Young formation age of a mantle plume source

Controlling DNA Fragmentation in MALDI-MS by Chemical Modification

Fragmentation has proven to be a major factor limiting accessible mass range, sensitivity, and mass resolution in the analysis of DNA by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Previous work has shown that this DNA fragmentation is strongly dependent on both the MALDI matrix and the nucleic acid sequence employed. Fragmentation is initiated by nucleobase protonation, leading to cleavage of the N-glycosidic bond with base loss, followed by cleavage of the phosphodiester backbone. In this study, asymmetric oligonucleotides incorporating cytidine and cytidine analogs such as 5-methyl-2'-deoxycytidine, 5-bromo-2'-deoxycytidine, aracytidine, and 2'-fluorodeoxycytidine nucleosides were used to systematically investigate the influence of the structural changes on the stability of the N-glycosidic bond. Modifications of the deoxyribose sugar ring by replacing the 2'-hydrogen with more electron-withdrawing groups such as the hydroxyl or fluoro group stabilize the N-glycosidic bond to a greater extent than the C5 nucleobase modifications. 2'-Hydroxyl and 2'-fluoro groups respectively are shown to partially or completely block fragmentation at the modified nucleosides. Mixtures of oligonucleotides incorporating such modifications demonstrate remarkably extended accessible mass range, as well as increased sensitivity and mass resolution. The stabilization provided by these chemical modifications also expands the range of matrices useful for nucleic acid analysis, yielding in some cases greatly improved performance.

Synthesis and analysis of oligonucleotides containing abasic site analogues

DNA damage results in the formation of abasic sites from the formal hydrolysis of the glycosidic bond (AP) and several oxidized abasic lesions. Previous studies on AP sites revealed that DNA polymerases preferentially incorporated dA opposite them in approximately 80% of the replication events in Escherichia coli. These results were consistent with the hypothesis that the AP sites are noninstructive lesions due to the absence of a Watson-Crick base whose bypass adheres to the "A-rule." Recent replication studies of the oxidized abasic lesion, 2-deoxyribonolactone (L), revealed that DNA polymerase(s) does not apply the A-rule when bypassing it and incorporates large amounts of dG opposite L. These studies suggested that abasic sites such as L do direct polymerases to selectively incorporate nucleotides opposite them. However, it was not possible to determine the structural basis for this molecular recognition from these experiments. A group of oligonucleotides containing analogues of the AP and L lesions were synthesized and characterized as probes to gain insight into the structural basis for the distinct effect of 2-deoxyribonolactone on replication. These molecules will be useful tools for studying replication in cells and in vitro.

Characteristic structure and environment in FAD cofactor of (6-4) photolyase along function revealed by resonance Raman spectroscopy

A pyrimidine-pyrimidone (6-4) photoproduct and a cyclobutane pyrimidine dimer (CPD) are major DNA lesions induced by ultraviolet irradiation, and (6-4) photolyase, an enzyme with flavin adenine dinucleotide (FAD) as a cofactor, repairs the former specifically by light illumination. We investigated resonance Raman spectra of (6-4) photolyase from Arabidopsis thaliana having neutral semiquinoid and oxidized forms of FAD, which were selectively intensity enhanced by excitations at 568.2 and 488.0 nm, respectively. DFT calculations were carried out for the first time on the neutral semiquinone. The marker band of a neutral semiquinone at 1606 cm(-1) in H(2)O, whose frequency is the lowest among various flavoenzymes, apparently splits into two comparable bands at 1594 and 1608 cm(-1) in D(2)O, and similarly, that at 1522 cm(-1) in H(2)O does into three bands at 1456, 1508, and 1536 cm(-1) in D(2)O. This D(2)O effect was recognized only after being oxidized once and photoreduced to form a semiquinone again, but not by simple H/D exchange of solvent. Some Raman bands of the oxidized form were observed at significantly low frequencies (1621, 1576 cm(-1)) and with band splittings (1508/1493, 1346/1320 cm(-1)). These Raman spectral characteristics indicate strong H-bonding interactions (at N5-H, N1), a fairly hydrophobic environment, and an electron-lacking feature in benzene ring of the FAD cofactor, which seems to specifically control the reactivity of (6-4) photolyase.

