Prebiotic Photochemical Coproduction of Purine Ribo- and Deoxyribonucleosides.

The hypothesis that life on Earth may have started with a heterogeneous nucleic acid genetic system including both RNA and DNA has attracted broad interest. The recent finding that two RNA subunits (cytidine, C, and uridine, U) and two DNA subunits (deoxyadenosine, dA, and deoxyinosine, dI) can be coproduced in the same reaction network, compatible with a consistent geological scenario, supports this theory. However, a prebiotically plausible synthesis of the missing units (purine ribonucleosides and pyrimidine deoxyribonucleosides) in a unified reaction network remains elusive. Herein, we disclose a strictly stereoselective and furanosyl-selective synthesis of purine ribonucleosides (adenosine, A, and inosine, I) and purine deoxynucleosides (dA and dI), alongside one another, via a key photochemical reaction of thioanhydroadenosine with sulfite in alkaline solution (pH 8-10). Mechanistic studies suggest an unexpected recombination of sulfite and nucleoside alkyl radicals underpins the formation of the ribo C2'-O bond. The coproduction of A, I, dA, and dI from a common intermediate, and under conditions likely to have prevailed in at least some primordial locales, is suggestive of the potential coexistence of RNA and DNA building blocks at the dawn of life.

Bisubstrate-Type Chemical Probes Identify GRP94 as a Potential Target of Cytosine-Containing Adenosine Analogs.

We synthesized affinity-based chemical probes of cytosine-adenosine bisubstrate analogs and identified several potential targets by proteomic analysis. The validation of the proteomic analysis identified the chemical probe as a specific inhibitor of glucose-regulated protein 94 (GRP94), a potential drug target for several types of cancers. Therefore, as a result of the use of bisubstrate-type chemical probes and a chemical-biology methodology, this work opens the way to the development of a new family of GRP94 inhibitors that could potentially be of therapeutic interest.

Effect of Pulsed Light Irradiation on Bioactive, Nonvolatile Components and Antioxidant Properties of Caterpillar Medicinal Mushroom Cordyceps militaris (Ascomycetes).

The caterpillar medicinal mushroom Cordyceps militaris contains many bioactive components, such as adenosine, cordycepin, and polysaccharides. In this study, C. militaris was exposed to 0, 3, 6, or 9 pulses of light irradiation to estimate changes in vitamin D2, bioactive compounds, nonvolatile taste components, and antioxidant properties. In addition, we compared the components and properties of C. militaris mycelia and solid waste medium that had been treated with pulsed light (PL) irradiation. Overall, PL irradiation of C. militaris increased the vitamin D2 content and increased the total amino acid levels 9-48%; the antioxidant properties of the mycelia treated with 0 pulses and of the solid waste medium treated with 3 pulses all exhibited lower half-maximal effective concentrations. Therefore, PL irradiation affected the amounts of bioactive compounds, but the irradiated samples still contained intense umami taste and a sufficient amount of antioxidant components.

Identification of the major degradation pathways of ticagrelor.

Ticagrelor is a direct-acting and reversible P2Y12-adenosine diphosphate (ADP) receptor blocker used as antiplatelet drug. Forced degradation under various stress conditions was carried out. The degradation products have been detected and identified by high-pressure liquid chromatography multistage mass spectrometry (LC-MS(n)) along with high-resolution mass spectrometry. C18 XTerra MS column combined with a linear gradient mobile phase composed of a mixture of 10 mM acetate ammonium/acetonitrile was shown suitable for drug and impurity determinations and validated as a stability indicating method. Structural elucidation of the degradation products relied on MS(n) studies and accurate mass measurements giving access to elemental compositions. Up to nine degradation products resulting from oxidation/auto-oxidation, S-dealkylation and N-dealkylation have been identified, covering a range of possible degradation pathways for derivatives with such functional groups. Kinetics was also studied in order to assess the molecule's shelf-life and to identify the most important degradation factors.

