Gas phase formation of carbon cluster (fullerenes and graphenes)/prebiotic sugar complexes.

Among the constituent molecular classes of proteins and nucleic acids, the presence of Ribose and deoxy-Ribose in space remains unclear. Here, we provide experimental evidence of astronomically related sugar derivatives - carbon cluster (fullerenes and graphenes)/prebiotic sugar complexes - and study their formation processes in the gas phase. The results show that, with PAH cations (dicoronylene, DC, C48H20+)/(2-deoxy-d-Ribose, dR, C5H10O4, and dehydrated 2-deoxy-d-Ribose, DedR, C5H8O3) and fullerene cations (C60+)/(dR and DedR) as the initial molecular precursors, two series of graphene-prebiotic sugar cluster cations (graphene/dR and graphene/DedR, e.g., (dR)Cn+ and (DedR)Cn+) and two series of fullerene-prebiotic sugar cluster cations (fullerene/dR and fullerene/DedR, e.g., (dR)(DedR)2Cn+, (DedR)3Cn+, and (dR)2(DedR)Cn+) are formed through an ion-molecule reaction pathway under the influence of a strong radiation field. The structures of the newly formed complexes and the binding energies of these formation reactions are initially theoretically calculated. These laboratory studies attest to the importance of ion-molecule reaction synthesis routes for the chemical complexity in space, demonstrating that the gas phase interstellar materials could directly lead to the formation of large and complex sugar derivatives in a bottom-up growth process. The chemical evolution in space in which single molecules are transformed into complex molecules produces a wide variety of organic compounds (e.g., carbon cluster (fullerenes and graphenes)/prebiotic sugar complexes). For their astrobiological implications, this opens up aromatic based biogenic chemistry that is available to the parent of PAHs or fullerenes in the interstellar environments.

Prebiotic synthesis of 2-deoxy-d-ribose from interstellar building blocks promoted by amino esters or amino nitriles.

Understanding the prebiotic genesis of 2-deoxy-d-ribose, which forms the backbone of DNA, is of crucial importance to unravelling the origins of life, yet remains open to debate. Here we demonstrate that 20 mol% of proteinogenic amino esters promote the selective formation of 2-deoxy-d-ribose over 2-deoxy-d-threopentose in combined yields of ≥4%. We also demonstrate the first aldol reaction promoted by prebiotically-relevant proteinogenic amino nitriles (20 mol%) for the enantioselective synthesis of d-glyceraldehyde with 6% ee, and its subsequent conversion into 2-deoxy-d-ribose in yields of ≥ 5%. Finally, we explore the combination of these two steps in a one-pot process using 20 mol% of an amino ester or amino nitrile promoter. It is hence demonstrated that three interstellar starting materials, when mixed together with an appropriate promoter, can directly lead to the formation of a mixture of higher carbohydrates, including 2-deoxy-d-ribose.

Practical and Reliable Synthesis of 1,2-Dideoxy-d-ribofuranose and its Application in RNAi Studies.

We developed a practical and reliable method for synthesizing an abasic deoxyribonucleoside, 1,2-dideoxy-d-ribofuranose (dR(H)) via elimination of nucleobase from thymidine. To synthesize oligonucleotides bearing dR(H) by the standard phosphoramidite solid-phase method, dR(H) was converted to the corresponding phosphoramidite derivative and linked to a solid support (controlled pore glass resin). Chemically modified small interfering RNAs (siRNAs) possessing dR(H) at their 3'-overhang regions were synthesized. Introducing dR(H) to the 3'-end of the antisense strand of siRNA reduced its knockdown effect.

Development of 2-Deoxy-2-[(18)F]fluororibose for Positron Emission Tomography Imaging Liver Function in Vivo.

