Preparation of short cytosine-modified oligonucleotides by nicking enzyme amplification reaction

A method for enzymatic production of short (10-20 nt) cytosine-modified oligonucleotides was developed by nicking enzyme amplification reaction using Vent(exo-) polymerase, Nt.BstNBI nicking endonuclease and 5-substituted dCTP derivatives. The methodology including isolation was scaled up to nanomolar amounts and was proved to be suitable for production of diverse base-modified short single-stranded oligonucleotides (inaccessible by other enzymatic methods) that are of potential interest as labelled primers or functionalized aptamers.     

1, 3-环己二烯与丙烯反应exo和endo机理的理论研究

采用从头算方法在3-21G基组上研究了1, 3-环己二烯与丙烯生成exo和endo产物的反应机理。该反应生成exo和endo产物各存在三条反应途径, 其中两条为分步途径, 一条为协同途径。经计算研究表明:1, 3-环己二烯与丙烯生成exo和endo产物的有利途径为经过一个双自由基中间体的分步过程, 由丙烯端位碳原子先进攻的分步过程最为容易。对应于该过程, 生成exo和endo产物的反应速控步骤的位垒值分别为80.69kJ/mol和75.58kJ/mol。表明生成endo产物的反应比生成exo产物的反应略为有利。     

Synthesis of Deoxynucleoside Triphosphates that Include Proline,Urea, or Sulfonamide Groups and Their Polymerase Incorporation into DNA

To expand the chemical array available for DNA sequences in the context of in vitro selection, I present herein the synthesis of five nucleoside triphosphate analogues containing side chains capable of organocatalysis. The synthesis involved the coupling of L ‐proline‐containing residues (dU^tPTP and dU^cPTP), a dipeptide (dU^FPTP), a urea derivative (dU^BpuTP), and a sulfamide residue (dU^BsTP) to a suitably protected common intermediate, followed by triphosphorylation. These modified dNTPs were shown to be excellent substrates for the Vent (exo^?) and Pwo DNA polymerases, as well as the Klenow fragment of E. coli DNA polymerase I, although they were only acceptable substrates for the 9°N_m polymerase. All of the modified dNTPs, with the exception of dU^BpuTP, were readily incorporated into DNA by the polymerase chain reaction (PCR). Modified oligonucleotides efficiently served as templates for PCR for the regeneration of unmodified DNA. Thermal denaturation experiments showed that these modifications are tolerated in the major groove. Overall, these heavily modified dNTPs are excellent candidates for SELEX.     

A facile graphene oxide-based DNA polymerase assay

The DNA polymerase assay is fundamental for related molecular biology investigations and drug screenings, however, the commonly used radioactive method is laborious and restricted. Herein, we report a novel, simple and cost-effective fluorometric DNA polymerase detection method by utilizing graphene oxide (GO) as a signal switch. In this strategy, in the absence of DNA polymerase, the fluorophore-labeled template ssDNA could be strongly adsorbed and almost entirely quenched by GO. However, as DNA polymerase exists, the polymerized dsDNA product might lead to a much lower quenching efficiency after addition of GO due to the much weaker interaction of dsDNA with GO than ssDNA, thus resulting in a much higher fluorescence signal detected. As proof of concept, the quantitative DNA polymerase activity assay was performed using the Klenow fragment exo(-) (KF(-)) as a model. It was confirmed that, after optimization of detection conditions, KF(-) activity could be sensitively detected through facile fluorescence measurements, with a detection limit of 0.05 U mL(-1) and a good linear correlation between 0.05-2.5 U mL(-1) (R(2) = 0.9928). In addition, this GO-based method was further inspected to evaluate the inhibitive behaviors of several drugs toward KF(-) activity, the result of which firmly demonstrated its potential application in polymerization-targeted drug screening.     

New chiral ferrocenyl P,S-ligands for highly diastereo-/enantioselective catalytic [3 + 2] cycloaddition of azomethine ylides with cyclic and acyclic enones

A new family of chiral ferrocenyl P,S-ligands has been developed and successfully applied in a highly endo-selective catalytic asymmetric cycloaddition of azomethine ylides with various enones, including cyclic and acyclic α-enones. For cyclic α-enones, a [Cu(CH(3)CN)(4)]ClO(4)/(R(c),S(Fc))-2f complex catalyzed the cycloaddition to give the sole endo-cycloadducts in perfect enantioselectivities (normally 99% ee), while an AgOAc/(R(c),S(Fc))-2f catalytic system exhibited good endo/exo selectivities (endo/exo = 91/9 to 96/4) and high enantiocontrol (up to 98% ee) for acyclic α-enones.     