Properties and reactivity of the adenosine radical generated by radiation-induced oxidation in aqueous solution.

The formation of oxidation products of DNA bases induced by hole injection into DNA duplexes is closely related to the characteristics of the radical species generated, especially those from purine bases possessing lower oxidation potentials than pyrimidines. To investigate the reactivities of adenosine base radicals generated from the radical cations of adenosine (Ado), we have conducted extensive pulse radiolysis and steady-state X-radiolysis investigations of Ado under the conditions generating oxidizing radical species such as the sulfate radical anion (SO(4)(-*)). Kinetic analysis of the transient absorption spectra demonstrated that the redox-neutral radical of adenosine [Ado(-H)(*)] decays via a homogeneous bimolecular reaction, recombines with an alkyl alcohol radical, or abstracts hydrogen from the phosphate ion, with rate constants of 2k = 4.2 x 10(8) M(-1) s(-1) and k = 6.4-8.5 x 10(8) and 10(3)-10(4) M(-1) s(-1), respectively. High-dose pulsed electron beam irradiation, which generates high concentrations of Ado(-H)(*) during the radiolysis, yielded 8-oxo-7,8-dihydroadenosine (8-oxo-Ado) with a G value of 0.018 x 10(-7) mol J(-1). It is thus proposed that the disproportionation of Ado(-H)(*) might lead to the formation of 8-oxo-Ado as a minor process, which is in addition to the widely accepted mechanism in which the addition of hydroxyl radical to Ado initiates its formation.

Photodynamic antisense regulation of mRNA having a point mutation with psoralen-conjugated oligonucleotide.

Nucleic acid-based drugs, such as antisense oligonucleotide, ribozyme, and small interfering RNA, are specific compounds that inhibit gene expression at the post-transcriptional level. To develop more effective nucleic acid-based drugs, we focused on photo-reactive antisense oligonucleotides. We have optimized the structure of psoralen-conjugated oligonucleotide to improve their sequence selectivity and photo-crosslinking efficiency. Previously, we reported that photo reactive oligonucleotides containing 2'-O-psoralenyl-methoxyethyl adenosine (2'-Ps-eom) showed drastic photo-reactivity with a strictly sequence specific manner in vitro. In this report, we evaluated the binding ability toward intracellular target mRNA. The 2'-Ps-eom selectively photo-cross-linked to the target mRNA extracted from cells. The 2'-Ps-eom also cross-linked to target mRNA in cells. Furthermore, 2'-Ps-eom did not cross-link to mRNA having a mismatch base. These results suggest that 2'-Ps-eom is a powerful antisense molecule to inhibit the expression of mRNA having a point mutation.

Properties of novel antisense oligonucleotides containing 2'-O-modified adenosine with a photo-reactive group.

In order to enhance the efficiency of antisense molecules for target RNA regulation, a novel photo-reactive antisense oligonucleotide was developed. We designed and synthesized a photo-reactive antisense oligonucleotide containing an adenosine in which 2'-OH was modified with 4,5',8-trimethylpsoralen (Ps) via an ethoxymethylene linkage (2'-Ps-eom). We evaluated the photo-cross-linking efficiency and sequence specificity toward complementary RNA (match-RNA). 2'-Ps-eom was selectively photo-cross-linked to the match-RNA. The photo-cross-linking efficiency was about 75% upon UVA-irradiation (365 nm) for 10 min. Previously, we reported oligonucleotides that had an adenosine anchoring Ps at 2'-O-position via a methylene linkage (2'-Ps-met). The photo-cross-linking efficiency of 2'-Ps-met and match-RNA was about 35% upon UVA-irradiation for 120 min. The photo-cross-linking efficiency of 2'-Ps-eom was dramatically enhanced in comparison with the one of 2'-Ps-met.

Characterization of the reactive intermediates in laser flash photolysis of adenine, adenosine and dAMP using acetone as photosensitizer.

