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Phylogenetic relationships among the six Iris subgenera were reconstructed by chloroplast trnL-F sequences data using maximum likelihood. The entire matrix of aligned bases analyzed includes 1043 characters and the length of all sequences varied from 747 bp to 893 bp, and mutation sites accounted for 18.79% of the total length. The cluster analysis results accorded well with the subgeneric classification of Chinese Iris species. Results suggested rhizomes and sepals lacking ornament are ancestral characters, and subg. Xyridion and subg. Limniris are more primordial than another four subgenera. Subgenus Nepalensis and subg. Xyridion were resolved as monophyletic.

8-OxodGuo and Fapy·dG induced 10-22% mutations, predominantly G → T transversions, in human embryonic kidney 293T cells in four TG*N sequence contexts, where N = C, G, A, or T. siRNA knockdown of pol λ resulted in 34 and 55% increases in the level of mutations in the progeny from the 8-oxodGuo construct in the TG*T and TG*G sequences, respectively, suggesting that pol λ is involved in error-free bypass of 8-oxodGuo. For Fapy·dG, in contrast, the level of G → T mutations was reduced by 27 and 46% in the TG*T and TG*G sequences, respectively, suggesting that pol λ is responsible for a significant fraction of Fapy·dG-induced G → T mutations.

Bioluminescence is a useful tool for imaging of cancer in in vivo animal models that endogenously express luciferase, an enzyme that requires a substrate for visual readout. Current bioluminescence imaging, using commonly available luciferin substrates, only lasts a short time (15–20 min). To avoid repeated administration of luciferase substrate during cancer detection and surgery, a long lasting bioluminescence imaging substrate or system is needed. A novel water-soluble biotinylated luciferase probe, B-YL (1), was synthesized. A receptor-targeted complex of B-YL with streptavidin (SA) together with a biotinylated epidermal growth factor short peptide (B-EGF) (SA/B-YL/B-EGF = 1:3:1, molar ratio) was then prepared to demonstrate selective targeting. The complex was incubated with brain cancer cell lines overexpressing the EGF receptor (EGFR) and transfected with the luciferase gene. Results show that the complex specifically detects cancer cells by bioluminescence. The complex was further used to image xenograft brain tumors transfected with a luciferase gene in mice. The complex detects the tumor immediately, and bioluminescence lasts for 5 days. Thus, the complex generates a long lasting bioluminescence for cancer detection in mice. The complex with selective targeting may be used in noninvasive cancer diagnosis and accurate surgery in cancer treatment in clinics in the future.

The small-molecule, water-soluble molecular beacon probe 1 is hydrolyzed by the lysate and living cells of human prostate cancer cell lines (LNCaP), resulting in strong green fluorescence. In contrast, probe 1 does not undergo significant hydrolysis in either the lysate or living cells of human nontumorigenic prostate cells (RWPE-1). These results, corroborated by UV-Vis spectroscopy and fluorescent microscopy, reveal that probe 1 is a sensitive and specific fluorogenic and chromogenic sensor for the detection of human prostate cancer cells among nontumorigenic prostate cells and that carboxylesterase activity is a specific biomarker for human prostate cancer cells.

In this study, we synthesized small-molecule, water-soluble, fluorescein-containing ureido compounds 6 and 8 as target receptors for cytosine free bases and then investigated the binding of cytosine free bases with the receptors using 15 N NMR spectroscopy and partially labeled cytosine-2,4- 13 C-1,3,4- 15 N-cytosine. Binding with the receptor 6a (the disodium form of 6 ) caused the chemical shift of the nitrogen atom of the amino group of cytosine to move downfield; binding of the receptor 8a (the disodium form of 8 ), which is possessing no corresponding aryl nitrogen atom, had no effect on this signal. Fluorescence spectroscopy revealed that binding of cytosine and its derivatives led to quenching of the fluorescence of receptor 6a ; in contrast, the quenching of receptor 8a was only slightly affected by cytosine. Because the fluorescence of 6a was not quenched by either deoxycytidine or uracil, it appears that this receptor is a specific for cytosine among the DNA bases. We used the fluorescence of 6a to measure the apparent binding constants for various cytosine derivatives, including the anticancer prodrug 5-fluorocytosine. Receptor 6a is the first small-molecule, water-soluble fluorescent receptor for the specific binding of cytosine free bases in aqueous solution.

Tobacco SABP2, a 29kDa protein catalyzes the conversion of methyl salicylic acid (MeSA) into salicylic acid (SA) to induce SAR. Pretreatment of plants with acibenzolar-S-methyl (ASM), a functional analog of salicylic acid induces systemic acquired resistance (SAR). Data presented in this paper suggest that SABP2 catalyzes the conversion of ASM into acibenzolar to induce SAR. Transgenic SABP2-silenced tobacco plants when treated with ASM, fail to express PR-1 proteins and do not induce robust SAR expression. When treated with acibenzolar, full SAR is induced in SABP2-silenced plants. These results show that functional SABP2 is required for ASM-mediated induction of resistance.

Two pyrene containing fluorescent receptors, 2-(1-pyrenyl)benzoic acid (FR-1) and 8-(1-pyrenyl)-1-naphthoic acid (FR-2), have been designed and synthesized to mimic a pyrene dinucleotide for molecular recognition of 9-butyladenine (9-BuA). The X-ray crystal structures of the receptors FR-1 and FR-2 along with the binding substrate 9-BuA have been determined. FR-1 has the carboxyl group in the same plane as the phenyl group whereas the pyrenyl group is perpendicular to the phenyl group. However, both carboxyl and pyrenyl groups in FR-2 are parallel to each other but perpendicular to the naphthyl group. The binding constant for FR-2 to 9-BuA was found to be 7896±2187 M−1, which is 8.3-fold greater than that for FR-1 (953±129 M−1). The results indicate that the complex of 9-BuA with FR-2 is more stable than that with FR-1 by 1.2 kcal/mol. In addition, the molecular recognition of 9-BuA with the receptors can also be observed using fluorescence spectroscopy.