Life-threatening acute liver failure can be triggered by a variety of factors, including common drugs such as acetaminophen. Positron emission tomography (PET) is rarely used to monitor liver function, in part because of a lack of specific imaging agents for liver function. Here we report a new PET probe, 2-deoxy-2-[(18)F]fluororibose ([(18)F]-2-DFR), for use in imaging liver function. [(18)F]-2-DFR was synthesized and validated as a competitive substrate for the ribose salvage pathway. [(18)F]-2-DFR was prepared through an efficient late stage radiofluorination. The desired selectivity of fluorination was achieved using an unorthodox protecting group on the precursor, which could withstand harsh SN2 reaction conditions with no side reactions. [(18)F]-2-DFR accumulated preferentially in the liver and was metabolized by the same enzymes as ribose. [(18)F]-2-DFR could distinguish between healthy liver and liver damaged by acetaminophen. [(18)F]-2-DFR is expected to be a useful PET probe for imaging and quantifying liver functions in vivo, with likely significant clinical utility.

Modular synthesis of 1-α- and 1-ß-(indol-2-yl)-2'-deoxyribose C-nucleosides.

A simple two-step method for the selective preparation of anomerically pure 1α- and 1ß-(indol-2-yl)deoxyribose derivatives was developed. The synthesis was based on the Sonogashira reaction of 1α- and 1ß-ethynyldeoxyribose and 2-haloanilines followed by a Pd-complex catalyzed cyclization to the corresponding indolyldeoxyribosides.

Synthesis and photochemical behavior of the tetrazolo tautomer of 2-azido-4-pyrimidinone-2'-deoxyriboside.

The 2-azido analogue of 2'-deoxyuridine was prepared in three steps from 2'-deoxy-2-thiouridine. The sulfur atom of the 2-thio nucleoside was methylated and then displaced by hydrazine to furnish the corresponding 2-hydrazino derivative. After diazotization, the 2-azido compound that exists as its tetrazolo tautomer was obtained. Upon UV irradiation in aqueous solution, the title compound led to isocytosine.

Thermodynamic potential for the abiotic synthesis of adenine, cytosine, guanine, thymine, uracil, ribose, and deoxyribose in hydrothermal systems.

The thermodynamic potential for the abiotic synthesis of the five common nucleobases (adenine, cytosine, guanine, thymine, and uracil) and two monosaccharides (ribose and deoxyribose) from formaldehyde and hydrogen cyanide has been quantified under temperature, pressure, and bulk composition conditions that are representative of hydrothermal systems. The activities of the precursor molecules (formaldehyde and hydrogen cyanide) required to evaluate the thermodynamics of biomolecule synthesis were computed using the concentrations of aqueous N2, CO, CO2 and H2 reported in the modern Rainbow hydrothermal system. The concentrations of precursor molecules that can be synthesized are strongly dependent on temperature with larger concentrations prevailing at lower temperatures. Similarly, the thermodynamic drive to synthesize nucleobases, ribose and deoxyribose varies considerably as a function of temperature: all of the biomolecules considered in this study are thermodynamically favored to be synthesized throughout the temperature range from 0 degrees C to between 150 degrees C and 250 degrees C, depending on the biomolecule. Furthermore, activity diagrams have been generated to illustrate that activities in the range of 10(-2)- 10(-6) for nucleobases, ribose and deoxyribose can be in equilibrium with a range of precursor molecule activities at 150 degrees C and 500 bars. The results presented here support the notion that hydrothermal systems could have played a fundamental role in the origin of life, and can be used to plan and constrain experimental investigation of the abiotic synthesis of nucleic-acid related biomolecules.

Repair of thymine glycol by hNth1 and hNeil1 is modulated by base pairing and cis-trans epimerization.