Acidity and Proton Affinity of Hypoxanthine in the Gas Phase versus in Solution: Intrinsic Reactivity and Biological Implications

Hypoxanthine is a mutagenic purine base that most commonly arises from the oxidative deamination of adenine. Damaged bases such as hypoxanthine are associated with carcinogenesis and cell death. This inevitable damage is counteracted by glycosylase enzymes, which cleave damaged bases from DNA. Alkyladenine DNA glycosylase (AAG) is the enzyme responsible for excising hypoxanthine from DNA in humans. In an effort to understand the intrinsic properties of hypoxanthine, we examined the gas-phase acidity and proton affinity using quantum mechanical calculations and gas-phase mass spectrometric experimental methods. In this work, we establish that the most acidic site of hypoxanthine has a gas-phase acidity of 332 +/- 2 kcal mol-1, which is more acidic than hydrochloric acid. We also bracket a less acidic site of hypoxanthine at 368 +/- 3 kcal mol-1. We measure the proton affinity of the most basic site of hypoxanthine to be 222 +/- 3 kcal mol-1. DFT calculations of these values are consistent with the experimental data. We also use calculations to compare the acidic and basic properties of hypoxanthine with those of the normal bases adenine and guanine. We find that the N9-H of hypoxanthine is more acidic than that of adenine and guanine, pointing to a way that AAG could discriminate damaged bases from normal bases. We hypothesize that AAG may cleave certain damaged nucleobases as anions and that the active site may take advantage of a nonpolar environment to favor deprotonated hypoxanthine as a leaving group versus deprotonated adenine or guanine. We also show that an alternate mechanism involving preprotonation of hypoxanthine is energetically less attractive, because the proton affinity of hypoxanthine is less than that of adenine and guanine. Last, we compare the acidity in the gas phase versus that in solution and find that a nonpolar environment enhances the differences in acidity among hypoxanthine, adenine, and guanine.

One-electron photooxidation and site-selective strand cleavage at 5-methylcytosine in DNA by sensitization with 2-methyl-1,4-naphthoquinone-tethered oligonucleotides

Photosensitized one-electron oxidation was applied to discriminate a specific base site of 5-methylcytosine (mC) generated in DNA possessing a partial sequence of naturally occurring p53 gene, using a sensitizing 2-methyl-1,4-naphthoquinone (NQ) chromophore tethered to an interior of oligodeoxynucleotide (ODN) strands. Photoirradiation and subsequent hot piperidine treatment of the duplex consisting of mC-containing DNA and NQ-tethered complementary ODN led to oxidative strand cleavage selectively at the mC site, when the NQ chromophore was arranged so as to be in close contact with the target mC. The target mC is most likely to be one-electron oxidized into the radical cation intermediate by the sensitization of NQ. The resulting mC radical cation may undergo rapid deprotonation and subsequent addition of molecular oxygen, thereby leading to its degradation followed by strand cleavage at the target mC site. In contrast to mC-containing ODN, ODN analogs with replacement of normal cytosine, thymine, adenine, or guanine at the mC site underwent less amount of such an oxidative strand cleavage at the target base site, presumably due to occurrence of charge transfer and charge recombination processes between the base radical cation and the NQ radical anion. Furthermore, well designed incorporation of the NQ chromophore into an interior of ODN could suppress a competitive strand cleavage at consecutive guanines, which occurred as a result of positive charge transfer. Thus, photosensitization by an NQ-tethered ODN led to one-electron oxidative strand cleavage exclusively at the target mC site, providing a convenient method of discriminating mC in naturally occurring DNA such as human p53 gene as a positive band on a sequencing gel.