A simple synthesis of fresh alkyl iodides using alcohols and hydriodic acid (HI) is reported. The alkyl iodides were obtained in quick and easy work-up with good to excellent yields (66–94%) and very high purities (97–99%). Freshly prepared iodomethane and 1-iodobutane were applied to synthesize biologically relevant 3,7-dimethyladenine and 9-butyladenine, which were characterized thoroughly using 1D and 2D NMR, individually.

Fapy.dG is produced in DNA as a result of oxidative stress from a precursor that also forms OxodG. Bypass of Fapy.dG in a shuttle vector in COS-7 cells produces G --T transversions slightly more frequently than does OxodG (Kalam, M. A., et al. (2006) Nucleic Acids Res. 34, 2305). The effect of Fapy.dG on replication in Escherichia coli was studied by transfecting M13mp7(L2) bacteriophage DNA containing the lesion within the lacZ gene in 4 local sequence contexts. For comparison, experiments were carried out side-by-side on OxodG. The efficiency of lesion bypass was determined relative to that of a genome containing native nucleotides. Fapy.dG was bypassed less efficiently than OxodG. Bypass efficiency of Fapy.dG and OxodG increased modestly in SOS-induced cells. Mutation frequencies at the site of the lesions in the originally transfected genomes were determined using the REAP assay (Delaney, J. C., Essigmann, J. M. (2006) Methods Enzymol. 408, 1). G --T transversions were the only mutations observed above background when either Fapy.dG or OxodG was bypassed. OxodG mutation frequencies ranged from 3.1% to 9.8%, whereas the G --T transversion frequencies observed upon Fapy.dG bypass wereor=1.9% in wild-type E. coli. In contrast to OxodG bypass, Fapy.dG mutation frequencies were unaffected by carrying out experiments in mutM/mutY cells. Overall, these experiments suggest that Fapy.dG is at most weakly mutagenic in E. coli. Steady-state kinetic experiments using the Klenow fragment of DNA polymerase I from E. coli suggest that a low dA misincorporation frequency opposite Fapy.dG and inefficient extension of a Fapy.dG:dA base pair work synergistically to minimize the levels of G --T transversions.

Proper maintenance of the genome is of great importance. Consequently, damaged nucleotides are repaired through redundant pathways. We considered whether the genome is protected from formamidopyrimidine nucleosides (Fapy*dA, Fapy*dG) via a pathway distinct from the Escherichia coli guanine oxidation system. The formamidopyrimidines are produced in significant quantities in DNA as a result of oxidative stress and are efficiently excised by formamidopyrimidine DNA glycosylase. Previous reports suggest that the formamidopyrimidine nucleosides are substrates for endonucleases III and VIII, enzymes that are typically associated with pyrimidine lesion repair in E.coli. We investigated the possibility that Endo III and/or Endo VIII play a role in formamidopyrimidine nucleoside repair by examining Fapy*dA and Fapy*dG excision opposite all four native 2'-deoxyribonucleotides. Endo VIII excises both lesions more efficiently than does Endo III, but the enzymes exhibit similar selectivity with respect to their action on duplexes containing the formamidopyrimidines opposite native deoxyribonucleotides. Fapy*dA is removed more rapidly than Fapy*dG, and duplexes containing purine nucleotides opposite the lesions are superior substrates compared with those containing formamidopyrimidine-pyrimidine base pairs. This dependence upon opposing nucleotide indicates that Endo III and Endo VIII do not serve as back up enzymes to formamidopyrimidine DNA glycosylase in the repair of formamidopyrimidines. When considered in conjunction with cellular studies [J. O. Blaisdell, Z. Hatahet and S. S. Wallace (1999) J. Bacteriol., 181, 6396-6402], these results also suggest that Endo III and Endo VIII do not protect E.coli against possible mutations attributable to formamidopyrimidine lesions.

The glycosidic bond hydrolysis reaction of the enzyme uracil DNA glycosylase (UDG) occurs by a two-step mechanism involving complete bond breakage to the uracil anion leaving group in the first step, formation of a discrete glycosyl cation-uracil anion intermediate, followed by water attack in a second transition-state leading to the enzyme-bound products of uracil and abasic DNA. We have synthesized and determined the binding affinities of unimolecular mimics of the substrate and first transition-state (TS1) in which the uracil base is covalently attached to the sugar, and in addition, bimolecular mimics of the second addition transition state (TS2) in which the base and sugar are detached. We find that the bipartite mimics of TS2 are superior to the TS1 mimics. These results indicate that bipartite TS2 inhibitors could be useful for inhibition of glycosylases that proceed by stepwise reaction mechanisms.

Abasic sites are often referred to as noninstructive lesions. The C1'-oxidized abasic site (2-deoxyribonolactone, L) is produced by several DNA damaging agents, including gamma-radiolysis and the neocarzinostatin chromophore (NCS). The effects of a C1'-oxidized abasic site incorporated at a defined site in single-stranded plasmid were examined in SOS polymerase-proficient and -deficient Escherichia coli. For comparison, experiments utilizing plasmids containing an abasic site (AP) were carried out side by side. In contrast to plasmid containing AP, dA and dG were incorporated most often when plasmid containing L was replicated. The ratio of dG:dA incorporation depended upon local sequence and varied from 0.9 to 2.2. High levels of translesion incorporation of dA are consistent with previous observations that treatment of DNA with the neocarzinostatin chromophore resulted in large amounts of G.C --> A.T transitions [Povirk and Goldberg (1986) Nucleic Acids Res. 14, 1417] and support the proposal that L is the source of these mutations. Both abasic lesions were 100% lethal in triple knockout cells lacking pol II, pol IV, and pol V. Analysis of translesion synthesis in repair-deficient cells revealed that pol V played a significant role in replication of L and AP. Significant levels of -1 frameshifts were formed in 5'-d(CL) sequences in the presence of pol V and were the exclusive product in pol V-deficient cells. Frameshift products were not formed when the nucleotide on the 5'-side of L was either dT or dG. Deleting pol II or pol IV had only modest effects on replication of L-containing plasmid but significantly decreased the amount of -1 frameshift product formed from an AP lesion. Experiments carried out side by side using otherwise identical plasmids containing an AP site illustrate the distinct properties of these two abasic lesions and that neither should be thought of as noninstructive.

