BG4 antibody can recognize telomeric G-quadruplexes harboring destabilizing base modifications and lesions.

BG4 is a single-chain variable fragment antibody shown to bind various G-quadruplex (GQ) topologies with high affinity and specificity, and to detect GQ in cells, including GQ structures formed within telomeric TTAGGG repeats. Here, we used ELISA and single-molecule pull-down (SiMPull) detection to test how various lengths and GQ destabilizing base modifications in telomeric DNA constructs alter BG4 binding. We observed high-affinity BG4 binding to telomeric GQ independent of telomere length, although three telomeric repeat constructs that cannot form stable intramolecular GQ showed reduced affinity. A single guanine substitution with 8-aza-7-deaza-G, T, A, or C reduced affinity to varying degrees depending on the location and base type, whereas two G substitutions in the telomeric construct dramatically reduced or abolished binding. Substitution with damaged bases 8-oxoguanine and O6-methylguanine failed to prevent BG4 binding although affinity was reduced depending on lesion location. SiMPull combined with FRET revealed that BG4 binding promotes folding of telomeric GQ harboring a G to T substitution or 8-oxoguanine. Atomic force microscopy revealed that BG4 binds telomeric GQ with a 1:1 stoichiometry. Collectively, our data suggest that BG4 can recognize partially folded telomeric GQ structures and promote telomeric GQ stability.

Theoretical and DFT Study of Atypical Pentanuclear [(iPr3P)Ni]5Hn (n = 4, 6, 8) Clusters: What are the Rules?

The structure, bonding, and properties of a series of atypical pentanuclear nickel hydride clusters supported by electron-rich iPr3P of the type [(iPr3P)Ni]5Hn (n = 4, 6, 8; H4, H6, H8) and their anionic models where iPr3P are substituted by H- (H4', H6', H8') were investigated by density functional theory (DFT) calculations. All clusters were calculated to adopt a similar square pyramidal core geometry. Calculations indicate singlet ground states with small singlet-triplet gaps for H4 and H6, similar to previously reported experimental values. Molecular orbital theory description clusters were investigated using the simplified model complexes [HNi]5Hn5- (n = 4, 6, 8; H4', H6', H8'). The results show that there are three skeletal electron pairs (SEPs) in H4'. The addition of two molecules of H2 to form H6' and H8' results in the partial or full occupation of two degenerate MOs (e* set) that give two SEPs and one SEP, respectively. Indeed, the occupation of these low-lying weakly antibonding orbitals governs the multielectron chemistry available for these clusters and plays a role in their unique reactivity.

Dismantling of Vinyl Ethers by Pentanuclear [(iPr3 P)Ni]5 H6 : Facile Cooperative C-O, C-C and C-H Activation Pathways.

The [(iPr3 P)Ni]5 H6 cluster (1) and H2 C=CHOtBu react at room temperature to form the new pentanuclear NiH carbide [(iPr3 P)Ni]5 H4 (C)(CO) (3), along with an equivalent of isobutylene. This transformation requires the activation of multiple unreactive bonds, including C-H, C-C, and C(sp3 )-O bond cleavage. Analysis of the reaction mixture by 1 H NMR revealed the production of two additional paramagnetic species, assigned as [(iPr3 P)Ni]4 H4 (C-CH3 )NiOtBu (4 a) and [(iPr3 P)Ni]4 H4 (C-CH2 OtBu)NiOtBu (5 a), which arise from C(sp2 )-O bond cleavage and CH bond rearrangements. The reaction of 1 with H2 C=CHOSiMe2 CH2 Ph produced the isolable 4 a analogue [(iPr3 P)4 Ni5 ]H4 (CCH3 )(OSiMe2 CH2 Ph) (4 c). An isolable analogue of 5 a was obtained from the reaction of 1 with H2 C=CHOAd (Ad=1-admantyl), which produced [(iPr3 P)4 Ni5 ]H4 (CCH2 OAd)(OAd) (5 d). The utilization of both cluster faces and vertices for bonding substrate fragments in these transformations demonstrates the remarkable flexibility of the robust Ni5 H4 core in the cooperative activation of multiple C-O, C-C and C-H bonds.