Specificity of human thymine DNA glycosylase depends on N-glycosidic bond stability

Initiating the DNA base excision repair pathway, DNA glycosylases find and hydrolytically excise damaged bases from DNA. While some DNA glycosylases exhibit narrow specificity, others remove multiple forms of damage. Human thymine DNA glycosylase (hTDG) cleaves thymine from mutagenic G.T mispairs, recognizes many additional lesions, and has a strong preference for nucleobases paired with guanine rather than adenine. Yet, hTDG avoids cytosine, despite the million-fold excess of normal G.C pairs over G.T mispairs. The mechanism of this remarkable and essential specificity has remained obscure. Here, we examine the possibility that hTDG specificity depends on the stability of the scissile base-sugar bond by determining the maximal activity (k(max)) against a series of nucleobases with varying leaving-group ability. We find that hTDG removes 5-fluorouracil 78-fold faster than uracil, and 5-chlorouracil, 572-fold faster than thymine, differences that can be attributed predominantly to leaving-group ability. Moreover, hTDG readily excises cytosine analogues with improved leaving ability, including 5-fluorocytosine, 5-bromocytosine, and 5-hydroxycytosine, indicating that cytosine has access to the active site. A plot of log(k(max)) versus leaving-group pK(a) reveals a Brønsted-type linear free energy relationship with a large negative slope of beta(lg) = -1.6 +/- 0.2, consistent with a highly dissociative reaction mechanism. Further, we find that the hydrophobic active site of hTDG contributes to its specificity by enhancing the inherent differences in substrate reactivity. Thus, hTDG specificity depends on N-glycosidic bond stability, and the discrimination against cytosine is due largely to its very poor leaving ability rather than its exclusion from the active site.

Base pairing and replicative processing of the formamidopyrimidine-dG DNA lesion

The 2,6-diamino-4-hydroxy-5-formamidopyrimidine of 2'-deoxyguanosine (FaPydG) is one of the major DNA lesions found after oxidative stress in cells. To clarify the base pairing and coding potential of this major DNA lesion with the aim to estimate its mutagenic effect, we prepared oligonucleotides containing a cyclopentane based analogue of the DNA lesion (cFaPydG). In addition, oligonucleotides containing the cyclopentane analogue of 2'-deoxyguanosine (cdG), and oligonucleotides containing 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) were synthesized. The thermodynamic stability of duplexes containing these building blocks and all canonical counterbases were determined by concentration dependent melting-point measurements (van't Hoff plots). The data reveal that cFaPydG greatly destabilizes a DNA duplex (DeltaDeltaG degrees (298K) approximately 2-4 kcal mol(-1)). The optimal base pairing partner for the cFaPydG lesion is dC. Investigation of duplexes containing dG and cdG shows that the effect of substituting the deoxyribose by a cyclopentane moiety is marginal. The data also provide strong evidence that the FaPydG lesion is unable to form a base pair with dA. Our computational studies indicate that the syn-conformation required for base pairing with dA is energetically unfavorable. This is in contrast to 8-oxodG for which the syn-conformation represents the energetic minimum. Kinetic primer extension studies using S. cerevisiae Pol eta reveal that cFaPydG is replicated in an error-free fashion. dC is inserted 2-3 orders of magnitude more efficiently than dT or dA, showing that FaPydG is a lesion which retains the coding potential of dG. This is also in contrast to 8-oxodG, for which base pairing with dC and dA was established.