The specific recognition mechanisms of DNA repair glycosylases that remove cationic alkylpurine bases in DNA are not well understood partly due to the absence of structures of these enzymes with their cognate bases. Here we report the solution structure of 3-methyladenine DNA glycosylase I (TAG) in complex with its 3-methyladenine (3-MeA) cognate base, and we have used chemical perturbation of the base in combination with mutagenesis of the enzyme to evaluate the role of hydrogen bonding and pi-cation interactions in alkylated base recognition by this DNA repair enzyme. We find that TAG uses hydrogen bonding with heteroatoms on the base, van der Waals interactions with the 3-Me group, and conventional pi-pi stacking with a conserved Trp side chain to selectively bind neutral 3-MeA over the cationic form of the base. Discrimination against binding of the normal base adenine is derived from direct sensing of the 3-methyl group, leading to an induced-fit conformational change that engulfs the base in a box defined by five aromatic side chains. These findings indicate that base specific recognition by TAG does not involve strong pi-cation interactions, and suggest a novel mechanism for alkylated base recognition and removal.

The DNA repair enzyme uracil DNA glycosylase has been crystallized with a cationic 1-aza-2‘-deoxyribose-containing DNA that mimics the ultimate transition state of the reaction in which the water nucleophile attacks the anomeric center of the oxacarbenium ion−uracil anion reaction intermediate. Comparison with substrate and product structures, and the previous structure of the intermediate determined by kinetic isotope effects, reveals an exquisite example of geometric strain, least atomic motion, and electrophile migration in biological catalysis. This structure provides a rare opportunity to reconstruct the detailed structural transformations that occur along an enzymatic reaction coordinate.

A novel site-specific cytosine DNA glycosylase has been rationally engineered from the active site scaffold of the DNA repair enzyme uracil DNA glycosylase (UDG). UDG, which operates by a nucleotide flipping mechanism, was first converted into a sequence nonspecific cytosine DNA glycosylase (CDG) by altering the base-specific hydrogen bond donor-acceptor groups in the active site. A second mutation that renders UDG defective in nucleotide flipping was then introduced, and the double mutant was rescued using a substrate with a “preflipped” cytosine base. Substrate-assisted flipping was engineered by incorporation of an unnatural pyrene nucleotide wedge (Y) into the DNA strand opposite to the target cytosine. This new enzyme, CYDG, can be used to target cleavage of specific cytosine residues in the context of a C/Y base pair in any DNA fragment.

The reaction catalyzed by the DNA repair enzyme uracil DNA glycosylase (UDG) proceeds through an unprecedented stepwise mechanism involving a positively charged oxacarbenium ion sugar and uracil anion leaving group. Here we use a novel approach to evaluate the catalytic contribution of electrostatic interactions between four essential phosphodiester groups of the DNA substrate and the cationic transition state. Our strategy was to substitute each of these phosphate groups with an uncharged (R)- or (S)-methylphosphonate linkage (MeP). We then compared the damaging effects of these methylphosphonate substitutions on catalysis with their damaging effects on binding of a cationic 1-azadeoxyribose (1-aza-dR(+)) oxacarbenium ion analogue to the UDG-uracil anion binary complex. A plot of log k(cat)/K(m) for the series of MeP-substituted substrates against log K(D) for binding of the 1-aza-dR(+) inhibitors gives a linear correlation of unit slope, confirming that the electronic features of the transition state resemble that of the 1-aza-dR(+), and that the anionic backbone of DNA is used in transition state stabilization. We estimate that all of the combined phosphodiester interactions with the substrate contribute 6-8 kcal/mol toward lowering the activation barrier, a stabilization that is significant compared to the 16 kcal/mol catalytic power of UDG. However, unlike groups of the enzyme that selectively stabilize the charged transition state by an estimated 7 kcal/mol, these phosphodiester groups also interact strongly in the ground state. To our knowledge, these results provide the first experimental evidence for electrostatic stabilization of a charged enzymatic transition state and intermediate using the anionic backbone of DNA.

Trifluoroacetic acid has been found to be an efficient and non-oxidative catalyst for the epimerization of pyrene and other C-nucleosides in dichloromethane at ambient temperature. Aspects of the epimerization mechanism are also elucidated.

We recently introduced a new substrate rescue tool for investigating enzymatic base flipping by uracil DNA glycosylase (UDG) in which a bulky pyrene nucleotide wedge (Y) was placed opposite a uracil in duplex DNA (i.e., a U/Y pair), thereby preorganizing the target base in an extrahelical conformation [Jiang, Y. L., et al. (2001) J. Biol. Chem. 276, 42347-54]. The pyrene wedge completely rescued the large catalytic defects resulting from removal of the natural Leu191 wedge, presumably mimicking the pushing and plugging function of this group. Here we employ the pyrene rescue method in combination with transient kinetic approaches to assess the functional roles of six conserved enzymatic groups of UDG that have been implicated in the "pinch, push, plug, and pull" base-flipping mechanism (see the preceding paper in this issue). We find that a U/Y base pair increases the apparent second-order rate constant for damaged site recognition by L191G pushing mutation by 45-fold as compared to a U/A pair, thereby fully rescuing the kinetic effects of the mutation. Remarkably, the U/Y pair also allows L191G to proceed through the conformational docking step that is severely comprised with the normal U/A substrate, and allows the active site of UDG to clamp around the extrahelical base. Thus, pyrene also fulfills the plugging role of the Leu191 side chain. Preorganization of uracil in an extrahelical conformation by pyrene allows diffusion-controlled damage recognition by all of these base-flipping mutants, and allows the UDG conformational change to proceed as rapidly as the rate of uracil flipping with the natural U/A base pair. Thus, the pyrene wedge substrate allows UDG to recognize uracil by a lock-and-key mechanism, rather than the natural induced-fit mechanism. Unnatural pyrene base pairs may provide a general strategy to promote site-specific targeting of other enzymes that recognize extrahelical bases.