Group 14 Metal Terminal Phosphides: Correlating Structure with |J(MP)|

A series of heavier group 14 element, terminal phosphide complexes, M(BDI)(PR(2)) (M = Ge, Sn, Pb; BDI = CH{(CH(3))CN-2,6-iPr(2)C(6)H(3)}(2); R = Ph, Cy, SiMe(3)) have been synthesized. Two different conformations (endo and exo) are observed in the solid-state; the complexes with an endo conformation have a planar coordination geometry at phosphorus (M = Ge, Sn; R = SiMe(3)) whereas the complexes possessing an exo conformation have a pyramidal geometry at phosphorus. Solution-state NMR studies reveal through-space scalar coupling between the tin and the isopropyl groups on the N-aryl moiety of the BDI ligand, with endo and exo exhibiting different J(SnC) values. The magnitudes of the tin-phosphorus and lead-phosphorus coupling constants, |J(SnP)| and |J(PbP)|, differ significantly depending upon the hybridization of the phosphorus atom. For Sn(BDI)(P{SiMe(3)}(2)), |J(SnP)| is the largest reported in the literature, surpassing values attributed to compounds with tin-phosphorus multiple-bonds. Low temperature NMR studies of Pb(BDI)(P{SiMe(3)}(2)) show two species with vastly different |J(PbP)| values, interpreted as belonging to the endo and exo conformations, with sp(2)- and sp(3)-hybridized phosphorus, respectively.     

Density functional computations of proton affinity and gas-phase basicity of proline

The proton affinity and gas-phase basicity of proline were evaluated by using density functional theory coupling the B3-LYP hybrid functional with the extended 6--311++G** basis set. Cis and trans conformations of the carboxyl moiety for both exo and endo ring structures were considered for the neutral proline. The results show that the most stable structure of proline has the endo ring conformation with the carboxyl group in the cis position. The structure at the global minimum is stabilized by an intramolecular hydrogen bond. The nitrogen of the ring in the exo form is the preferred protonation site. The calculated proton affinity (924.3 kJ mol(-1)) and gas-phase basicity (894.4 kJ mol(-1)) are in very good agreement with the experimental counterparts.     

Palladium(II)‐Catalyzed Aminotrifluoromethoxylation of Alkenes: Mechanistic Insight into the Effect of N‐Protecting Groups

An efficient palladium‐catalyzed regioselective 5‐exo aminotrifluoromethoxylation of alkenes has been established herein, which provides a practical route towards the synthesis of OCF₃‐containing pyrrolidines. tert‐Butyloxycarbonyl (Boc) as an amino protecting group plays a significant role in both the chemo‐ and regioselectivities. In addition, preliminary mechanistic studies reveal that the amino protecting group of substrates and the counter anion of palladium catalyst play critical roles in reaction efficiency presumably due to an isomerization of alkyl‐ Pd(II) intermediates. Moreover, the asymmetric 5‐exo aminotrifluoromethoxylation reaction has also been achieved by introducing a sterically bulky pyridinyl‐oxazoline ligand.     

exo-selective asymmetric Diels-Alder reaction catalyzed by diamine salts as organocatalysts

[reaction: see text] A novel binaphthyl-based diamine (R)-2 was designed and synthesized. A protonic acid-(R)-2 salt catalyst has the advantage of exhibiting unprecedented high exo selectivity in the asymmetric Diels-Alder reaction of alpha,beta-unsaturated aldehydes. For instance, the reaction between cinnamaldehyde and cyclopentadiene in the presence of 12 mol % of binaphthyl-based diamine (R)-2 and 10 mol % of p-TsOH.H(2)O in alpha,alpha,alpha-trifluorotoluene at -20 degrees C gave the corresponding exo cycloadduct with 92% ee as a major diastereomer (exo/endo = 13/1).     