Synthesis of Surface-Analogue Square-Planar Tetranuclear Nickel Hydride Clusters and Bonding to µ4-NR, -O and -BH Ligands.

Tetranuclear Ni complexes were synthesized with bonding to BH, NR, and O in atypical surface-like geometries. The previously reported electron-deficient cluster [( iPr3P)Ni]5H6 (1) reacts with N-methylmorpholine oxide to give [( iPr3P)Ni]4H4(µ4-O) (2), which contains O coordinated in the center of a square-plane arrangement of Ni atoms. Reaction of 1 with benzonitrile gave the square-planar tetranuclear Ni cluster [( iPr3P)Ni]4H4(µ4-NCH2Ph) (3), which contains an imido donor in a square-based-pyramidal geometry. This reaction also gives [( iPr3P)Ni(N≡CPh)]3 (4), with bridging benzonitrile ligands. Trimer 4 was independently synthesized from the reaction of Ni(COD)2, iPr3P, and PhC≡N. The addition of dihydrogen to a 1:1 mixture of [( iPr3P)2Ni]2(N2) and ( iPr3P)2NiCl2 yielded [( iPr3P)Ni]4(µ3-H)4(µ2-Cl)2 (5), with a tetrahedral Ni core, in contrast to the square-planar geometries of 2 and 3. The solid-state structure of 5 was determined using both X-ray and neutron diffraction. Reaction of 5 with LiBH4 gave [( iPr3P)Ni]4H4(µ4-BH)2] (6) via loss of LiCl and H2.

Novel m4C modification in type I restriction-modification systems.

We identify a new subgroup of Type I Restriction-Modification enzymes that modify cytosine in one DNA strand and adenine in the opposite strand for host protection. Recognition specificity has been determined for ten systems using SMRT sequencing and each recognizes a novel DNA sequence motif. Previously characterized Type I systems use two identical copies of a single methyltransferase (MTase) subunit, with one bound at each half site of the specificity (S) subunit to form the MTase. The new m4C-producing Type I systems we describe have two separate yet highly similar MTase subunits that form a heterodimeric M1M2S MTase. The MTase subunits from these systems group into two families, one of which has NPPF in the highly conserved catalytic motif IV and modifies adenine to m6A, and one having an NPPY catalytic motif IV and modifying cytosine to m4C. The high degree of similarity among their cytosine-recognizing components (MTase and S) suggest they have recently evolved, most likely from the far more common m6A Type I systems. Type I enzymes that modify cytosine exclusively were formed by replacing the adenine target recognition domain (TRD) with a cytosine-recognizing TRD. These are the first examples of m4C modification in Type I RM systems.

Nickel-Catalyzed C-H Silylation of Arenes with Vinylsilanes: Rapid and Reversible ß-Si Elimination.

The reaction of C6F5H and H2C═CHSiMe3 with catalytic [iPr2Im]Ni(η2-H2C═CHSiMe3)2 (1b) exclusively forms the C-H silylation product C6F5SiMe3 with ethylene as a byproduct ([iPr2Im] = 1,3-di(isopropyl)imidazole-2-ylidene). Catalytic C-H bond silylation is facile with partially fluorinated aromatic substrates containing two ortho fluorine substituents adjacent to the C-H bond and 1,2,3,4-tetrafluorobenzene. Less fluorinated substrates react slower. Under the same reaction conditions, catalytic [IPr]Ni(η2-H2C═CHSiMe3)2 (1a) ([IPr] = 1,3-bis[2,6-diisopropylphenyl]-1,3-dihydro-2H-imidazol-2-ylidene) provided only the alkene hydroarylation product C6F5CH2CH2SiMe3. Mechanistic studies reveal that the C-H activation and ß-Si elimination steps are reversible under catalytic conditions with both catalysts 1a and 1b. With catalytic 1a, reversible ethylene loss after ß-Si elimination was also observed despite its inability to catalyze C-H silylation; the reductive elimination step to form the silylation product is much slower than reductive elimination to form the alkene hydroarylation product. Reversible ethylene loss was not observed with 1b, which suggests that the rate-limiting step in the reaction is neither C-H activation nor ß-Si elimination but either ethylene loss or reductive elimination of cis-disposed aryl and SiMe3 moieties.

