Real-time monitoring of double-stranded DNA cleavage using molecular beacons

Traditional methods to assay enzymatic cleavage of DNA are discontinuous, time-consuming and laborious. Here, we report a new approach for real-time monitoring of double-stranded DNA cleavage by restriction endonuclease based on nucleic acid ligation using molecular beacon. Upon cleavage of DNA, the cleavage product can be ligated by DNA ligase, which results in a fluorescence enhancement of the molecular beacon. This method permits real-time monitoring of DNA cleavage and makes it easy to characterize the activity of restriction endonuclease and to study the cleavage reaction kinetics.     

Characterization of bleomycin cleavage sites in strongly bound hairpin DNAs

The first complete, systematic study of DNA degradation by bleomycin under conditions analogous to those likely in a therapeutic setting has been carried out. Hairpin DNAs selected for their ability to bind strongly to BLM A(5) were used to determine the relationship between high-affinity DNA binding sites and the cleavage efficiency and selectivity of BLM A(5) and deglycoBLM A(5) on these DNAs. Of the 10 hairpin DNAs examined, 8 contained at least one 5'-GC-3' or 5'-GT-3' cleavage site, which have traditionally been associated with strong cleavage by Fe·BLM. In the hairpin DNAs, these included the strongest cleavage sites for BLM A(5) and were generally among those for deglycoBLM A(5). However, numerous additional cleavages were noted, many at sequences not usually associated with (deglyco)BLM-mediated cleavage. The remaining DNAs lacked the preferred (5'-GC-3' or 5'-GT-3') BLM cleavage sequences; however, strong cleavage was nonetheless observed at a number of unusual cleavage sites. The most prominent cleavage sequences were 5'-AT-3', 5'-AA-3', 5'-GA-3', and 5'-TT-3'; treatment with Fe(II)·BLM A(5) or Fe(II)·deglycoBLM A(5) resulted in strong cleavage at these sequences. Additionally, in contrast with BLM A(5), which produced cleavage within the randomized and flanking invariant regions, deglycoBLM A(5) showed a preference for cleavage in the randomized region of the DNAs. Previous reports have established that deglycoBLM exhibits decreased DNA cleavage efficiency relative to BLM. This was also generally observed when comparing cleavage efficiencies for the strongly bound hairpin DNAs. However, some cleavage bands produced by Fe·deglycoBLM A(5) were stronger in intensity than those produced by BLM A(5) at concentrations optimal for both compounds. To investigate the chemistry of DNA degradation, selected hairpin DNAs were treated with n-butylamine following cleavage with Fe(II)·BLM A(5) or Fe(II)·deglycoBLM A(5) to explore the alkali labile pathway of DNA degradation by BLM. While all 10 DNAs showed evidence of alkali labile products, five DNA hairpins afforded some products formed solely via the alkali labile pathway.     

Element coding based accurate evaluation of CRISPR/Cas9 initial cleavage

As a powerful gene editing tool, the kinetic mechanism of CRISPR/Cas9 has been the focus for its further application. Initial cleavage events as the first domino followed by nuclease end trimming significantly affect the final on-target rate. Here we propose EC-CRISPR, element coding CRISPR, an accurate evaluation platform for initial cleavage that directly characterizes the cleavage efficiency and breaking sites. We benchmarked the influence of 19 single mismatch and 3 multiple mismatch positions of DNA-sgRNA on initial cleavage, as well as various reaction conditions. Results from EC-CRISPR demonstrate that the PAM-distal single mismatch is relatively acceptable compared to the proximal one. And multiple mismatches will not only affect the cleavage efficiency, but also generate more non-site #3 cleavage. Through in-depth research of kinetic behavior, we uncovered an abnormally higher non-#3 proportion at the initial stage of cleavage by using EC-CRISPR. Together, our results provided insights into cleavage efficiency and breaking sites, demonstrating that EC-CRISPR as a novel quantitative platform for initial cleavage enables accurate comparison of efficiencies and specificities among multiple CRISPR/Cas enzymes.

Initial cleavage events as the first domino of CRISPR/Cas9 kinetic behaviors. To accurately evaluate the initial cleavage of Cas9, element coding CRISPR platform-enabled direct characterization of the cleavage efficiency and cleavage sites was proposed.     