Hydrophobicity, shape, and pi-electron contributions during translesion DNA synthesis

Translesion DNA synthesis, the ability of a DNA polymerase to misinsert a nucleotide opposite a damaged DNA template, represents a common route toward mutagenesis and possibly disease development. To further define the mechanism of this promutagenic process, we synthesized and tested the enzymatic incorporation of two isosteric 5-substituted indolyl-2'deoxyriboside triphosphates opposite an abasic site. The catalytic efficiency for the incorporation of the 5-cyclohexene-indole derivative opposite an abasic site is 75-fold greater than that for the 5-cyclohexyl-indole derivative. The higher efficiency reflects a substantial increase in the k(pol) value (compare 25 versus 0.5 s(-1), respectively) as opposed to an influence on ground-state binding of either non-natural nucleotide. The faster k(pol) value for the 5-cyclohexene-indole derivative indicates that pi-electron density enhances the rate of the enzymatic conformational change step required for insertion opposite the abasic site. However, the kinetic dissociation constants for the non-natural nucleotides are identical and indicate that pi-electron density does not directly influence ground-state binding opposite the DNA lesion. Surprisingly, each non-natural nucleotide can be incorporated opposite natural templating bases, albeit with a greatly reduced catalytic efficiency. In this instance, the lower catalytic efficiency is caused by a substantial decrease in the k(pol) value rather than perturbations in ground-state binding. Collectively, these data indicate that the rate of the conformational change during translesion DNA synthesis depends on pi-electron density, while the enhancement in ground-state binding appears related to the size and shape of the non-natural nucleotide.

Formation of Intrastrand Cross-Link Products between Cytosine and Adenine from UV Irradiation of d(BrCA) and Duplex DNA Containing a 5-Bromocytosine

Here, we showed that Pyrex-filtered UV light irradiation of d((Br)CA) gave rise to three types of intrastrand cross-link products, that is, d(C[5-N6]A), d(C[5-2]A), and d(C[5-8]A), where the C5 carbon atom of cytosine is covalently bonded to the N6 nitrogen atom, C2, and C8 carbon atoms of adenine, respectively. Furthermore, we demonstrated by LC-MS/MS that the UV irradiation of a 5-bromocytosine-containing duplex oligodeoxynucleotide (ODN) led to the formation of five cross-link products, that is, C[5-N6]A, C[5-2]A, C[5-8]A, A[2-5]C, and A[8-5]C, under both aerobic and anaerobic conditions. LC-MS/MS quantification results showed that the yields for the formation of these cross-link products are different. The presence of molecular oxygen reduces the yields for the formation of all cross-link products except A[2-5]C. To our knowledge, this is the first report about the formation of intrastrand cross-link products between cytosine and adenine in duplex DNA. The chemistry discovered here may facilitate the future preparations of oxidative cross-link lesion-bearing substrates for biochemical and biophysical studies.

Selective detection of 2-deoxyribonolactone in DNA

2-Deoxyribonolactone (L) is an oxidized abasic lesion that is produced by a variety of DNA damaging agents. It exhibits unique biological effects with respect to its proclivity to form DNA-protein cross-links and promutagenic base pairs. Recent evidence suggests that the levels of this lesion caused by oxidative stress are underestimated. We have developed a simple, selective method for detecting subpicomole amounts of L in DNA. The method takes advantage of the selective reaction of the butenolide (2) derived from beta-elimination from L with a biotinylated derivative of cysteine. This method will be useful for analyzing the levels of this oxidized abasic site in DNA.

Independent generation and characterization of a C2'-oxidized abasic site in chemically synthesized oligonucleotides

Abasic lesions, which are formed endogenously and as a consequence of exogenous agents, are lethal and mutagenic. Hydrogen atom abstraction from C2' in DNA under aerobic conditions produces an oxidized abasic lesion (C2-AP), along with other forms of DNA damage. The effects of C2-AP on DNA structure and function are not well understood. A method for the solid-phase synthesis of oligonucleotides containing C2-AP lesions is reported. The lesion is released via periodate oxidation of a triol containing a vicinal diol. The triol is introduced via a phosphoramidite that is compatible with standard oligonucleotide synthesis and deprotection conditions. UV-melting studies indicate that the C2-AP lesion has a comparable effect on the thermal stability of duplex DNA as other abasic lesions. The C2-AP lesion is rapidly cleaved by piperidine at 90 degrees C. However, cleavage by NaOH (0.1 M, 37 degrees C) shows that C2-AP is considerably less labile (t(1/2) = 3.3 +/- 0.2 h) than other abasic lesions.

