxycytidine-5′-Triphosphates and Their Properties as Substrates for DNA Polymerases

Modified 2′-deoxyribonucleotide triphosphates (dNTPs) have widespread applications in both existing and emerging biomolecular technologies. For such applications it is an essential requirement that the modified dNTPs be substrates for DNA polymerases. To date very few examples of C5-modified dNTPs bearing negatively charged functionality have been described, despite the fact that such nucleotides might potentially be valuable in diagnostic applications using Si-nanowire-based detection systems. Herein we have synthesised C5-modified dUTP and dCTP nucleotides each of which are labelled with an dianionic reporter group. The reporter group is tethered to the nucleobase via a polyethylene glycol (PEG)-based linkers of varying length. The substrate properties of these modified dNTPs with a variety of DNA polymerases have been investigated to study the effects of varying the length and mode of attachment of the PEG linker to the nucleobase. In general, nucleotides containing the PEG linker tethered to the nucleobase via an amide rather than an ether linkage proved to be the best substrates, whilst nucleotides containing PEG linkers from PEG₆ to PEG₂₄ could all be incorporated by one or more DNA polymerase. The polymerases most able to incorporate these modified nucleotides included Klentaq, Vent(exo-) and therminator, with incorporation by Klenow(exo-) generally being very poor.     

Optimization of non-natural nucleotides for selective incorporation opposite damaged DNA

The promutagenic process known as translesion DNA synthesis reflects the ability of a DNA polymerase to misinsert a nucleotide opposite a damaged DNA template. To study the underlying mechanism of nucleotide selection during this process, we quantified the incorporation of various non-natural nucleotide analogs opposite an abasic site, a non-templating DNA lesion. Our kinetic studies using the bacteriophage T4 DNA polymerase reveal that the pi-electron surface area of the incoming nucleotide substantially contributes to the efficiency of incorporation opposite an abasic site. A remaining question is whether the selective insertion of these non-hydrogen-bonding analogs can be achieved through optimization of shape and pi-electron density. In this report, we describe the synthesis and kinetic characterization of four novel nucleotide analogs, 5-cyanoindolyl-2'-deoxyriboside 5'-triphosphate (5-CyITP), 5-ethyleneindolyl-2'-deoxyriboside 5'-triphosphate (5-EyITP), 5-methylindolyl-2'-deoxyriboside 5'-triphosphate (5-MeITP), and 5-ethylindolyl-2'-deoxyriboside 5'-triphosphate (5-EtITP). Kinetic analyses indicate that the overall catalytic efficiencies of all four nucleotides are related to their base-stacking properties. In fact, the catalytic efficiency for nucleotide incorporation opposite an abasic site displays a parabolic trend in the overall pi-electron surface area of the non-natural nucleotide. In addition, each non-natural nucleotide is incorporated opposite templating DNA approximately 100-fold worse than opposite an abasic site. These data indicate that selectivity for incorporation opposite damaged DNA can be achieved through optimization of the base-stacking properties of the incoming nucleotide.     

Synthesis of Deoxynucleoside Triphosphates that Include Proline,Urea, or Sulfonamide Groups and Their Polymerase Incorporation into DNA

To expand the chemical array available for DNA sequences in the context of in vitro selection, I present herein the synthesis of five nucleoside triphosphate analogues containing side chains capable of organocatalysis. The synthesis involved the coupling of L ‐proline‐containing residues (dU^tPTP and dU^cPTP), a dipeptide (dU^FPTP), a urea derivative (dU^BpuTP), and a sulfamide residue (dU^BsTP) to a suitably protected common intermediate, followed by triphosphorylation. These modified dNTPs were shown to be excellent substrates for the Vent (exo^?) and Pwo DNA polymerases, as well as the Klenow fragment of E. coli DNA polymerase I, although they were only acceptable substrates for the 9°N_m polymerase. All of the modified dNTPs, with the exception of dU^BpuTP, were readily incorporated into DNA by the polymerase chain reaction (PCR). Modified oligonucleotides efficiently served as templates for PCR for the regeneration of unmodified DNA. Thermal denaturation experiments showed that these modifications are tolerated in the major groove. Overall, these heavily modified dNTPs are excellent candidates for SELEX.     