The DNA repair enzyme uracil DNA glycosylase (UDG) locates unwanted uracil bases in genomic DNA using a remarkable base-flipping mechanism in which the entire deoxyuridine nucleotide is rotated from the DNA base stack into the enzyme active site. Enzymatic base flipping has been described as a three-step process involving phosphodiester backbone pinching, base extrusion through active pushing and plugging by a leucine side chain that inserts in the DNA minor groove, and, finally, pulling by hydrogen-bonding groups that interact with the extrahelical base. Here we employ mutagenesis in combination with transient kinetic approaches to assess the functional roles of six conserved enzymatic groups of UDG that have been implicated in the "pinch, push, plug, and pull" base-flipping mechanism. Our results show that these mutant enzymes are capable of flipping the uracil base from the duplex, but that many of these mutations prevent a subsequent induced fit conformational step in which catalytic groups of UDG dock with the flipped-out base. These studies support our previous model for base flipping in which a conformational gating step closely follows base extrusion from the DNA duplex [Stivers, J. T., et al. (1999) Biochemistry 38, 952-963]. A model that accounts for the temporal and functional roles of these side chain interactions along the reaction pathway for base flipping is presented.

The DNA repair enzyme uracil DNA glycosylase (UDG) hydrolyzes the glycosidic bond of deoxyuridine in DNA by a remarkable mechanism involving formation of a positively charged oxacarbenium ion-uracil anion intermediate. We have proposed that the positively charged intermediate is stabilized by being sandwiched between the combined negative charges of the anionic uracil leaving group and a conserved aspartate residue that are located on opposite faces of the sugar ring. Here we establish that a duplex DNA oligonucleotide containing a cationic 1-aza-deoxyribose (I) oxacarbenium ion mimic is a potent inhibitor of UDG that binds tightly to the enzyme-uracil anion (EU(-)) product complex (K(D) of EU(-) = 110 pm). The tight binding of I to the EU(-) complex results from its extremely slow off rate (k(off) = 0.0008 s(-1)), which is 25,000-fold slower than substrate analogue DNA. Removal of Asp(64) and His(187), which are involved in stabilization of the cationic sugar and the anionic uracil leaving group, respectively, specifically weakens binding of I to the UDG-uracil complex by 154,000-fold, without significantly affecting substrate or product binding. These results suggest that electrostatic effects can effectively stabilize such an intermediate by at least -7 kcal/mol, without leading to anticatalytic stabilization of the substrate and products.

The intramolecular hydrogen bonding of a series of linked uracil, thymine and adenine derivatives is described. The nucleoside bases have been linked by semi-flexible spacers and the chemical shifts and ΔδNH/ΔT values for the nucleoside NH protons confirm the strong intramolecular hydrogen bonding motif.

The site-specific DNA cleavage and religation activities of the vaccinia virus type IB topoisomerase at (C/T)CCTT(+1)X(-1) sites in duplex DNA have allowed detailed investigations of the chemical and conformational steps on the reaction pathway of this enzyme (see accompanying article (Kwon, K., and Stivers, J. T. (2002) J. Biol. Chem. 277, 345-352)). To extend these studies to the DNA substrate, we have performed 19F NMR experiments using substrates in which the +1 T has been replaced with the NMR-sensitive thymidine base analogue 5-fluoro-2'-deoxyuridine (5-F-dUrd). Substitution of 5-F-dUrd has little effect on the binding affinity of topoisomerase I for DNA, results in small changes in the cleavage and religation rate constants, and produces a net 3-fold decrease in the cleavage equilibrium constant as compared with the CCCTT consensus DNA. One-dimensional 19F NMR experiments show that the +1 5-F-dUrd is in a dynamic equilibrium between a stacked and unstacked state in both the noncovalent complex and the covalent phosphotyrosine complex. These NMR observations are supported by the selective sensitivity of the +1 T and +1 5-F-dUrd to KMnO4 oxidation. A role for localized DNA distortion in the topoisomerase I mechanism is suggested.

Background Cancer cell esterases are often overexpressed and can have chiral specificities different from that of the corresponding normal cells and can, therefore, be useful targets for activating chemotherapeutic prodrug esters. Prodrug esters are inactive compounds that can be preferentially activated by esterase enzymes. Moreover, cancer cells often exhibit a high level of intrinsic oxidative stress due to an increased formation of reactive oxygen species (ROS) and a decreased expression of some enzymatic antioxidants. Prodrugs designed to induce additional oxidative stress can selectively induce apoptosis in cancer cells already exhibiting a high level of intrinsic oxidative stress. This study focused on the in vitro evaluation of four novel prodrug esters: the R- and S- chiral esters of 4-[(nitrooxy)methyl]phenyl N-acetylalaninate (R- and S-NPAA) and the R- and S- chiral esters of 4-[(nitrooxy)methyl]naphth-1-yl N-acetylalaninate (R- and S-NQM), which are activated, to varying extents, by oxidized protein hydrolase (OPH, EC 3.4.19.1) yielding a quinone methide (QM) intermediate capable of depleting glutathione (GSH), a key intracellular antioxidant. OPH is a serine esterase/protease that is overexpressed in some human tumors and cancer cell lines. Methods To evaluate the chiral ester prodrugs, we monitored cellular GSH depletion, cellular protein carbonyl levels (an oxidative stress biomarker) and cell viability in tumorigenic and nontumorigenic prostate cancer cell lines. Results We found that the prodrugs were activated by OPH and subsequently depleted GSH. The S-chiral ester of NPAA (S-NPAA) was two-fold more effective than the R-chiral ester (R-NPAA) in depleting GSH, increasing oxidative stress, inducing apoptosis, and decreasing cell viability in tumorigenic prostate LNCaP cells but had little effect on non-tumorigenic RWPE-1 cells. In addition, we found that that S-NPAA induced apoptosis and decreased cell viability in tumorigenic DU145 and PC3 prostate cell lines. Similar results were found in a COS-7 model that overexpressed active human OPH (COS-7-OPH). Conclusions Our results suggest that prostate tumors overexpressing OPH and/or exhibiting a high level of intrinsic oxidative stress may be susceptible to QM generating prodrug esters that are targeted to OPH with little effect on non-tumorigenic prostate cells.