Mass spectrometry in structural and stereochemical problems—CCXLIV : The influence of substituents and stereochemistry on the mass spectral fragmentation of progesterone

The complete high resolution mass spectra of progesterone (Δ⁴-pregnene-3,20-dione) and twenty-nine stereoisomers and alkyl substituted analogs have been analyzed with the aid of the recently developed computer program INTSUM. Progesterone analogs with “normal” configuration at the six chiral skeletal carbon atoms give rise to abundant ions corresponding to cleavage of the 1–2 and 3–4 bonds (ketene elimination), to cleavage of the 6–7 and 9–10 bonds (ring B cleavage), and to cleavage of the 13–17 and 15–16 bonds (partial ring D cleavage); these reactions are frequently followed by elimination of alkyl radicals. Alkyl groups at C-6 and C-10 exert a pronounced influence on the formation and fragmentation of the [M-ketene] ions. Reversal of configuration at C-10 increases the importance of ring B cleavage, whereas reversal at C-17 favors the partial cleavage of ring D. The fragmentation of 17-alkylprogesterones differs significantly from the general pattern, with acetyl loss (cleavage of the 17–20 bond) and partial ring D cleavage as the predominating reactions. Loss of ring D by cleavage of the 13–17 and 14–15 bonds is not an important reaction of progesterones. Direct interaction of the two ketonic functions was not observed.     

Synthesis of well-defined telechelic trans-1,4-polyisoprene by oxidative cleavage

Synthesis of telechelic trans-1,4-polyisoprenes(TPI: trans-structure 95%) was evaluated based on two different methods of oxidative cleavage(indirect cleavage: first epoxidation of TPI, then the selective cleavage of epoxidized units in epoxidized trans-1,4-polyisoprene(ETPI) and direct cleavage of isoprene units in TPI). The influence of solvents and the ratio of oxidative agents was investigated by 1H-NMR and 13C-NMR. A series of well-defined telechelic TPI with double terminated functional groups and less side reaction(molecular weight distribution range: 1.96?2.26) were synthesized by indirect cleavage in chloroform. Telechelic TPI showed similar crystallization behavior with TPI and interesting cold crystallization behavior characterized by DSC.     

Specificity of immobilized porcine pepsin in H/D exchange compatible conditions

Statistical analysis of data from 39 proteins (13 766 amino acid residues) digested with immobilized porcine pepsin under conditions compatible with hydrogen/deuterium (H/D) exchange (<1 degrees C, <30 s) was performed to examine pepsin cleavage specificity. The cleavage of pepsin was most influenced by the amino acid residue at position P1. Phe and Leu are favored residues each with a cleavage probability greater than 40%. His, Lys, Arg, or Pro residues prohibit cleavage when found at the P1 position. Pro also cannot be at position P2 (cleavage probability <0.3%). Occupation of the P3 position by His, Lys, or Arg, or occupation of the P2' position by Pro, also leads to very little cleavage (cleavage probability <1.7%). The average cleavage probability over the entire data set was 13.6%, which is slightly lower than the value previously obtained by Powers et al. (14.8%). This is due, in part, to the larger protein sizes used in the current study. While the specificity of pepsin was similar to that previously observed, higher selectivity was observed in the present study due to less experimental variation in the conditions used to generate our database.     

Determination of Alkylphenols Originated from Alkylphenol Ethoxylates by Cleavage Treatment Combined with GC-MS

A chemical cleavage technique was developed for the determination of alkylphenol ethoxylates (APEOs) in environmental samples involving the conversion of APEOs to alkylphenols (APs). Aluminum triiodide (AlI₃) and trimethylsilyl iodide were selected as cleavage reagents and the former was found to be highly reactive and suitable. With AlI₃ as cleavage reagent, nonylphenol ethoxylates (NPEOs) and octylphenol ethoxylates (OPEOs) were equivalently converted to the corresponding origins—nonylphenol (NP) and octylphenol (OP), which were detected by gas chromatography—mass spectrometry (GC-MS). The cleavage process was completed under refluxing condition. Water and methanol influenced the cleavage reaction significantly and should be removed prior to the cleavage reaction. The analytical approach was applied for the estimation of APEOs contents in wastewater by normalizing to APs and presented satisfactory recovery and reproducibility. This cleavage technique provides a common and reliable means to assess the environmental significance of samples contaminated by APEOs based on the presence of APs.     

结合丝组二肽的树状多肽对λDNA的切割

以Fmoc手工固相合成法合成了以多聚赖氨酸为骨架, 表面结合丝组二肽的四分支和二分支树状多肽, 以高效液相色谱提纯, 电喷雾电离质谱表征, 并通过凝胶电泳法研究了其对λDNA的切割活性.     