Transient absorption spectra of adenine, adenosine and 2'-deoxyadenosine 5'-monophosphate (dAMP) arising from 248 nm laser flash photolysis using acetone as a photosensitizer have been observed. The intermediates recorded are assigned to the excited triplet states and dehydrogenated radicals of adenine and its nucleoside and nucleotide. The excited triplet states of adenine and its derivatives are produced via triplet-triplet excitation transfer and observed for the first time, while the dehydrogenated radicals stemming from the interaction of triplet acetone with adenine and its derivatives via electron transfer through a five-member-ring electron donor-acceptor intermediate. The site of dehydrogenation is suggested to be the hydrogen atom on C(8) of the adenine moiety. Moreover, three sets of kinetic parameters of the triplet decay have been determined. The rate constants of the unimolecular decay (k0), the triplet quenching by the ground state (ksq) and by the triplet quencher Mn2+ (kq) are 1.1 x 10(5), 7.9 x 10(4), 3.7 x 10(4) s-1, 6.9 x 10(8), 8.3 x 10(8), 3.6 x 10(8) dm3 mol-1 s-1 and 4.2 x 10(8), 3.5 x 10(8), 6.0 x 10(8) dm3 mol-1 s-1 respectively for adenine, adenosine and dAMP.

Adenosine-mediated photoreaction of 4,5',8-trimethylpsoralen with alcohols.

Irradiation of thin films consisting of 4,5',8-trimethylpsoralen (TMP), adenosine and small amounts of alcohols led to TMP-alcohol photoadducts in addition to TMP-adenosine photoadducts. Four TMP-ethanol and two TMP-methanol adducts have been separated and characterized. Covalent bonds were formed between the 4-carbon of TMP and the alpha-carbon to the hydroxy group in the alcohols. The TMP-alcohol photoadducts were formed only in the TMP film containing small amounts of alcohol and adenosine. Furthermore, no photoadduct of TMP and ribose was detected upon photolysis of a TMP-ribose film, suggesting that the adenine moiety plays a specific role in the reaction. The interaction of adenosine with psoralens in a dry film may be related to the DNA sequence selectivity observed for the photoreaction of psoralens with DNA.

[The role of ultraviolet and gamma radiation in the abiogenic synthesis of nucleotides in the solid state]. / Rol' UF- i gamma-radiatsii v abiogennom sinteze nukleotidov v tverdom sostoianii.

A possibility of abiogenic synthesis of natural nucleotides in solid state under the influence of UV and gamma radiation has been shown for a mixture of nucleosides and dihydrophosphate. Adenosine and deoxyadenosine were used as initial substances. During adenosine and deoxyadenosine phosphorylation under the action of UV radiation (lambda = 254 nm), only 5'-monophosphates were formed, a yield of 0.094 and 0.36% respectively. Under the action of gamma radiation, 2',3'-cAMP (0.12%), 2'-AMP (0.08%) and 3'-AMP (0.14%) were produced together with 5'AMP (0.41%).

Free radicals from polycrystalline pyrimidines and purines upon heavy ion bombardment at low temperatures: an electron spin resonance study.

The formation of free radicals in polycrystalline samples of the DNA constituents thymine, cytosine, and adenosine after bombardment with heavy ions at about 100 K was investigated by electron spin resonance (ESR) spectroscopy. Spectra were observed at 77 K after irradiation at 100 K, upon annealing to 300 K and after storage at 300 K. Individual radical patterns were isolated from the spectra by computer manipulation and assigned to structures by powder-simulations based on literature data. The spectra of thymine contain an allyl radical, the octet pattern of the 5-thymyl radical and contributions of the 6-yl radical formed by net hydrogen gain at carbon C5. The latter species is also present in cytosine which in addition displays the pattern due to H-addition at the carboxyl oxygen C2. Adenosine exhibits two H-addition radicals, one at C2, the other at C8. Additionally, the spectra of all DNA subunits studied contain as a radical component a Gaussian singlet of about 0.9 mT line width. The spectra obtained at low temperature already contain the secondary radicals but exhibit a large linewidth. This feature is attributed to dipolar coupling caused by radicals in close proximity.