Facile Deep and Ultradeep Hydrodesulfurization by the [((i)Pr3P)Ni]5H6 Cluster Compared to Mononuclear Ni Sources.

The pentanuclear nickel cluster [((i)Pr3P)Ni]5H6 facilitates the room-temperature hydrodesulfurization of dibenzothiophene, 4-methyldibenzothiophene, and 4,6-dimethydibenzothiophene. These reactions provide the new tetranuclear nickel hydride sulfide [((i)Pr3P)Ni]4(µ-H)4(µ4-S) (1). In comparison, the dinuclear dinitrogen nickel complex [((i)Pr3P)2Ni]2(µ-N2) undergoes oxidative addition of the C-S bonds of dibenzothiophene and 4-methyl dibenzothiophene to provide the metallacycles Ni3(P(i)Pr3)3C12H8S (2) and Ni3(P(i)Pr3)3C13H10S (3), respectively, but 4,6-dimethydibenzothiophene is unreactive, even with heating to 70 °C for a week. The reaction of [((i)Pr3P)Ni]5H6 with SP(i)Pr3 in toluene provided [((i)Pr3P)Ni]5H6(S) (4), which was observed and characterized by NMR spectroscopy. The addition of vinyltrimethylsilane to 4 provided the best synthetic route to 1, with ((i)Pr3P)Ni(η(2)-CH2═CHSiMe3)2 (5) generated as a byproduct.

Breaking bonds and breaking rules: inert-bond activation by [(iPr3P)Ni]5H4 and catalytic stereospecific norbornene dimerization.

The facile carbon atom abstraction reaction by [(iPr3P)Ni]5H6 (1) with various terminal alkenes to give [(iPr3P)Ni]5H4(µ5-C) (2) occurs via a common highly reactive intermediate [(iPr3P)Ni]5H4 (3), which was isolated by the reaction of 1 with norbornene. Temperature dependent 1H and 31P{1H} NMR chemical shifts of 3 are consistent with a thermally populated triplet excited state only 2 kcal mol-1 higher energy than the diamagnetic ground state. Complex 3 catalyzes the dimerization of norbornene to stereoselectively provide exclusively (Z) anti-(bis-2,2'-norbornylidene).

Roles for the 8-Oxoguanine DNA Repair System in Protecting Telomeres From Oxidative Stress.

Telomeres are protective nucleoprotein structures that cap linear chromosome ends and safeguard genome stability. Progressive telomere shortening at each somatic cell division eventually leads to critically short and dysfunctional telomeres, which can contribute to either cellular senescence and aging, or tumorigenesis. Human reproductive cells, some stem cells, and most cancer cells, express the enzyme telomerase to restore telomeric DNA. Numerous studies have shown that oxidative stress caused by excess reactive oxygen species is associated with accelerated telomere shortening and dysfunction. Telomeric repeat sequences are remarkably susceptible to oxidative damage and are preferred sites for the production of the mutagenic base lesion 8-oxoguanine, which can alter telomere length homeostasis and integrity. Therefore, knowledge of the repair pathways involved in the processing of 8-oxoguanine at telomeres is important for advancing understanding of the pathogenesis of degenerative diseases and cancer associated with telomere instability. The highly conserved guanine oxidation (GO) system involves three specialized enzymes that initiate distinct pathways to specifically mitigate the adverse effects of 8-oxoguanine. Here we introduce the GO system and review the studies focused on investigating how telomeric 8-oxoguanine processing affects telomere integrity and overall genome stability. We also discuss newly developed technologies that target oxidative damage selectively to telomeres to investigate roles for the GO system in telomere stability.