Mass spectrometric analysis of DNA mixtures: instrumental effects responsible for decreased sensitivity with increasing mass

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry has demonstrated great potential to replace gel electrophoresis for DNA sequence analysis. A current limitation in this method is, however, the decreased sensitivity with increasing mass of DNA molecules. In the present study, instrumental effects on the mass analysis of DNA molecules were investigated quantitatively using an equimolar DNA mixture. It is shown that detection efficiency, detector saturation, and ion beam divergence account for the entirety of the observed falloff in signal intensity with increasing mass. Although the present study focused upon the analysis of DNA mixtures, the instrumental effects observed apply equally to other macromolecular mixtures (e.g., proteins, polymers).

Probing the Requirements for Recognition and Catalysis in Fpg and MutY with Nonpolar Adenine Isosteres

The Escherichia coli DNA repair enzymes Fpg and MutY are involved in the prevention of mutations resulting from 7,8-dihydro-8-oxo-2'-deoxyguanosine (OG) in DNA. The nonpolar isosteres of 2'-deoxyadenosine, 4-methylbenzimidazole beta-deoxynucleoside (B), and 9-methyl-1H-imidazo[4,5-b]pyridine beta-deoxynucleoside (Q), were used to examine the importance of hydrogen bonding within the context of DNA repair. Specifically, the rate of base removal under single-turnover conditions by the MutY and Fpg glycosylases from duplexes containing OG:B and OG:Q mismatches, relative to OG:A mismatches, was evalulated. The reaction of Fpg revealed a 5- and 10-fold increase in rate of removal of OG from duplexes containing OG:B and OG:Q base pairs, respectively, relative to an OG:A mispair. These results suggest that the lack of the ability to hydrogen bond to the opposite base facilitates removal of OG. In contrast, adenine removal catalyzed by MutY was much more efficient from an OG:A mispair-containing duplex (k2 = 12 +/- 2 min(-1)) compared to the removal of B from an OG:B duplex (k(obs) < 0.002 min(-1)). Surprisingly, MutY was able to catalyze base removal from the OG:Q-containing substrate (k2 = 1.2 +/- 0.2 min(-1)). Importantly, the B and Q analogues are not deleterious to high-affinity DNA binding by MutY. In addition, the B and Q analogues are more susceptible to acid-catalyzed depurination illustrating that the enzyme-catalyzed mechanism is distinct from the nonenzymatic mechanism. Taken together, these results point to the importance of both N7 and N3 in the mechanism of adenine excision catalyzed by MutY.

Oscillating formation of 8-oxoguanine during DNA oxidation

Oxidation of free guanine and guanine in salmon testes ds-DNA by hydroxyl radicals generated with Fenton reagent resulted in oscillating 8-oxoguanine concentrations. These oscillations were superimposed on a general trend of decreasing ratio of [8-oxoguanine]/{[8-oxoguanine] + [guanine]} with time, suggesting that a steady state 8-oxoguanine concentration would not be achieved. Mass spectrometry detected 8-oxoguanine and 5-guanidinohydantoin as products, suggesting that the latter was the product of oxidation of 8-oxoguanine. Guanidinohydantoin and other possible intermediates and products may be involved in a complex mechanism leading to the observed behavior. Oscillatory fluctuations in 8-oxoguanine may need to be considered in assessing its clinical significance as a biomarker for oxidative DNA damage.