Evaluation of gaseous hydrogen fluoride as a convenient reagent for parallel cleavage from the solid support

We have tested the limits of gaseous hydrogen fluoride as an agent for parallel detachment of organic molecules from the solid support. Peptides were chosen as relatively sensitive models for this reaction. Acid-catalyzed amide bond hydrolysis, side chain modification (tryptophan and other unnatural amino acids) by the protecting group residues as well as dehydration of serine and asparagine was followed. The technique of cleavage of side chain protection prior to the resin cleavage has given satisfactory results. Two-step deprotection and cleavage from benzhydrylamine resin by TFA and HF was compared to the deprotection and cleavage by TFA from Knorr resin.     

Alteration of the selectivity of DNA cleavage by a deglycobleomycin analogue containing a trithiazole moiety

The bleomycin (BLM) group of antitumor antibiotics effects DNA cleavage in a sequence-selective manner. Previous studies have indicated that the metal-binding and bithiazole moieties of BLM are both involved in the binding of BLM to DNA. The metal-binding domain is normally the predominant structural element in determining the sequence selectivity of DNA binding, but it has been shown that replacement of the bithiazole moiety with a strong DNA binder can alter the sequence selectivity of DNA binding and cleavage. To further explore the mechanism by which BLM and DNA interact, a trithiazole-containing deglycoBLM analogue was synthesized and tested for its ability to relax supercoiled DNA and cleave linear duplex DNA in a sequence-selective fashion. Also studied was cleavage of a novel RNA substrate. Solid-phase synthesis of the trithiazole deglycoBLM A(5) analogue was achieved using a TentaGel resin containing a Dde linker and elaborated from five key intermediates. The ability of the resulting BLM analogue to relax supercoiled DNA was largely unaffected by introduction of the additional thiazole moiety. Remarkably, while no new sites of DNA cleavage were observed for this analogue, there was a strong preference for cleavage at two 5'-GT-3' sites when a 5'-(32)P end-labeled DNA duplex was used as a substrate. The alteration of sequence selectivity of cleavage was accompanied by some decrease in the potency of DNA cleavage, albeit without a dramatic diminution. In common with BLM, the trithiazole analogue of deglycoBLM A(5) effected both hydrolytic cleavage of RNA in the absence of added metal ion and oxidative cleavage in the presence of Fe(2+) and O(2). In comparison with BLM A(5), the relative efficiencies of hydrolytic cleavage at individual sites were altered.     

硅-芳键的断裂反应

利用等摩尔竞争法我们研究了五种芳基三甲基硅烷与氯化氢的非均相断裂反应。用气体色谱法对各竞争反应产物进行定量分析,求出各断裂产物的相对性产率,结果表明其活性顺序是与相应的均相断裂反应相一致的。     

In Situ Raman Monitoring of Silver(I)‐Aided Laser‐Driven Cleavage Reaction of Cyclobutane

The cyclobutane cleavage reaction is an important process and has received continuous interest. Herein, we demonstrate the visible laser‐driven cleavage reaction of cyclobutane in crystal form by using in situ Raman spectroscopy. Silver(I) coordination‐induced strain and thermal effects from the laser irradiation are the two main driving forces for the cleavage of cyclobutane crystals. This work may open up a new avenue for studying cyclobutane cleavage reactions, as compared to the conventional routes using ex situ techniques.     

Asymmetric catalytic oxidative cleavage of polycyclic systems: the synthesis of atropisomeric diazonanes and diazecanes

Oxidative cleavage of internal double bonds in polycyclic systems can give access to compounds containing medium- to large-sized rings. In this example, the nine- and ten-membered ring containing compounds that resulted from the mCPBA-mediated (mCPBA=meta-chloroperoxybenzoic acid) oxidative cleavage reaction were shown to exhibit atropisomerism. The reaction of the polycyclic system with catalytic amounts of ruthenium tetraoxide followed by diol cleavage achieved the same synthetic goal. Use of the Nishiyama-Beller ruthenium-based catalysts enabled the synthesis of optically-enriched samples, providing the first example of an atropselective oxidative cleavage reaction.     