Catalytic C-H bond stannylation: a new regioselective pathway to C-Sn bonds via C-H bond functionalization.

The ubiquitous Stille coupling reaction utilizes Sn-C bonds and is of great utility to organic chemists. Unlike the B-C bonds used in the Miyaura-Suzuki coupling reaction, which are readily obtained via direct borylation of C-H bonds, routes to organotin compounds via direct C-H bond functionalization are lacking. Here we report that the nickel-catalyzed reaction of fluorinated arenes and pyridines with vinyl stannanes does not provide the expected vinyl compounds via C-F activation but rather provides new Sn-C bonds via C-H functionalization with the loss of ethylene. This mechanism provides a new unanticipated methodology for the direct conversion of C-H bonds to carbon-heteroatom bonds.

Solid-state 91Zr NMR spectroscopy studies of zirconocene olefin polymerization catalyst precursors.

(91)Zr (I = 5/2) solid-state NMR (SSNMR) spectra of the zirconocene compounds, Cp(2)ZrCl(2), Cp*(2)ZrCl(2) (1), Cp(2)ZrBr(2) (2), (Me(3)SiC(5)H(4))(2)ZrBr(2) (3), O(Me(2)SiC(5)H(4))(2)ZrBr(2) (4), (1,3-C(5)H(3))(SiMe(2)OSiMe(2))(2)(1,3-C(5)H(3))ZrBr(2) (5), Ind(2)ZrCl(2) (6), Cp(2)ZrMeCl (7), Cp(2)ZrMe(2) (8), and [Cp(2)ZrMe][MeB(C(6)F(5))(3)] (9) have been acquired. Static (91)Zr SSNMR spectra have been acquired for all complexes at magnetic fields of 9.4 and 21.1 T. Cp(2)ZrCl(2) and complexes 1 to 5 possess relatively narrow central transition powder patterns which allows for magic-angle spinning (MAS) (91)Zr solid-state NMR spectra to be acquired at a moderate field strength of 9.4 T. Complexes 6 to 9 possess ultrawideline central transition SSNMR spectra necessitating piece-wise acquisition techniques. From the static and MAS (91)Zr SSNMR spectra, it is possible to measure (91)Zr electric field gradient (EFG) and chemical shift (CS) tensor parameters, as well as the Euler angles which describe their relative orientation. Basis sets and methods for the accurate quantum chemical calculation of (91)Zr EFG and CS tensors have been identified. The origin of the observed EFG and CS tensor parameters are further investigated by visualization of the EFG and CS tensor orientations within the molecular frames. Correlations between the observed and calculated NMR tensor parameters and molecular symmetry and structure are made. All of these observations suggest that (91)Zr SSNMR spectroscopy can be utilized to probe the molecular structure of a variety of homogeneous and heterogeneous olefin polymerization catalysts.

Mechanisms of nucleotide selection by telomerase.

Telomerase extends telomere sequences at chromosomal ends to protect genomic DNA. During this process it must select the correct nucleotide from a pool of nucleotides with various sugars and base pairing properties, which is critically important for the proper capping of telomeric sequences by shelterin. Unfortunately, how telomerase selects correct nucleotides is unknown. Here, we determined structures of Tribolium castaneum telomerase reverse transcriptase (TERT) throughout its catalytic cycle and mapped the active site residues responsible for nucleoside selection, metal coordination, triphosphate binding, and RNA template stabilization. We found that TERT inserts a mismatch or ribonucleotide ~1 in 10,000 and ~1 in 14,000 insertion events, respectively. At biological ribonucleotide concentrations, these rates translate to ~40 ribonucleotides inserted per 10 kilobases. Human telomerase assays determined a conserved tyrosine steric gate regulates ribonucleotide insertion into telomeres. Cumulatively, our work provides insight into how telomerase selects the proper nucleotide to maintain telomere integrity.

Mesityl alkyne substituents for control of regiochemistry and reversibility in zirconocene couplings: new synthetic strategies for unsymmetrical zirconacyclopentadienes and conjugated polymers.