Ionization of adenine derivatives: EPR and ENDOR studies of X-irradiated adenine.HCl.1/2H2O and adenosine.HCl.

Following X irradiation of adenine.HCl.H2O at 10 K, evidence for five distinct radical products was present in the EPR/ENDOR. (In both adenine.HCl.1/2H2O and adenosine.HCl, the adenine base is present in a cationic form as it is protonated at N1). From ENDOR data, radical R1, stable at temperatures up to 250 K, was identified as the product of net hydrogen loss from N1. This product, evidently formed by electron loss followed by proton loss, is equivalent to the radical cation of the neutral adenine base. Radical R2, unstable at temperatures above 60 K, was identified as the product of net hydrogen addition to N3, and evidently formed by electron addition followed by proton addition. Radicals R3-R5 could not be identified with certainty. Similar treatment of adenosine.HCl provided evidence for six identifiable radical products. Radical R6, stable to ca. 150 K, was identified as the result of net hydrogen loss from the amino group, and evidently was the product of electron loss followed by proton loss. Radical R7 was tentatively identified as the product of net hydrogen addition to C4 of the adenine base. Radical R8 was found to be the product of net hydrogen addition to C2 of the adenine base, and R9 was the product of net hydrogen addition to C8. Radical R10 was identified as the product of net hydrogen abstraction from C1' of the ribose, and R11 was an alkoxy radical formed from the ribose. With the exception of R11, all products were also found following irradiation at 65 K. Only radical R8 and R9 were stable at room temperature. Most notable is the different deprotonation behavior of the primary electron-loss products (radical R1 vs. R6) and the different protonation behavior of the primary electron-gain products (radical R2 vs. no similar product in adenosine.HCl). The major structural difference in the two crystals is the electrostatic environment of the adenine base. Therefore, this study provides further evidence that environmental influences are important in determining proton transfer processes.

Enhancement of radiation-induced base release from nucleosides in alkaline solution: essential role of the O.- radical.

The effect of pH on base release in the gamma-radiolysis of N2O-saturated solutions of a number of nucleosides (including uridine, 3-methyluridine, 2',3'-O-isopropylidene-uridine, and adenosine) has been investigated. For all these nucleotides, independent of the base or sugar moiety, base release is very low at pH below 10 (G approximately (0.3-0.7) x 10(-7) mol J-1), but increases drastically to G approximately (3-4) x 10(-7) mol J-1 at pH greater than or equal to 13. This phenomenon had already been previously reported and attributed to an OH(-)-induced transfer of a base radical into a sugar radical. However, it is now shown that at pH 12, where base release starts to increase, a lowering of the dose-rate does not affect the yield of free base. The increase in base release is accompanied by an overall reduction of chromophore loss of similar magnitude (with 2',3'-O-isopropylidene-uridine and 3-methyluridine), as well as by an increase in the yield of oxidizing radicals by a factor of 2 (with uridine). The measured rate constant of the reaction of .OH/O.- with the nucleosides is also pH-dependent, as .OH reacts faster than O.- with the nucleosides by a factor of 6-7. It is concluded that the increase in base release at high pH is caused by the increasing participation of O.-, which, unlike .OH, attacks the nucleosides preferentially at their sugar moieties, and is not due to an OH(-)-induced radical transfer from the base to the sugar moiety.

A novel photoadduct of 4,5',8-trimethylpsoralen and adenosine.

A novel photoadduct of 4,5',8-trimethylpsoralen (TMP) and adenosine was isolated and purified by reverse-phase liquid chromatography. The structure of the photoproduct was determined by various spectral methods and found to be a TMP-adenosine 1:1 adduct resulting from the covalent bond formation between the carbon C(4) of TMP and ribose 4'-carbon of adenosine.