The genetic secrets some fossils hold

Most animals that once lived have gone extinct. The remains of a few of these can be found in museum collections worldwide. As modern evolutionary biology is limited to the use of extant taxa, retrieving DNA from extinct or subfossil organisms can add significant insight into past population history and resolve phylogenies that can be tentative by morphology alone. DNA is a relatively weak molecule, comparatively speaking, yet under certain conditions it persists in the fossil record, despite what in vitro chemistry predicts. While most fossil remains do not contain DNA, museum specimens can be screened for the presence of conditions that would be conducive for nucleic acid preservation by measuring the extent of amino acid racemization and by looking at the extent of protein hydrolysis by pyrolysis gas chromatography/mass spectrometry. Results from these types of analyses suggest that the preservation of DNA is linked to the temperature and its constancy at a site rather than its age. Chemical analyses of coprolites from extinct herbivores from the late Pleistocene, as well as Archaic Native Americans, show the presence of compounds from the Maillard reaction. Upon the cleaving of these products, the defecator can be identified and his diet analyzed.

Theoretical study on the stability of N-glycosyl bonds: why does N7-platination not promote depurination?

The depurination reaction of guanosine, protonated or modified with cisplatin at the N7 position, has been studied by density functional theory (DFT), coupled with a continuum treatment of solvation. Protonation accelerates the depurination reaction whereas N7-platination, the initial product of cisplatin binding to DNA, does not. The computed reaction energy profiles demonstrate that N7-platination has only a minor effect on the energetics of the transition state, whereas protonation lowers it by approximately 10 kcal mol(-1). The orbitals involved in N7-Pt/H bonding are examined, and electronic differences between the two substituted guanines are identified. Natural bond orbital analysis, fragment orbital analysis, and extended transition-state theory reveal how the electronically different substituents at the N7 position control the stability of the N9-C1' bond. The detailed description of the electronic structure of the N7-substituted guanosines and the computational protocol developed to obtain a realistic model for these systems not only explain a longstanding enigma but also provide guidelines for further studies toward understanding the interactions of cisplatin with DNA.

Site-specific generation of deoxyribonolactone lesions in DNA oligonucleotides

[reaction: see text] An efficient method for the site-specific generation of 2-deoxyribonolactone oxidative DNA damage lesions from a "photocaged" nucleoside analogue was developed. A nucleoside phosphoramidite bearing a C-1' nitrobenzyl cyanohydrin was prepared and incorporated into DNA oligonucleotides using automated DNA synthesis. The caged analogue, which was stable in aqueous solution, was converted to the 2-deoxyribonolactone lesion by UV irradiation. DNA containing the caged analogue and the deoxyribonolactone site were characterized by electrospray mass spectrometry (ES-MS).

DNA identification of commercial ginseng samples

An investigation was performed with the objective of developing a DNA-based protocol for the identification of commercial samples of the herbal compound ginseng. There are currently two major herbal products referred to as ginseng. They are Korean or Chinese ginseng (Panax ginseng) and American ginseng (Panax quinquefolius). The market for ginseng in the United States is estimated to be approximately $300 million annually. Current tests for ginseng species identification rely on expert botanical identification of fresh plant/root specimens or on biochemical characterization of active and marker compounds (e.g., ginsenosides). For the determination of the feasibility of ginseng identification by DNA analysis, a strategy based on the direct DNA sequence analysis of the nuclear ribosomal internal transcribed spacer region was developed. Other genetic tests included sequence analysis of the chloroplast ribulose 1,5-bisphosphate carboxylase large subunit gene and DNA fingerprinting by the rapid amplification of polymorphic DNA technique. To confirm the results, each ginseng sample was identified using high-performance liquid chromatography. All methods were successful in distinguishing American from Korean ginseng. In addition, the protocol was improved for the isolation of genomic and plastid DNA from commercial ginseng preparations by incorporating an impact homogenization step into the standard column chromatography purification procedure.