Reaction of 2 equivs of MesC[triple bond]CPh with Cp(2)Zr(eta(2)-Me(3)SiC[triple bond]CSiMe(3))(pyr) afforded the zirconacyclopentadiene Cp(2)Zr[2,5-Ph(2)-3,4-Mes(2)C(4)]. The regiochemistry of this isomer (betabeta with respect to the mesityl substituents) was determined through single-crystal X-ray analysis and 2D (NOESY, HSQC, HMBC) NMR experiments. This selectivity is attributed largely to a steric-based directing effect of the o-methyl ring substituents since coupling of 1,3-dimethyl-2-(phenylethynyl)benzene with zirconocene gave a single regioisomer (o-xylyl groups in both beta-positions) while coupling of 1,3-dimethyl-5-(phenylethynl)benzene gave a statistical distribution of zirconacyclopentadiene regioisomers. The coupling reaction of 2 equivs of MeC[triple bond]CMes or PrC[triple bond]CMes with Cp(2)Zr(eta(2)-Me(3)SiC[triple bond]CSiMe(3))(pyr) at ambient temperature gave the betabeta regioisomers, Cp(2)Zr[2,5-Me(2)-3,4-Mes(2)C(4)] and Cp(2)Zr[2,5-Pr(2)-3,4-Mes(2)C(4)], respectively, as the major products. Heating solutions of these zirconacycles at 80 degrees C for several hours resulted in an increase in the amount of the unsymmetrical product. For reaction mixtures of PrC[triple bond]CMes and Cp(2)Zr(eta(2)-Me(3)SiC[triple bond]CSiMe(3))(pyr) the major (and apparently thermodynamic) product under these reaction conditions was Cp(2)Zr[2,4-Mes(2)-3,5-Pr(2)C(4)]. The steric strain in the mesityl-substituted zirconacycles allowed for facile substitution reactions of MesC[triple bond]CPh or PrC[triple bond]CMes by less bulky alkynes (i.e., tolan and 3-hexyne) to give the unsymmetrical ziconacyclopentadienes Cp(2)Zr[2,4,5-Ph(3)-3-MesC(4)], Cp(2)Zr[2-Ph-3-Mes-4,5-Et(2)C(4)], and Cp(2)Zr[2-Pr-3-Mes-4,5-Ph(2)C(4)]. Reaction of a mesityl-terminated diyne containing a rigid dihexylfluorenylene spacer with zirconocene afforded poly(p-fluorenylenedienylene) after demetalation with benzoic acid.

Selective C-F bond activation of tetrafluorobenzenes by nickel(0) with a nitrogen donor analogous to N-heterocyclic carbenes.

N, not NHC: A neutral, basic, strong sigma-donor nitrogen ancillary ligand with properties analogous to those of N-heterocyclic carbenes (NHCs) was developed to aid in the oxidative additions of challenging substrates to late transition metals. Selective, room-temperature C-F bond activation was observed with hexa-, penta-, and all three isomers of tetrafluorobenzene using a nickel(0) source in the presence of this donor.

Unexpected intermediates and products in the C-F bond activation of tetrafluorobenzenes with a bis(triethylphosphine)nickel synthon: direct evidence of a rapid and reversible C-H bond activation by Ni(0).

The reaction of (PEt(3))(2)Ni(eta(2)-C(14)H(10)), a source of the reactive Ni(PEt(3))(2) moiety, with 1,2,4,5-F(4)C(6)H(2) yields a mixture of three C-F bond activation products that include the unexpected products (PEt(3))(2)NiF-2,3,5,6-F(4)C(6)H and (PEt(3))(2)NiF-2,3,5-F(3)C(6)H(2). Monitoring the reaction mixture via (19)F and (1)H NMR also reveals the presence of the C-H bond activation product, (PEt(3))(2)NiH-2,3,5,6-F(4)C(6)H which is produced in a rapid equilibrium reaction. This observation provides insight into the steps necessary to modify nickel complexes for selective C-F bond activation in a variety of polyfluorinated aromatic substrates, but also expands the potential of simple nickel compounds for C-H bond activation and functionalization reactions.