A series of potential receptor molecules based on the dipurinyl-2,6-pyridinedicarboxamide motif has been prepared and the intramolecular hydrogen bonding characterised by 1 H NMR and FT-IR spectroscopies. The hydrogen bonding gives rise to a preferential planar, cis conformation for the molecules. The planar nature of the unit also gives rise to π-π stacking as shown by 1 H NMR dilution experiments.

The palladium-catalysed couplings of aryl halides and triflates with propargyl amino amides and the couplings of aryl and vinyl halides and triflates with an ethynyl oxazolidine are reported.

Protein serine-threonine kinase casein kinase II (CK2) is involved in a myriad of cellular processes including cell growth and proliferation through its phosphorylation of hundreds of substrates, yet how CK2 function is regulated is poorly understood. Here we report that the CK2 catalytic subunit CK2α is modified by O-linked β-N-acetyl-glucosamine (O-GlcNAc) on Ser347, proximal to a cyclin-dependent kinase phosphorylation site (Thr344). We use protein semisynthesis to show that phosphorylation of Thr344 increases the cellular stability of CK2α by strengthening its interaction with Pin1, whereas glycosylation of Ser347 seems to be antagonistic to Thr344 phosphorylation and permissive to proteasomal degradation. By performing kinase assays with site-specifically phospho- and glyco-modified CK2α in combination with CK2β and Pin1 binding partners on human protein microarrays, we show that the kinase substrate selectivity of CK2 is modulated by these specific post-translational modifications. This study suggests how a promiscuous protein kinase can be regulated at multiple levels to achieve particular biological outputs.

Covalent interstrand DNA cross links (ICLs) between complementary stands of the DNA double helix constitute a major and particularly cytotoxic class of DNA damage (1). As these crosslinks affect both DNA strands, the redundant information normally safeguarded by the DNA double helix is jeopardized, and cellular repair processes can induce double strand breaks and other potentially deleterious lesions in the process of removing the lesion (2, 3, 4). These highly toxic ICLs primarily disrupt rapidly dividing cells as they pose physical obstacles to strand separation at the replication fork and to transcriptional bubble formation. Consequently, structurally diverse agents such as psoralen, mitomycin C, cisplatin, and nitrogen mustards that induce ICLs have become important chemotherapeutics and frontline weapons against many types of cancer (1, 2, 3). ICL repair in mammalian cells proceeds via several overlapping pathways, and the precise repair mechanism depends upon the nature of the crosslink, and the stage of the cell cycle when the damage is discovered (2, 5, 6). Prominent among these pathways is replication-dependent repair (S phase), where the ICL poses a physical barrier to the progressing replication fork, and stalled replication complexes lead to the recruitment of repair machinery that initiates repair via ICL-induced double-strand breaks (5). Similarly, ICLs encountered at or near actively transcribed regions of the genome during Go or G1 stages of the cell cycle can prevent transcriptional bubble formation and stall transcriptional machinery (2, 3, 7). Such transcription-coupled repair (TCR) processes involve recruitment of nucleotide excision repair (NER) factors to the stalled complex (8, 9, 10, 11). Finally, ICL detection in Go or G1 can also occur in unperturbed DNA in a process known as the global genome repair (GGR) pathway of NER, which occurs in the absence of transcription (7, 10, 11, 12). The GGR pathway has only been completely worked out in prokaryotes, and involves NER-dependent incision events on a single DNA strand on both the 5′ and 3′ sides of the ICL resulting in “unhooking” of the crosslink. However, previous studies using mammalian cell extracts showed that NER only leads to dual incisions on the 5′ side of the ICL that do not result in crosslink unhooking (Figure 1) (13). Figure 1 Schematic illustrating NER-dependent and -independent processing of ICLs observed in mammalian cell extracts (32). Interstrand crosslinks prevent mammalian NER enzymes from making incisions surrounding the crosslink. Instead, unknown repair enzyme activities ... Recently there has been increased interest in the process of ICL detection using model ICL-containing duplexes that serve as defined substrates for DNA repair factors present in mammalian cells(Fig. 1) (11, 14, 15). A model ICL that has been very useful in ex vivo repair studies is one in which the exocyclic N4 nitrogen atoms of staggered cytosine bases on opposite strands of the DNA duplex are connected by an ethyl covalent linker (Fig. 2). This defined crosslink can be site-specifically incorporated using a convertible nucleoside approach and has been extensively characterized using structural and biochemical methodology (2, 16, 17, 18). Due to the inherent anti-parallel nature of the DNA duplex, two different orientations of the staggered CC ICL can be generated, one in which the crosslink is placed in a 5′-CG-3′ sequence and one in which the crosslink is placed in a 5′-GC-3′ sequence. Because of the relative geometries of the staggered cytosine bases in these two forms, only the 5′-CG-3′ orientation allows an ethyl linker geometry that optimally positions the N4 atoms of the linked cytosine bases to maintain normal Watson-Crick hydrogen bonding contacts with their cross strand partner guanine, thereby maintaining the B-form DNA structure (Fig. 2b). 5′-CG-3′ ICL-DNA has been structurally characterized in different sequence contexts using x-ray crystallography, solution state NMR spectroscopy, and atomic force microscopy, and found to adopt a structure that is essentially identical to canonical B-form DNA (16, 18, 19). In contrast, the non-optimal 5′-GC-3′ ICL-DNA form has been found to have a highly distorted duplex structure (16). Figure 2 Structure of DNA duplex containing the N4C-ethyl-N4C crosslink. (a) Crystallographic model of duplex DNA (pdb accession name 2OKS) containing a central staggered 5′–CG-3′ N4C-ethyl-N4C interstrand crosslink in the major groove. ... When these staggered CC ICL duplexes were exposed to mammalian cell extracts it was observed that the disordered 5′-GC-3′ construct and the B form 5′-CG-3′ ICL-DNA were incised in two distinct ways (14, 20), but a matched normal DNA was not incised. The first set of incisions occurred on a single strand, 5′ to the ICL and produced a set of oligonucleotides 24–32 nucleotides in length (Fig. 1), similar to those previously reported by Sancar and coworkers (13). The second set of apparent incisions appeared on both the 5′ and 3′ sides of the ICL and led to unhooking of the ICL (Fig. 1) 2. Through the use of extracts derived from cells that were deficient in NER enzymes, it was established that the dual 5′ incisions require NER, while the highly-specific 5′ and 3′ incision activity that leads to unhooking is novel, and not attributable to known DNA repair pathways (14). The disordered 5′-GC-3′ ICL was unhooked with an initial rate that was 6-fold grater than that of the B-form 5′-CG-3′ ICL-DNA, suggesting that DNA distortion plays a role in detection, however the remarkable aspect of both NER-dependent and independent incision events is that the normal matched DNA duplex is never detectably incised (14). Thus, subtle differences in the structure and/or dynamic properties of the B form ICL and the normal duplex must give rise to incision specificity. While the gross structural distortions provided by the 5′-GC-3′ ICL could lead to its preferred incision (14, 16), the detection of specific incision events in the structurally undistorted 5′-CG-3′ ICL duplex demonstrates that structural distortions can not be the sole determining factor guiding incision. Since structural methods only yield information on the time-averaged conformation of a macromolecule, they are insensitive to short-lived high-energy states that may be present and critical to biological recognition (21, 22, 23, 24). Here we use NMR imino proton exchange measurements to probe the dynamics of B-form and non-B-form duplexes containing staggered CC ICLs. We find that the intrinsic dynamic properties of these ICL-DNAs do not provide an adequate explanation for their specific endonucleolytic incision by DNA repair factors in mammalian cell extracts. The findings suggest that the covalent nature of the two linked DNA strands is the essential determining feature for incision of both ICL’s, and that the differences in the dynamic and structural properties of the two ICL duplexes plays a lesser role. A model for recognition and incision is proposed based on these findings.