Oxidation of thymine yields 5,6-dihydroxy-5,6-dihydrothymine (thymine glycol. Tg) which, as cis 5S,6R and 5R,6S 2'-deoxyribonucleoside diastereoisomers (dTg1, dTg2), are in equilibrium with their trans 5S,6S and 5R,6R epimers. The stereoselective excision of Tg from DNA by the mammalian orthologs of E. coli DNA N-glycosylase/AP lyases Nth and Nei was reported using substrates in which Tg opposed adenine. Since we showed that Tg is the major product of oxidation of 5-methylcytosine, we asked if the opposing purine influenced stereospecific enzymatic excision. The human ortholog hNth1 released Tg2 much more rapidly than Tg1 regardless of the opposing purine. In contrast, hNeil1 released Tg non-stereoselectively, but the rate of excision was much greater when Tg opposed guanine. Remarkably, the kinetics of excision of Tg by hNth1 and hNeil1 were biphasic, describing a double exponential curve which yielded two rate constants. We suggest that the greater rate constant describes the rate of enzymatic excision of Tg. The smaller rate constant represents the equilibrium constant for the cis and trans epimerization of dTg1 and dTg2 in high molecular weight DNA. Thus, only one of the epimers of dTg1 and dTg2 are enzymatically processed but it is not yet known whether it is cis or trans. Thus, base excision repair of Tg in mammals is mediated by at least two DNA N-glycosylase/AP lyases which are affected by the nature of the diastereoisomer of dTg, the rate of cis-trans epimerization of each diastereoisomer, and the nature of the opposing purine.

An extremely stable and orthogonal DNA base pair with a simplified three-carbon backbone.

A nucleotide C3HQ with a minimal three-carbon backbone displays unprecedented pairing strength and orthogonality in a homopair C3HQ:C3HQ in the presence of one equivalent of Cu2+. The pairing stability in DNA even exceeds the related base pair having the regular 2'-deoxyribose backbone. This discovery of a synergy between an artificial backbone and base-pairing scheme opens new avenues for the economical design of modified oligonucleotides with tailored properties.

Nile Red nucleoside: novel nucleoside analog with a fluorophore replacing the DNA base.

A solvatochromic dye is very useful in studies of local polarity and dynamics in biological systems. A novel solvatochromic chromophore, Nile Red beta-C-2'-deoxyriboside, has been synthesized to act as a photophysical probe, and incorporated site-selectively into an oligodeoxynucleotide. The absorption and fluorescence spectra of Nile Red nucleoside showed a remarkable sensitivity to the solvent polarity.

A practical synthesis of L-ribose.

L-Ribose was synthesized by a simple four-step method with overall yield of 76.3% from a protected L-arabinose derivative, which is a compatible intermediate for the synthesis of L-deoxyribose. The key step of this strategy is the Swern oxidation and subsequent stereoselective reduction accompanied by inversion of the 2-hydroxy group of protected L-arabinose.

Efficient synthesis of 2-deoxy-L-erythro-pentose (2-deoxy-L-ribose) from L-arabinose.

An efficient and practical route for the large-scale synthesis of 2-deoxy-L-erythro-pentose (2-deoxy-L-ribose) starting from L-arabinose was developed using Barton-type free-radical deoxygenation reaction as a key step. The radical precursor, a phenoxythiocarbonyl ester, was prepared in situ, and the most efficient deoxygenation was achieved by slow addition of tributyltin hydride to the reaction mixture.

Convenient method for the preparation of 2'-deoxyribosylurea by thymidine oxidation and NMR study of both anomers.

The synthesis of 2'-deoxyribosylurea by thymidine oxidation with potassium permanganate followed by alkaline hydrolysis of intermediates is described. The anomeric configuration of the resulting products was studied by NMR spectroscopy.

Synthesis of an aza analogue of 2-deoxy-D-ribofuranose and its homologues.