Regioselective functionalization of iminophosphoranes through Pd-mediated C-H bond activation: C-C and C-X bond formation

The orthopalladation of iminophosphoranes [R(3)P=N-C(10)H(7)-1] (R(3) = Ph(3) 1, p-Tol(3) 2, PhMe(2) 3, Ph(2)Me 4, N-C(10)H(7)-1 = 1-naphthyl) has been studied. It occurs regioselectively at the aryl ring bonded to the P atom in 1 and 2, giving endo-[Pd(μ-Cl)(C(6)H(4)-(PPh(2=N-1-C(10)H(7))-2)-κ-C,N](2) (5) or endo-[Pd(μ-Cl)(C(6)H(3)-(P(p-Tol)(2)=N-C(10)H(7)-1)-2-Me-5)-κ-C,N](2) (6), while in 3 the 1-naphthyl group is metallated instead, giving exo-[Pd(μ-Cl)(C(10)H(6)-(N=PPhMe(2))-8)-κ-C,N](2) (7). In the case of 4, orthopalladation at room temperature affords the kinetic exo isomer [Pd(μ-Cl)(C(10)H(6)-(N=PPh(2)Me)-8)-κ-C,N](2) (11exo), while a mixture of 11exo and the thermodynamic endo isomer [Pd(μ-Cl)(C(6)H(4)-(PPhMe=N-C(10)H(7)-1)-2)-κ-C,N](2) (11endo) is obtained in refluxing toluene. The heating in toluene of the acetate bridge dimer [Pd(μ-OAc)(C(10)H(6)-(N=PPh(2)Me)-8)-κ-C,N](2) (13exo) promotes the facile transformation of the exo isomer into the endo isomer [Pd(μ-OAc)(C(6)H(4)-(PPhMe=N-C(10)H(7)-1)-2)-κ-C,N](2) (13endo), confirming that the exo isomers are formed under kinetic control. Reactions of the orthometallated complexes have led to functionalized molecules. The stoichiometric reactions of the orthometallated complexes [Pd(μ-Cl)(C(10)H(6)-(N=PPhMe(2))-8)-κ-C,N](2) (7), [Pd(μ-Cl)(C(6)H(4)-(PPh(2)[=NPh)-2)](2) (17) and [Pd(μ-Cl)(C(6)H(3)-(C(O)N=PPh(3))-2-OMe-4)](2) (18) with I(2) or with CO results in the synthesis of the ortho-halogenated compounds [PhMe(2)P=N-C(10)H(6)-I-8] (19), [I-C(6)H(4)-(PPh(2)=NPh)-2] (21) and [Ph(3)P=NC(O)C(6)H(3)-I-2-OMe-5] (23) or the heterocycles [C(10)H(6)-(N=PPhMe(2))-1-(C(O))-8]Cl (20), [C(6)H(5)-(N=PPh(2)-C(6)H(4)-C(O)-2]ClO(4) (22) and [C(6)H(3)-(C(O)-1,2-N-PPh(3))-OMe-4]Cl (24).     

Characterization of a Family B DNA Polymerase from the Hyperthermophilic Crenarchaeon Ignicoccus hospitalis KIN4/I and Its Application to PCR

A family B DNA polymerase gene from the hyperthermophilic crenarchaeon Ignicoccus hospitalis KIN4/I was highly expressed under the control of T7lac promoter of pET-28ARG in Escherichia coli BL21-CodonPlus(DE3)-RIL cells. The produced I. hospitalis (Iho) DNA polymerase was purified by heat treatment followed by HisTrap? HP column and HiTrap? SP column chromatographies. The molecular mass of the purified Iho DNA polymerase was 88 kDa as estimated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The optimal pH for Iho DNA polymerase activity was 7.0 and the optimal temperature was 70 °C. Iho DNA polymerase was strongly activated by the presence of magnesium ion at an optimum concentration of 3 mM. The optimal concentration of KCl for Iho DNA polymerase activity was 60 mM. The half-life of the enzyme at 94 °C was about 2 h. The optimal conditions for polymerase chain reaction (PCR) were determined. Iho DNA polymerase possesses 3′?→?5′ exonuclease activity, and the fidelity of the Iho DNA polymerase was similar to that of Pfu and Vent DNA polymerases. However, Iho DNA polymerase provided more enhanced efficiency of PCR amplification than Pfu and Vent DNA polymerases. Iho DNA polymerase could successfully amplify a 2-kb λ DNA target with a 10-s extension time and could amplify a DNA fragment up to 8 kb λ DNA.     