2',3'-Dideoxy-3'-thionucleoside triphosphates: syntheses and polymerase substrate activities

All four 2',3'-dideoxy-3'-thio-nucleosides (ddtNTPs) function as substrates for the Y410F mutant of Deep Vent (exo-) DNA polymerase. Not only are the ddtNTPs incorporated to form the N + 1 product, but further elongations are observed in which the key step is attack of the 3'-thiol on the 5'-triphosphate. Although other polymerases are likely to differ in their use of the ddtNTPs, there does not appear to be a fundamental prohibition against using a thiol nucleophile on a phosphate anhydride electrophile. The syntheses of four ddtNTPs (C, T, A, G) are described. [structure: see text]     

Organostannoxane-supported multiferrocenyl assemblies: synthesis, novel supramolecular structures, and electrochemistry

Organostannoxane-based multiredox assemblies containing ferrocenyl peripheries have been readily synthesized by a simple one-pot synthesis, either by a solution method or by room-temperature solid-state synthesis, in nearly quantitative yields. The number of ferrocenyl units in the multiredox assembly is readily varied by stoichiometric control as well as by the choice of the organotin precursors. Thus, the reaction of the diorganotin oxides, R2SnO (R = Ph, nBu and tBu) with ferrocene carboxylic acid affords tetra-, di-, and mononuclear derivatives [{Ph2Sn[OC(O)Fc]2}2] (1), [{[nBu2SnOC(O)Fc]2O}2] (2), [nBu2Sn{OC(O)Fc}2] (3), [{tBu2Sn(OH)OC(O)Fc}2] (4), and [tBu2Sn{OC(O)Fc}2] (5) (Fc = eta(5)C5H4-Fe-eta(5)C5H5). The reaction of triorganotin oxides, R3SnOSnR3 (R = nBu and Ph) with ferrocene carboxylic acid leads to the formation of the mono-nuclear derivatives [Ph3SnOC(O)Fc] (6) and [{nBu3SnOC(O)Fc}(n)] (7). Molecular structures of the compounds 1-4 and 6 have been determined by single-crystal X-ray analysis. The molecular structure of compound 1 is new among organotin carboxylates. In this compound, ferrocenyl carboxylates are involved in both chelating and bridging coordination modes to the tin atoms to form an eight-membered cyclic structure. In all of these compounds, the acidic protons of the cyclopentadienyl groups are hydrogen bonded to the carboxylate oxygens (C-HO) to form rich supramolecular assemblies. In addition to this, pi-pi, T-shaped, L-shaped, and side-to-face stacking interactions involving ferrocenyl groups also occur. Compound 6 shows an interesting and novel intermolecular CO2-pi stacking interaction. Electrochemical analysis of the compounds 1-4, 6, and 7 shows a single, quasi-reversible oxidation peak corresponding to the simultaneous oxidation of four, two, and one ferrocenyl substituents, respectively. Compound 5 shows two quasi-reversible oxidation peaks. This is attributed to the positional difference among the ferrocenyl substituents on the tin atom. Additionally, while compounds 2 and 4 are electrochemically quite robust and do not decompose even after ten continuous CV cycles, compounds 1, and 3, 5-7 start to show decomposition after five cycles.     

Synthesis and photophysical properties of biaryl-substituted nucleos(t)ides. Polymerase synthesis of DNA probes bearing solvatochromic and pH-sensitive dual fluorescent and 19F NMR labels