Versatile (η6-arene)Ni(PCy3) nickel monophosphine precursors.

Nickel monophosphine arene adducts have been proposed as highly reactive intermediates capable of difficult C-O bond activation steps in Ni catalyzed cross-coupling reactions. The addition of N-methylmorpholine N-oxide to arene solutions of ([Cy3P)2Ni]2N2 allows for the synthesis of stable (η6-arene)Ni(PCy3) complexes. The isolation of these species demonstrates their viability as intermediates and provides an experimental means to test the hypothesized importance of the Ni(PCy3) moiety in bond activation and catalysis.

Facile assembly of a Cu9 amido complex: a new tripodal ligand design that promotes transition metal cluster formation.

A tripodal amido ligand with a central non-chelating phosphorus donor allows for the facile assembly of a pentane soluble organometallic copper cluster with a central copper atom surrounded by a nonplanar chain of eight copper atoms and two terminal amido-copper bonds.

Diamagnetic molybdenum nitride complexes supported by diligating tripodal triamido-phosphine ligands as precursors to paramagnetic phosphine donors.

The reaction of the ligand precursors P[CH2NHAr(R)]3 () with (Me2N)3Mo[triple bond, length as m-dash]N generated the complexes P(CH2NAr(R))3Mo[triple bond, length as m-dash]N (), where Ar(R) = 3,5-(CH3)2C6H3 (), Ph (), and 3,5-(CF3)2C6H3 (), with (Me2N)3Mo[triple bond, length as m-dash]N generated the complexes P(CH2NAr(R))3Mo[triple bond, length as m-dash]N (). Complex was obtained in poor yield, due to the formation of P(CH2N-3,5-(CF3)2C6H3)2(CH2NH-3,5-(CF3)2C6H3)(NMe2H)(NMe2)Mo[triple bond, length as m-dash]N () as the major product. Reaction of with VMes3THF generated the paramagnetic complexes P(CH2NAr(R))3Mo(µ-N)V(Mes)3 (). The reaction of with Ni(acac)2 generated the Ni(0) complexes Ni[P(CH2NAr(R))3Mo[triple bond, length as m-dash]N]4 () in poor yield. These complexes were synthesized in higher yields from the reaction of with Ni(COD)2, where COD = 1,5-cyclooctadiene. Reaction of either with V(Mes)3THF or with Ni(COD)2 generated the paramagnetic nonanuclear complex Ni[P(CH2NAr(R))3Mo(µ-N)VMes3]4 ().

Study of Bond Angles and Bond Lengths in Disiloxane and Related Molecules in Terms of the Topology of the Electron Density and Its Laplacian.

We have calculated the electron density distributions for the series of molecules H(n)XOXH(n), X = Li to F and Na to Cl, and some related molecules. We have analyzed these distributions and their Laplacian to obtain atomic charges, electron densities at the bond critical point, and the charge concentrations revealed by the Laplacian. On the basis of this information and an analysis of the X-O bond lengths and angles, we have examined the factors that determine the lengths of the X-O bonds and the XOX bond angles. The XO bond length reaches a minimum value at boron in period 2 and at silicon in period 3 when the product of the charges on X and O reaches a maximum value, consistent with a predominately ionic model for the molecules X = Li, Be, B, Na, Mg, Al, and Si. In the remaining molecules of both series, the XO bonds have an increasing covalent character. The bond length and the bond angle in disiloxane are consistent with the ionic character of the molecule, and there is no evidence for the frequently quoted back-bonding model. In disiloxane and related molecules in which the ligand is considerably less electronegative than oxygen the electrons in the valence shell of oxygen are not well localized into pairs, so the bond angle is intermediate between the tetrahedral angle expected when the valence shell electrons of oxygen are strongly localized into four tetrahedral pairs and the 180 degrees bond angle expected on the basis of the electrostatic and/or steric repulsion between the positively charged X atoms. The effects on the bond lengths and angles of substituting oxygen by sulfur and hydrogen by fluorine are discussed.