Isotopic evidence for Late Cretaceous plume-ridge interaction at the Hawaiian hotspot

When a mantle plume interacts with a mid-ocean ridge, both are noticeably affected. The mid-ocean ridge can display anomalously shallow bathymetry, excess volcanism, thickened crust, asymmetric sea-floor spreading and a plume component in the composition of the ridge basalts. The hotspot-related volcanism can be drawn closer to the ridge, and its geochemical composition can also be affected. Here we present Sr-Nd-Pb isotopic analyses of samples from the next-to-oldest seamount in the Hawaiian hotspot track, the Detroit seamount at 51 degrees N, which show that, 81 Myr ago, the Hawaiian hotspot produced volcanism with an isotopic signature indistinguishable from mid-ocean ridge basalt. This composition is unprecedented in the known volcanism from the Hawaiian hotspot, but is consistent with the interpretation from plate reconstructions that the hotspot was located close to a mid-ocean ridge about 80 Myr ago. As the rising mantle plume encountered the hot, low-viscosity asthenosphere and hot, thin lithosphere near the spreading centre, it appears to have entrained enough of the isotopically depleted upper mantle to overwhelm the chemical characteristics of the plume itself. The Hawaiian hotspot thus joins the growing list of hotspots that have interacted with a rift early in their history.

Recognition of the nonpolar base 4-methylindole in DNA by the DNA repair adenine glycosylase MutY

[formula: see text] The DNA repair adenine glycosylase MutY efficiently recognizes 7-deaza-2'-deoxyadenosine (Z) and its nonpolar isostere 4-methylindole beta-deoxynucleoside (M) opposite 7,8-dihydro-8-oxo-2'-deoxyguanosine (OG) and G in DNA. Both wild-type and truncated MutY exhibit a 10- to 20-fold higher affinity for a duplex containing OG:M than OG:Z. More efficient recognition of M over Z by MutY may be to due the lack of hydrogen bonding with the OG that facilitates nucleotide flipping during the substrate recognition process.

Synthesis of a chemiluminescent acridinium hydroxylamine (AHA) for the direct detection of abasic sites in DNA

[structure: see text] The synthesis of a chemiluminescent acridinium hydroxylamine (AHA) for the direct detection of abasic sites in damaged nucleic acids is described. The reagent reacts readily with abasic sites of damaged calf thymus DNA generated in a time-dependent manner under acid/heat depurination conditions. Preliminary results indicate the sensitivity of the direct chemiluminescent detection format is approximately 0.1 abasic sites detected per 10(6) nucleotides using as little as 200 ng of DNA.

Synthesis and Properties of C-Azalyxonucleosides

1-beta-(4-Imidazoyl)- and 1-beta-(5-uracilyl)-1,4-dideoxy-1,4-imino-L-lyxitols were synthesized stereoselectively via a sequential procedure by the addition of the corresponding metal salts of heterocycles, Swern oxidation, reductive aminocyclization, and deprotection. Their structures were determined based on X-ray crystallography. From the NMR measurements of their N-acyl derivatives, two rotational isomers were observed. Their bioassay is also described.

A model to explain the various paradoxes associated with mantle noble gas geochemistry

As a result of an energetic accretion, the Earth is a volatile-poor and strongly differentiated planet. The volatile elements can be accounted for by a late veneer ( approximately 1% of total mass of the Earth). The incompatible elements are strongly concentrated into the exosphere (atmosphere, oceans, sediments, and crust) and upper mantle. Recent geochemical models invoke a large primordial undegassed reservoir with chondritic abundances of uranium and helium, which is clearly at odds with mass and energy balance calculations. The basic assumption behind these models is that excess "primordial" 3He is responsible for 3He/4He ratios higher than the average for midocean ridge basalts. The evidence however favors depletion of 3He and excessive depletion of 4He and, therefore, favors a refractory, residual (low U, Th) source Petrological processes such as melt-crystal and melt-gas separation fractionate helium from U and Th and, with time, generate inhomogeneities in the 3He/4He ratio. A self-consistent model for noble gases involves a gas-poor planet with trapping of CO2 and noble gases in the shallow mantle. Such trapped gases are released by later tectonic and magmatic processes. Most of the mantle was depleted and degassed during the accretion process. High 3He/4He gases are viewed as products of ancient gas exsolution stored in low U environments, rather than products of primordial reservoirs.