As one of the natural polyphenols, resveratrol possesses hydroxyl substituted trans-stilbene structure and exerts impact on health by inhibiting multiple human enzymes, such as cyclooxygenase, F1 ATPase, and tyrosinase. Resveratrol has to be bound by human serum albumin (HSA) to keep a high concentration in serum, since its solubility is low in water. To improve water solubility and bioavailability, two resveratrol aliphatic acids and their esters have been designed and synthesized. The solubilities of the resveratrol and its derivatives have been measured using a standard procedure. The two aliphatic acids showed better solubilities in pure water and phosphate buffer (pH 7). The binding affinities of resveratrol derivatives for HSA were also measured, and the drug–protein interaction mechanism was investigated using fluorescence, UV–vis, and NMR spectroscopies. Interestingly, resveratrol hexanoic acid (5) was found to be a much better ligand (Ka = (6.70 ± 0.10) × 106 M−1) for HSA than resveratrol (Ka = (1.64 ± 0.07) × 105 M−1), and there was 41-fold improvement for the binding affinity. It was the first time that the increase of fluorescence of resveratrol moiety was observed during the binding to HSA, suggesting that 5 should be bound tightly by HSA. The UV–vis absorption spectroscopy revealed a maximum absorption shift from 318 to 311 nm with decreasing intensity by 20% upon complexation, suggesting that the π–π conjugation of the stilbene structure was impaired during the binding. Although HSA was reported to have only one binding site for resveratrol, the Job’s and molar ratio plots suggested that HSA should bind two molecules of 5. NMR study suggested that phenyl group (B ring) in the center of the molecule of 5 should be involved in the π–π stacking interactions with HSA aromatic amino acid residues. Molecular geometry calculation of 5 with Spartan software showed that the stilbene structure had two conformers, orthogonal and planar ones. The former (E = −1.432 KJ/mol) was more stable than the latter (E = −0.128 KJ/mol), suggesting that the former should be the conformer of 5 in the complexation with HSA.

The nucleoside triphosphates of N6-(2-deoxy-α,β-d-erythro-pentofuranosyl)-2,6-diamino-4-hydroxy-5-formamidopyrimidine (Fapy·dGTP) and its C-nucleoside analogue (β-C-Fapy·dGTP) were synthesized. The lability of the formamide group required that nucleoside triphosphate formation be carried out using an umpolung strategy in which pyrophosphate was activated toward nucleophilic attack. The Klenow fragment of DNA polymerase I from Escherichia coli accepted Fapy·dGTP and β-C-Fapy·dGTP as substrates much less efficiently than it did dGTP. Subsequent extension of a primer containing either modified nucleotide was less affected compared to when the native nucleotide is present at the 3′-terminus. The specificity constants are sufficiently large that nucleoside triphosphate incorporation could account for the level of Fapy·dG observed in cells if 1% of the dGTP pool is converted to Fapy·dGTP. Similarly, polymerase-mediated introduction of β-C-Fapy·dG could be useful for incorporating useful amounts of this nonhydrolyzable analogue for use as an inhibitor of base excision repair. The kinetic viability of these processes is enhanced by inefficient hydrolysis of Fapy·dGTP and β-C-Fapy·dGTP by MutT, the E. coli enzyme that releases pyrophosphate and the corresponding nucleoside monophosphate upon reaction with structurally related nucleoside triphosphates.