The design of four new fluorinated biaryl fluorescent labels and their attachment to nucleosides and nucleoside triphosphates (dNTPs) by the aqueous cross-coupling reactions of biarylboronates is reported. The modified dNTPs were good substrates for KOD XL polymerase and were enzymatically incorporated into DNA probes. The photophysical properties of the biaryl-modified nucleosides, dNTPs, and DNA were studied systematically. The different substitution pattern of the biaryls was used for tuning of emission maxima in the broad range of 366-565 nm. Using methods of computational chemistry the emission maxima were reproduced with a satisfactory degree of accuracy, and it was shown that the large solvatochromic shifts observed for the studied probes are proportional to the differences in dipole moments of the ground (S(0)) and excited (S(1)) states that add on top of smaller shifts predicted already for these systems in vacuo. Thus, we present a set of compounds that may serve as multipurpose base-discriminating fluorophores for sensing of hairpins, deletions, and mismatches by the change of emission maxima and intensities of fluorescence and that can be also conviently studied by (19)F NMR spectroscopy. In addition, aminobenzoxazolyl-fluorophenyl-labeled nucleotides and DNA also exert dual pH-sensitive and solvatochromic fluorescence, which may imply diverse applications.     

Synthesis, structure and electrochemistry of ferrocene-peptide macrocycles

Redox active cyclopeptides Fc[CSA]2 (5), Fc[Gly-CSA]2 (6), Fc[Ala-CSA]2 (7), Fc[Val-CSA](2) and Fc[Leu-CSA]2 (9) (CSA = cysteamine) which are formed by the reaction of ferrocenedicarboxylic acid with peptide cystamines at high dilutions. These systems exhibit H-bonding involving the amide NH in solution as shown by their temperature dependent NMR spectra. With the exception of 5, the ferrocene macrocycles display intramolecular N...O cross-ring H-bonding in the solid state involving the amino acids proximal to the ferrocene.     

1,3,2-Diazaborolyl-functionalized thiophenes and dithiophenes: synthesis, structure, electrochemistry and luminescence

Reaction of 2-bromo-1,3-diethyl-1,3,2-benzodiazaborole (1) with equimolar amounts of thienyl lithium or 2,2-dithienyl lithium led to the generation of benzodiazaboroles 2 and 3 which are functionalized at the boron atom by a 2-thienyl or a 5-(2,2-dithienyl) unit. Similarly 2-bromo-1,3-diethyl-1,3,2-naphthodiazaborole (4) and thienyl lithium or 2,2-dithienyl lithium afforded the naphthoborolyl-substituted thiophene 5 or dithiophene 6. Treatment of 2,5-bis(dibromoboryl)-thiophene 7 with 2 eq. of tBuN=CH-CH=NtBu in n-hexane followed by sodium amalgam reduction of the obtained bis(diazaborolium) salt 8 gave the 2,5-bis(diazaborolyl)thiophene 9. The 2,5-bis(diazaborolidinyl)-thiophene 10 resulted from the cyclocondensation of 7 with 2 eq. of N,N-di-tert-butylethylenediamine in the presence of NEt3. Analogously, cyclocondensation of 7 with N,N-diethylphenylenediamine gave the bis(benzodiazaborolyl) functionalized thiophene 11. The novel compounds were characterized by elemental analysis and spectroscopy (1H-, 11B-, 13C-NMR, MS and UV-VIS). The molecular structure of 3 was elucidated by X-ray diffraction. Cyclovoltammograms show an irreversible oxidation wave at 298-598 vs. Fc/Fc+. The borolylated thiophenes and dithienyls show intense blue luminescence with Stokes shifts of 30-107 nm.     

Synthesis and characterization of the oxidized dGTP lesions spiroiminodihydantoin-2'-deoxynucleoside-5'- triphosphate and guanidinohydantoin-2'-deoxynucleoside-5'- triphosphate

Two convenient synthetic routes to the oxidized guanosine triphosphate lesions spiroiminodihydantoin-2'-deoxynucleoside-5'-triphosphate (dSpTP) and guanidinohydantoin-2'-deoxynucleoside-5'-triphosphate (dGhTP) are reported. Both two-electron oxidation of 2'-deoxy-7,8-dihydro-8-oxoguanosine-5'-triphosphate (dOGTP) using SO4*- generated photolytically from K2S2O8 or four-electron oxidation of 2'-deoxyguanosine-5'-triphosphate (dGTP) from singlet oxygen provide either dSpTP or dGhTP at pH 8.0 or 4.4, respectively. Highly purified triphosphates are obtained by ion pair reversed-phase HPLC.