Cyclododecatetraene tetraepoxide: highly diastereofacial epoxidation of all-(Z)-1,4,7,10-cyclododecatetraene and selective synthesis of bridged bis-oxocanes

Epoxidation of all-(Z)-1,4,7,10-cyclododecatetraene has been investigated with use of m-CPBA and dimethyldioxirane in anhydrous solvent. The diastereoselectivity of multiple epoxidation steps is complete affording only exo,exo,exo,endo-1,4,7,10-tetraepoxide. To understand this result, the step-by-step epoxidation reaction was investigated and each step was found to be highly regio- and stereoselective. Finally, a Lewis acid-catalyzed ethanolysis or treatment with HBr/KBr of the tetraepoxide gave rearranged diepoxy-oxabicyclo[5.5.1]tridecane (bridged bis-oxocanes) in which eight stereocenters were controlled.     

CpRu((R)-Binop-F)(H2O)][SbF6], a new fluxional chiral Lewis acid catalyst: synthesis, dynamic nmr, asymmetric catalysis, and theoretical studies

The C(2)-symmetric electron-poor ligand (R)-BINOP-F (4) was prepared by reaction of (R)-BINOL with bis(pentafluorophenyl)-phosphorus bromide in the presence of triethylamine. The iodo complex [CpRu((R)-BINOP-F)(I)] ((R)-6) was obtained by substitution of two carbonyl ligands by (R)-4 in the in situ-prepared [CpRu(CO)(2)H] complex followed by reaction with iodoform. Complex 6 was reacted with [Ag(SbF(6))] in acetone to yield [CpRu((R)-BINOP-F)(acetone)][SbF(6)] ((R)-7). X-ray structures were obtained for both (R)-6 and (R)-7. The chiral one-point binding Lewis acid [CpRu((R)-BINOP-F)][SbF(6)] derived from either (R)-7 or the corresponding aquo complex (R)-8 activates methacrolein and catalyzes the Diels-Alder reaction with cyclopentadiene to give the [4 + 2] cycloadduct with an exo/endo ratio of 99:1 and an ee of 92% of the exo product. Addition occurs predominantly to the methacrolein C(alpha)-Re face. In solution, water in (R)-8 exchanges readily. Moreover, a second exchange process renders the diastereotopic BINOP-F phosphorus atoms equivalent. These processes were studied by the application of variable-temperature (1)H, (31)P, and (17)O NMR spectroscopy, variable-pressure (31)P and(17)O NMR spectroscopy, and, using a simpler model complex, density functional theory (DFT) calculations. The results point to a dissociative mechanism of the aquo ligand and a pendular motion of the BINOP-F ligand. NMR experiments show an energy barrier of 50.7 kJ mol(-1) (12.2 kcal mol(-1)) for the inversion of the pseudo-chirality at the ruthenium center.     

An experimental and theoretical study of stereoselectivity of furan-maleic anhydride and furan-maleimide diels-alder reactions

The stereoselectivity of the reaction of furan (1) with maleic anhydride (2) and maleimide (3) was studied experimentally and theoretically. Although the two reactions are highly similar with regard to their preference for endo and exo steroisomers, notable differences were experimentally observed and explained on the basis of calculated reaction-free energies and transition-state barriers. The experimental values of rate constants (k(1+2endo) = (1.75 +/- 0.48) x 10(-5); mol(-1) l s(-1); k(1+2exo) = (3.10 +/- 0.55) x 10(-5); mol(-1) l s(-1); k(1+3endo) = (1.93 +/- 0.082) x 10(-5); mol(-1) l s(-1), k(1+3exo) = (1.38 +/- 0.055) x 10(-5); mol(-1) l s(-1) all at 300 K) and the observed reaction course clearly confirm that neither of these reactions are prototypical examples of Diels-Alder [4 + 2] cycloadditions, whose dominant preference is for endo isomers. However, only by comparing their energetics-calculated at the CCSD(T) level of theory-with the analogous reactions involving cyclopentadiene (8) as a diene can these observations be understood. The low thermodynamic stability of furan [4 + 2] adducts opens retro-Diels-Alder reaction channels and overrules the very small kinetic preference (calculated and measured here) of initial formation for endo stereoisomers. On a macroscopic scale "an irregular"-thermodynamically more stable-exo stereoisomer was consequently observed as a dominant species.     