The mechanism of cleavage and isomerisation of RNA promoted by an efficient dinuclear Zn2+ complex

The cleavage and isomerisation of uridine 3'-alkylphosphates was studied in the presence of a dinuclear Zn(2+) complex, 3. The rate acceleration of the cleavage by 1 mM 3 is approximately 10(6)-fold under neutral conditions. Most remarkably, the complex also promotes the isomerisation of phosphodiester bonds, although the rate-enhancement is more modest: under neutral conditions complex 3 (1 mM) catalyses isomerisation by about 500-fold. The observation of this reaction shows that the reactions of these substrates catalysed by 3 proceed through a stepwise mechanism involving an intermediate phosphorane. A β(lg) value of -0.92 was determined for the 3-promoted cleavage reaction, and modest kinetic solvent deuterium isotope effects ranging from 1.5 to 2.8 were observed. Isomerisation was less sensitive to the nature of the esterifying group, with a β value of -0.5, and the kinetic solvent deuterium isotope effects were less than 1.5. Most of these characteristics of the 3-promoted cleavage are very similar to those for the cleavage of nucleoside 3'-phosphotriesters. These data are explained by a mechanism in which the complex primarily acts as an electrophilic catalyst neutralising the charge on the phosphate and stabilising an intermediate phosphorane, with general acid catalysis promoting the cleavage reaction. In contrast to the behaviour of triesters, isomerisation is significantly slower than cleavage; this suggests that the changes in geometry that occur during isomerisation lead to a much less stable complex between 3 and the phosphorane intermediate.     

Unimolecular decompositions of even-electron ions

Fragmentations of even-electron ions of lifetimes ≥10^?5s caused by electron and chemical ionization and by collisional activation have been correlated. Proposed reaction classifications include: cleavage of one bond with charge migration; cleavage of one bond through cyclization-displacement; cleavage of two bonds in a cyclic ion with charge retention; and cleavage of two bonds in an acyclic ion with rearrangement and charge retention. Such reactions are compared with those of odd-electron ions; despite a higher tendency for rearrangement, the decompositions of a positive even-electron ion, in particular as displayed in its collisional activation spectrum, have substantial utility for characterizing its structure.     

Promoting Tag Removal of a MBP-Fused Integral Membrane Protein by TEV Protease

Tag removal is a prerequisite issue for structural and functional analysis of affinity-purified membrane proteins. The present study took a MBP-fused membrane protein, MrpF, as a model to investigate the tag removal by TEV protease. Influences of the linking sequence between TEV cleavage site and MrpF on protein expression and predicted secondary structure were investigated. The steric accessibility of TEV protease to cleavage site of MBP-fused MrpF was explored. It was found that reducing the size of hydrophilic group of detergents and/or extending the linking sequence between cleavage site and target protein can significantly improve the accessibility of the cleavage site and promote tag removal by TEV protease.     

Regioselective cleavage of myoglobin with copper(II) compounds at neutral pH

Selective hydrolytic cleavage of myoglobin was studied with CuCl2, Cu(ClO4)2, Cu(AC)2, and binuclear Cu(II) complexes of 3,6,9,16,19,22-hexaaza-6,19-bis (2-hydroxyethyl)-tricyclo- [22,2,2,2(11,14)]-triaconta-1,11,13,24,27,29-hexaene (1) and 3,6,9,16,19,22-hexaaza-tricyclo-[22,2,2,2(11,14)]-triaconta- 1,11,13,24,27,29-hexaene (2). The sites of cleavage were precisely determined by LC-ESIMS and further confirmed by an MS/MS method through fragmentation from both the N-terminal and C-terminal. The peptide bonds of Gln91-Ser92 and Ala94-Thr95 were remarkably cleaved by Cu(II) anchored to the side chain of the His93 residue. The data presented in this study show that Cu(II)-mediated cleavage of myoglobin is able to proceed at neutral pH, more selectively than Pd(II)-mediated cleavage, and buffer solution of phosphate and NH4HCO3 accelerates the cleavage reaction.     

Studies on Model Interaction of Keggin-type Polyoxometalates with Nucleic Acid

Keggin anions behave differently from each other when they react with nucleic acids. The molybdenum series exhibits oxidative cleavage activity towards AMP and DNA. The mechanism of AMP damage and DNA cleavage caused by the molybdenum series is mainly oxidation and the oxidation sites are on the ribose parts other than on the adenine parts, while the hydrolysis probably makes significant contributions to the cleavage of DNA and to the damage of AMP caused by the tungsten series.     

环三聚磷腈多齿配体的合成及DNA的切割活性

为了得到具有核酸切割功能的人工核酸酶, 设计合成了5种环三聚磷腈多齿配体, 并初步检测了其对DNA的切割活性. 目标化合物的结构由IR, 1H NMR, 31P NMR, 13C NMR和ESI-MS确认. 在生理条件下对pUC19 DNA切割活性的初步实验结果表明, 在化合物5a～5e的Cu(Ⅱ)配合物存在下, 保温24 h后, pUC19 DNA由Form Ⅰ断裂为Form Ⅱ, 即合成目标化合物有明显的DNA切割活性. 同时, 考察了配合物5b+Cu在不同时间下对DNA的切割活性的影响.