Direct radiation action of heavy ions on DNA as studied by ESR-spectroscopy.

The effects of heavy ions on the mechanisms of free radical formation in DNA-constituents as compared to low-LET irradiation are investigated by means of Electron Spin Resonance (ESR) spectroscopy. Dose-yield curves were measured at low (T < 100 K) and ambient temperatures in order to obtain the G-value, that is number of radicals formed per 100 eV absorbed energy. These G-values show a characteristic LET-dependence and are one to two orders of magnitude lower than for low-LET irradiation. Measurements on 2'Deoxycytidine at 300 K using combined heavy ion and X-ray irradiation methods suggested that this effect can be partially explained by a destruction of radicals during the irradiation.

The degree of ultraviolet light damage to DNA containing iododeoxyuridine or bromodeoxyuridine is dependent on the DNA sequence.

The sequence selectivity of 300 nm ultraviolet light damage to DNA containing bromodeoxyuridine or iododeoxyuridine was examined on DNA sequencing gels. This was accomplished using a system where an M13 template was employed to direct synthesis of DNA in which thymidine was fully substituted with bromodeoxyuridine or iododeoxyuridine. The sites of damage corresponded to the positions of analogue incorporation. The extent of damage varied considerably at different sites of cleavage and ranged from the undetectable to over fifteen times the limit of detection (as assessed by laser densitometer scans). Strong damage sites had the "consensus" sequence CTT while sites of no detectable damage had the "consensus" sequence GTR. Bromodeoxyuridine and iododeoxyuridine had the same sites of damage although the extent of damage varied at different sites and bromodeoxyuridine damage was slightly greater than iododeoxyuridine. DNA containing thymidine was not damaged to any detectable level in this system with 300 nm ultraviolet light. The use of three closely related DNA sequences as targets for damage confirmed that (1) the sites of analogue incorporation are the cause of ultraviolet damage; and (2) that the neighbouring DNA sequence is an important parameter in determining the extent of damage. It is proposed that the microstructure of DNA--in particular the distance between the 5-carbon of the pyrimidine base (which is attached to the halogen) and hydrogen on the 2' carbon of the 5'-deoxyribose--ultimately determines the degree of cleavage with large distances giving a small degree of damage and smaller distances a large degree of damage.

ESR and ENDOR study of adenosine single crystals X-irradiated at 10 K.

Single crystals of adenosine were X-irradiated at 10 K and investigated between 10 and 300 K using K-band ESR and ENDOR spectroscopy. Two free radicals were analyzed. Radical I exhibits small hyperfine couplings to the C8-H, C2-H, and a N3-H protons, and was identified as the N3 protonated base anion radical. Radical II exhibits small hyperfine couplings to a C8-H and an exocyclic -N10-H proton. It is suggested that this is therefore the N10 deprotonated base cation radical. Enough data were not available to analyze a third primary radical believed to be located on the ribose moiety. Upon warming Radical I decays at ca. 40 K with no apparent successor. Likewise, no successor was identified for Radical II, which decays at ca. 100 K. At ca. 200 K there is ESR evidence for the C2 and C8 H-addition radicals. Their precursors have not been identified.

Heavy-ion-induced free radical formation in solid DNA-constituents: quantitative and structural aspects.

Electron spin resonance (ESR) spectroscopy was used to study free radical formation in solid, polycrystalline pellets of DNA-constituents. Dose-yield curves were obtained at low (ca 90 K) and ambient temperatures, and were analyzed for initial G-values (radicals per 100 eV absorbed energy). At both temperatures, values of one or more orders of magnitude below the corresponding x-ray values were found. Combination of x-ray and heavy-ion irradiation indicated an enhanced radical destruction as probable cause of reduced G-values. Structural aspects as analyzed from the ESR-powder spectra revealed differences in initial, low-temperature radical population and in decay reactions upon annealing between heavy-ion bombardment and low-LET irradiation.