Azasugars were obtained in one-pot reactions by catalytic reduction reactions of amino group precursors in aldosugars followed by intramolecular reductive amino alkylation reactions. (3R,4S)-4-[(1S)-1,2-Dihydroxyethyl]pyrrolidin-3-ol was obtained from D-xylose by two different strategies through 3-C-cyano-3-deoxy-D-ribo-pentofuranose or 3-C-azidomethyl-3-deoxy-D-ribo-pentofuranose in 6 and 16% overall yields, respectively. The oxidative cleavage of the diol group in the corresponding Fmoc-azasugar followed by deprotection afforded (3R,4R)-4-(hydroxymethyl)pyrrolidin-3-ol. (3R,4S)-4-[(1S,2R)-1,2,3-Trihydroxypropyl]pyrrolidin-3-ol was synthesized from diacetone-D-glucose through 3-deoxy-3-C-nitromethyl-D-allose and the overall yield was 7%.

Efficient synthesis of 2-deoxy L-ribose from L-arabinose: mechanistic information on the 1,2-acyloxy shift in alkyl radicals.

[formula: see text] Conversion of the inexpensive L-arabinose 1 into the ethylthio ortho ester 7 followed by generation of the dialkoxyalkyl radical III produces the desired 2-deoxy-L-ribose triester 4 in excellent overall yield. It has been shown that the similar dialkoxyalkyl radical IV is not an intermediate in the 1,2-acyloxy shift of anomeric radical I.

An improved route to 1,2-dideoxy-beta-1-phenyl-D-ribofuranose.

An efficient synthesis of the aryl nucleoside analogue 1,2-dideoxy-beta-1-phenyl-D-ribofuranose (1) is described. This route utilizes the addition of phenyllithium to a protected 2-deoxyribonolactone followed by reduction with triethylsilane/boron trifluoride etherate to selectively produce the beta-anomer. Deprotection yields the desired aryl C-nucleoside in 27% overall yield from 2-deoxy-D-ribose.

Non-hydrogen bonding 'terminator' nucleosides increase the 3'-end homogeneity of enzymatic RNA and DNA synthesis.

We report the use of novel non-polar nucleoside analogues as terminators of enzymatic RNA and DNA synthesis. Standard 'runoff' RNA synthesis by T7 RNA polymerase gives RNA products which have ragged ends as a result of transcription which often extends beyond the end of the template DNA strand. Similarly, the Klenow fragment of Escherichia coli DNA polymerase I tends to run past the end of the template strand during DNA synthesis. We report here that certain non-hydrogen-bonding nucleoside analogues, when placed at the downstream 5'-end of a template DNA strand, cause the polymerases to stop more abruptly at the last coding nucleotide. This results in a considerably more homogeneous oligonucleotide being produced. Three novel nucleosides are tested as potential terminators: 4-methylindole beta-deoxynucleoside (M), 1-naphthyl alpha-deoxynucleoside (N) and 1-pyrenyl alpha-deoxynucleoside (P). Comparison is made to an abasic nucleoside (phi) and to unterminated synthesis. Of these, M is found to be the most efficient at terminating transcription, and both P and M are highly effective at terminating DNA synthesis. It is also found that the ability of a nucleoside to stall synthesis when it is internally placed in the template strand is not necessarily a good predictor of terminating ability at the end of a template. Such terminator nucleosides may be useful in the preparative enzymatic synthesis of RNA and DNA, rendering purification simpler and lowering the cost of synthesis by preventing the uptake of potentially costly nucleotides into unwanted products.

Incorporation by chemical synthesis and characterization of deoxyribosylformylamine into DNA.

2-deoxyribosylformylamine is a major oxidative DNA damage type which occurs upon the action of ionizing radiation on DNA. The protected 2-deoxyribosylformylamine phosphoramidite was synthesized and used in conjunction with previously reported alkali labile base protected phosphoramidites ('PAC phosphoramidites') for the preparation of oligodeoxyribonucleotides containing this lesion. Final deprotection of the oligonucleotides was performed under mild alkaline conditions to preserve the integrity of the fragile defect. The presence of formylamino deoxyribosyl residue was confirmed by FAB mass spectrometry sequencing. Oligonucleotides bearing deoxyribosyl formylamine were used as templates for studying in vitro replication. They direct the insertion of guanine or induce a deletion opposite the lesion.