Uracil DNA glycosylase (UNG) locates uracil and its structural congener thymine in the context of duplex DNA using a base flipping mechanism. NMR imino proton exchange measurements were performed on free and UNG-bound DNA duplexes in which a single thymine (T) was paired with a series of adenine analogues (X) capable of forming one, two, or three hydrogen bonds. The base pair opening equilibrium for the free DNA increased 55-fold as the number of hydrogen bonds decreased, but the opening rate constants were nearly the same in the absence and presence of UNG. In contrast, UNG was found to slow the base pair closing rate constants (kcl) compared to each free duplex by a factor of 3- to 23-fold. These findings indicate that regardless of the inherent thermodynamic stability of the TX pair, UNG does not alter the spontaneous opening rate. Instead, the enzyme holds the spontaneously expelled thymine (or uracil) in a transient extrahelical sieving site where it may partition forward into the enzyme active site (uracil) or back into the DNA base stack (thymine).

Human nuclear uracil DNA glycosylase (UNG2) and deoxyuridine triphosphate nucleotidohydrolase (dUTPase) are the primary enzymes that prevent the incorporation and accumulation of deoxyuridine in genomic DNA. These enzymes are desirable targets for small molecule inhibitors given their roles in a wide range of biological processes ranging from chromosomal rearrangements that lead to cancer, viral DNA replication, and the formation of toxic DNA strand breaks during anticancer drug therapy. To accelerate the discovery of such inhibitors, we have developed a high-throughput approach for directed library synthesis and screening. In this efficient technology, a uracil-aldehyde ligand is covalently tethered to one position of a trivalent alkyloxyamine linker via an oxime linkage, and then the vacant linker positions are derivatized with a library of aldehydes. The resulting triskelion oximes were directly screened for inhibitory activity and the most potent of these showed micromolar binding affinities to UNG2 and dUTPase.

Uracil DNA glycosylase (UNG) is an important DNA repair enzyme that recognizes and excises uracil bases in DNA using an extrahelical recognition mechanism. It is emerging as a desirable target for small-molecule inhibitors given its key role in a wide range of biological processes including the generation of antibody diversity, DNA replication in a number of viruses, and the formation of DNA strand breaks during anticancer drug therapy. To accelerate the discovery of inhibitors of UNG we have developed a uracil-directed ligand tethering strategy. In this efficient approach, a uracil aldehyde ligand is tethered via alkyloxyamine linker chemistry to a diverse array of aldehyde binding elements. Thus, the mechanism of extrahelical recognition of the uracil ligand is exploited to target the UNG active site, and alkyloxyamine linker tethering is used to randomly explore peripheral binding pockets. Since no compound purification is required, this approach rapidly identified the first small-molecule inhibitors of human UNG with micromolar to submicromolar binding affinities. In a surprising result, these uracil-based ligands are found not only to bind to the active site but also to bind to a second uncompetitive site. The weaker uncompetitive site suggests the existence of a transient binding site for uracil during the multistep extrahelical recognition mechanism. This very general inhibitor design strategy can be easily adapted to target other enzymes that recognize nucleobases, including other DNA repair enzymes that recognize other types of extrahelical DNA bases.

2-deoxyribonolactone (L) and 2-deoxyribose (AP) are abasic sites that are produced by ionizing radiation, reactive oxygen species and a variety of DNA damaging agents. The biological processing of the AP site has been examined in the yeast Saccharomyces cerevisiae. However, nothing is known about how L is processed in this organism. We determined the bypass and mutagenic specificity of DNA containing an abasic site (AP and L) or the AP analog tetrahydrofuran (F) using an oligonucleotide transformation assay. The tetrahydrofuran analog and L were bypassed at 10-fold higher frequencies than the AP lesions. Bypass frequencies of lesions were greatly reduced in the absence of Rev1 or Polzeta (rev3 mutant), but were only marginally reduced in the absence of Poleta (rad30 mutant). Deoxycytidine was the preferred nucleotide inserted opposite an AP site whereas dA and dC were inserted at equal frequencies opposite F and L sites. In the rev1 and rev3 strains, dA was the predominant nucleotide inserted opposite these lesions. Overall, we conclude that both Rev1 and Polzeta are required for the efficient bypass of abasic sites in yeast.

The DNA repair enzyme uracil DNA glycosylase (UDG) utilizes base flipping to recognize and remove unwanted uracil bases from the genome but does not react with its structural congener, thymine, which differs by a single methyl group. Two factors that determine whether an enzyme flips a base from the duplex are its shape and hydrogen bonding properties. To probe the role of these factors in uracil recognition by UDG, we have synthesized a DNA duplex that contains a single difluorophenyl (F) nucleotide analogue that is an excellent isostere of uracil but possesses no hydrogen bond donor or acceptor groups. By using binding affinity measurements, solution 1 9 F NMR, and solid state 3 1 P{ 1 9 F} rotational-echo double-resonance (REDOR) NMR measurements, we establish that UDG partially unstacks F from the duplex. However, due to the lack of hydrogen bonding groups that are required to support an open-to-closed conformational transition in UDG, F cannot stably dock in the UDG active site. We propose that F attains a metastable unstacked state that mimics a previously detected intermediate on the uracil-flipping pathway and suggest structural models of the metastable state that are consistent with the REDOR NMR measurements.

Uracil DNA glycosylase (UDG) removes uracil from U·A or U·G base pairs in genomic DNA by extruding the aberrant uracil from the DNA base stack. A question in enzymatic DNA repair is whether UDG and related glycosylases also use an extrahelical recognition mechanism to inspect the integrity of undamaged base pairs. Using NMR imino proton exchange measurements we find that UDG substantially increases the equilibrium constant for opening of T-A base pairs by almost two orders of magnitude relative to free B-DNA. This increase is brought about by enzymatic stabilization of an open state of the base pair without increasing the rate constant for spontaneous base pair opening. These findings indicate a passive search mechanism in which UDG uses the spontaneous opening dynamics of DNA to inspect normal base pairs in a rapid genome-wide search for uracil in DNA.