A simple approach to micropatterning and surface modification of poly(dimethylsiloxane)

Ozone treatment is an efficient economical, alternative method for surface activation of poly(dimethylsiloxane) (PDMS). This is illustrated by the derivatization of a PDMS surface with (3-aminopropyl)triethoxysilane (APTES). The apparent surface concentration of amino groups was found to be ca. 10(-8) mol/cm2 using UV/visible spectroscopy of the product from the reaction of the amino groups and fluorescamine. Potential application for micropatterning of biologically active interfaces was demonstrated by the covalent immobilization of oligonucleotides. A simple process for photolithographic patterning on PDMS surfaces has been developed.     

C-甲基硝酮与丙烯腈1,3-偶极环加成反应从头算研究

用从头算方法在MP2 / 6 31G(d)水平上研究了C 甲基硝酮与丙烯腈 1,3 偶极环加成反应 ,该反应可生成endo 4,exo 4,endo 5 ,exo 5四种不同的产物 ,反应势垒分别为 8.35、17.2 3、-0 .18和 4.88kJ/mol。在C 甲基硝酮与丙烯腈接近的过程中 ,首先生成 3个不同的氢键复合物 ,相对能量为 -4 7.8、-4 6 .6和 -33 .7kJ/mol。由这 3个不同的氢键复合物导致了 4个不同的过渡态而形成 4个不同的产物     

Pendant bases as proton relays in iron hydride and dihydrogen complexes

The complex trans-[HFe(PNP)(dmpm)(CH(3)CN)]BPh(4), 3, (where PNP is Et(2)PCH(2)N(CH(3))CH(2)PEt(2) and dmpm is Me(2)PCH(2)PMe(2)) can be successively protonated in two steps using increasingly strong acids. Protonation with 1 equiv of p-cyanoanilinium tetrafluoroborate in acetone-d(6) at -80 degrees C results in ligand protonation and the formation of endo (4a) and exo (4b) isomers of trans-[HFe(PNHP)(dmpm)(CH(3)CN)](BPh(4))(2). The endo isomer undergoes rapid intramolecular proton/hydride exchange with an activation barrier of 12 kcal/mol. The exo isomer does not exchange. Studies of the reaction of 3 with a weaker acid (anisidinium tetrafluoroborate) in acetonitrile indicate that a rapid intermolecular proton exchange interconverts isomers 4a and 4b, and a pK(a) value of 12 was determined for these two isomers. Protonation of 3 with 2 equiv of triflic acid results in the protonation of both the PNP ligand and the metal hydride to form the dihydrogen complex [(H(2))Fe(PNHP)(dmpm)(CH(3)CN)](3+), 11. Studies of related complexes [HFe(PNP)(dmpm)(CO)](+) (12) and [HFe(depp)(dmpm)(CH(3)CN)](+) (10) (where depp is bis(diethylphosphino)propane) confirm the important roles of the pendant base and the ligand trans to the hydride ligand in the rapid intra- and intermolecular hydride/proton exchange reactions observed for 4. Features required for an effective proton relay and their potential relevance to the iron-only hydrogenase enzymes are discussed.     

Stereocontrol in rare earth metal triflate-catalyzed 1,3-dipolar cycloaddition reaction of 2-benzopyrylium-4-olate with aldehydes

Exo-cycloadduct was obtained with high stereoselectivity by the addition of ytterbium triflate (Yb(OTf)(3)) (10 mol %) in the rhodium(II) acetate (Rh(2)(OAc)(4))-catalyzed decomposition of o-(methoxycarbonyl)-alpha-diazoacetophenone in the presence of benzaldehyde. In the reaction in the absence of Yb(OTf)(3), almost no selectivity was obtained. Stereoselectivity in the reactions with p-nitrobenzaldehyde, p-anisaldehyde, and benzyloxyacetaldehyde could be also controlled to high exo preference by the addition of Yb(OTf)(3).     

Effect of the leaving group on the reaction of 2-aminopyrroles with electron deficient heteroaromatic azadienes: substitution by addition-elimination versus cycloaddition

When a good leaving group is present in the heteroaromatic azadiene, reaction with 2-aminopyrroles occurs by substitution by addition-elimination instead of cycloaddition. This novel reaction is sensitive to steric effects and takes place in 2-amino-1-methylpyrrole at C-5 and the exo amino group but at C-3 in 2-amino-1-t-butylpyrrole.