Methyl Transfer to Mercury Thiolates: Effects of Coordination Number and Ligand Dissociation

The complexes [(CH(3))(4)N](2)[Hg(SC(6)H(5))(4)] and [(C(4)H(9))(4)N][Hg(SC(6)H(5))(3)] demethylate (CH(3)O)(3)PO as revealed by (1)H, (31)P{(1)H}, and (199)Hg{(1)H} NMR spectroscopy in DMSO-d(6) solution. The products of the [(CH(3))(4)N](2)[Hg(SC(6)H(5))(4)] reaction are CH(3)SC(6)H(5), (CH(3)O)(2)PO(2)(-), and [Hg(SC(6)H(5))(3)](-), whereas [Hg(SC(6)H(5))(3)](-) demethylates (CH(3)O)(3)PO to yield CH(3)SC(6)H(5) and {Hg(SC(6)H(5))(2)[(CH(3)O)(2)PO(2)]}(-). Kinetic and solution studies of [(CH(3))(4)N](2)[Hg(SC(6)H(5))(4)] reveal a rapid equilibrium between bound and free thiolate. The dissociated thiolate is the nucleophile active toward (CH(3)O)(3)PO. These results imply that the metal center of the inactive mercury derivative of the Escherichia coli Ada DNA alkylation repair protein may comprise a three-coordinate [Hg(S-cysteine)(3)](-) moiety and an unbound, protonated cysteine (HS-Cys69).

Alkyl Transfer to Metal Thiolates: Kinetics, Active Species Identification, and Relevance to the DNA Methyl Phosphotriester Repair Center of Escherichia coli Ada

The Ada protein of Escherichia coli employs a [Zn(S-cys)(4)](2)(-) site to repair deoxyribonucleic acid alkyl phosphotriester lesions. The alkyl group is transferred to a cysteine thiolate in a stoichiometric reaction. We describe a functional model for this chemistry in which a thiolate of [(CH(3))(4)N](2)[Zn(SC(6)H(5))(4)] accepts a methyl group from (CH(3)O)(3)PO. The thiolate salt (CH(3))(4)N(SC(6)H(5)) is also active in methyl transfer, but the thiol C(6)H(5)SH fails to react. Conductivity measurements and kinetic studies demonstrate that [(CH(3))(4)N](2)[Zn(SC(6)H(5))(4)] forms ion pairs in dimethyl sulfoxide (DMSO) solution (K(IP) = 13 +/- 4 M(-)(1)) which exhibit diminished reactivity. The reaction of [Zn(SC(6)H(5))(4)](2)(-) with (CH(3)O)(3)PO is first order with respect to each reagent. A second-order rate constant for this reaction, k(Zn), was determined to be (1.6 +/- 0.3) x 10(-)(2) M(-)(1) s(-)(1). From kinetic data and equilibria studies, all reactivity of [(CH(3))(4)N](2)[Zn(SC(6)H(5))(4)] toward (CH(3)O)(3)PO could be attributed to dissociated thiolate. Metal complexes representing alternative protein sites were prepared and displayed the following kinetic trend of methyl transfer ability: [(CH(3))(4)N](2)[Zn(SC(6)H(5))(4)] > [(CH(3))(4)N](2)[Co(SC(6)H(5))(4)] approximately [(CH(3))(4)N](2)[Cd(SC(6)H(5))(4)] > [(CH(3))(4)N][Zn(SC(6)H(5))(3)(MeIm)] > [Zn(SC(6)H(5))(2)(MeIm)(2)], where MeIm = 1-methylimidazole. These results are consistent with a dissociated thiolate being the active species and suggest that a similar mechanism might apply to alkyl phosphotriester repair by Ada.