Trifluoroacetic acid and benzenesulfonic acid in dichloromethane at ambient temperature have been found to be efficient co-catalysts for the epimerization of C -nucleosides with electron-withdrawing substituents. This approach provides a convenient route to the β anomer of the nucleosides with high yields in the range 54–78%. Synthesis of the 3′-phosphoramidite of 2,4-difluorophenyl C -nucleoside suitable for solid-phase DNA synthesis is described.

We have investigated the inhibition of the DNA repair enzyme uracil DNA glycosylase (UDG) by an 11-mer oligonucleotide (AIA) containing a cationic 1-aza-deoxyribose (I) residue designed to be a stable mimic of the high-energy oxacarbenium ion reaction intermediate [Werner, R. M., and Stivers, J. T. (2000) Biochemistry 39, 14054-14064]. Inhibition kinetics and direct binding studies indicate that AIA binds weakly to the free enzyme (K(D) = 2 microM) but binds 4000-fold more tightly to the enzyme-uracil anion (EU) product complex (K(D) = 500 pM). The importance of the positive charge on the 1-nitrogen in binding is established by the observation that AIA binds30 000-fold more tightly to the EU complex than the corresponding neutral tetrahydrofuran (F) abasic site product analogue (AFA). The unusual inhibition mechanism for AIA results in a time dependence that resembles slow-onset inhibition even though the apparent on-rate of the inhibitor for the EU(-) binary product complex is moderate (1 microM(-1) x s(-1)). Accordingly, the low K(D) of AIA for the EU complex is largely due its very slow off-rate (5 x 10(-4) x s(-1)). These results support previous kinetic isotope effect measurements that indicate UDG stabilizes a discrete oxacarbenium ion-uracil anion intermediate. This oxacarbenium ion mimic represents the tightest binding inhibitor of UDG yet identified.

The DNA repair enzyme uracil DNA glycosylase (UDG) is a powerful N-glycohydrolase that cleaves the glycosidic bond of deoxyuridine in DNA. We have investigated the role of substrate binding energy in catalysis by systematically dismantling the optimal substrate Ap(+1)UpA(-1)pA(-2) by replacing the nucleotides at the +1, -1, or -2 position with a tetrahydrofuran abasic site nucleotide (D), a 3-hydroxypropyl phosphodiester spacer (S), a phosphate monoester (p), or a hydroxyl group (h). Contrary to previous reports, the minimal substrate for UDG is 2'-deoxyuridine (hUh). UDG has a significant catalytic efficiency (CE) for hUh of 4 x 10(7) M(-1) [CE = (k(cat)/K(m))(1/k(non)), where k(non) is the rate of the spontaneous hydrolysis reaction of hUh at 25 degrees C]. Addition of +1 and -1 phosphate monoanions to form pUp increases k(cat)/K(m) by 45-fold compared to that of hUh. The k(cat)/K(m) for pUp, but not pU or Up, is found to decrease by 20-fold over the pH range of 6-9 with a pK(a) of 7.1, which is identical to the pK(a) values for deprotonation of the +1 and -1 phosphate groups determined by the pH dependence of the (31)P NMR chemical shifts. This pH dependence indicates that binding of the pUp tetraanion is disfavored, possibly due to unfavorable desolvation or electrostatic properties of the highly charged +1 and -1 phosphate groups. Addition of flexible hydroxypropyl groups to the +1 and -1 positions to make SpUpS increases k(cat)/K(m) by more than 10(5)-fold compared to that of hUh, which is a 20-fold greater effect than observed with rigid D substituents in these positions (i.e., DpUpD). The -2 phosphoester or nucleotide is found to increase the reactivity of trimer substrates with rigid furanose rings or nucleotides in the +1 and -1 positions by 1300-270000-fold (i.e., DpUpD --DpUpDpA or ApUpA --ApUpApA). In contrast, the -2 nucleotide provides only an 8-fold rate enhancement when appended to the substrate containing the more flexible +1 and -1 S substituents (SpUpS --SpUpSpA). These context-dependent effects of a -2 nucleotide are interpreted in terms of a mechanism in which the binding energy of this "handle" is used drive the rigid +1 and -1 A or D substituents into their binding pockets, resulting in a net catalytic benefit of -4.3 to -7.5 kcal/mol. Taken together, these results systematically track how UDG uses distant site binding interactions to produce an overall four billion-fold increase in CE compared to that of the minimal substrate hUh.

The DNA repair enzyme uracil DNA glycosylase (UDG) pinches the phosphodiester backbone of damaged DNA using the hydroxyl side chains of a conserved trio of serine residues, resulting in flipping of the deoxyuridine from the DNA helix into the enzyme active site. We have investigated the energetic role of these serine-phosphodiester interactions using the complementary approaches of crystallography, directed mutagenesis, and stereospecific phosphorothioate substitutions. A new crystal structure of UDG bound to 5'-HO-dUAAp-3' (which lacks the 5' phosphodiester group that interacts with the Ser88 pinching finger) shows that the glycosidic bond of dU has been cleaved, and that the enzyme has undergone the same specific clamping motion that brings key active site groups into position as previously observed in the structures of human UDG bound to large duplex DNA substrates. From this structure, it may be concluded that glycosidic bond cleavage and the induced fit conformational change in UDG can occur without the 5' pinching interaction. The S88A, S189A, and S192G "pinching" mutations exhibit 360-, 80-, and 21-fold damaging effects on k(cat)/K(m), respectively, while the S88A/S189A double mutant exhibits an 8200-fold damaging effect. A free energy analysis of the combined effects of nonbridging phosphorothioate substitution and mutation at these positions reveals the presence of a modest amount of strain energy between the compressed 5' and 3' phosphodiester groups flanking the bound uridine. Overall, these results indicate a role for these serine-phosphodiester interactions in uracil flipping and preorganization of the sugar ring into a reactive conformation. However, in contrast to a recent proposal [Parikh, S. S., et al. (2000) Proc Natl. Acad. Sci. 94, 5083], there is no evidence that conformational strain of the glycosidic bond induced by serine pinching plays a major role in the 10(12)-fold rate enhancement brought about by UDG.