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.     

Reduction of nitroarenes,azoarenes and hydrazine derivatives by an organic super electron donor

Reduction of nitrobenzene by excess organic electron donor, 12, affords diphenylhydrazine in a reaction where azobenzene oxide and azobenzene are likely intermediates. No cleavage of the N-N σ-bond is seen under photoactivation conditions, whereas traces are seen under thermal activation. Hydrazone derivatives were prepared to explore the cleavage of N-N σ-bonds; the results show that a low-lying LUMO assists the transition state for accepting an electron, and the stabilisation that the potential fragments from N-N bond cleavage afford to the fragments is important in determining whether cleavage is observed.     

Selective Cleavage of the HIV-1 TAR-RNA with a Peptide–Cyclen Conjugate

Covalent linkage of the arginine-rich fragment of the Tat protein to 1,4,7,10-tetraazacyclododecane (cyclen) results in the selective cleavage of the TAR-RNA of HIV-1 (see picture; the biotin at the 5′ end acts as a label for the subsequent analysis of the cleavage fragments). The cleavage occurs at room temperature and is diminished when Eu^III ions are present—at a concentration of about 1/10 of the concentration of the peptide–cyclen conjugate. The pH dependence indicates that two ammonium ions are responsible for the cleavage reaction. The white arrows in the schematic diagram mark the cleavage sites in RNase T1, and the black arrows the sites in the peptide–cyclen conjugate.     

Cuprous Oxide Catalyzed Oxidative CC Bond Cleavage for CN Bond Formation: Synthesis of Cyclic Imides from Ketones and Amines

Selective oxidative cleavage of a C? C bond offers a straightforward method to functionalize organic skeletons. Reported herein is the oxidative C? C bond cleavage of ketone for C? N bond formation over a cuprous oxide catalyst with molecular oxygen as the oxidant. A wide range of ketones and amines are converted into cyclic imides with moderate to excellent yields. In‐depth studies show that both α‐C? H and β‐C? H bonds adjacent to the carbonyl groups are indispensable for the C? C bond cleavage. DFT calculations indicate the reaction is initiated with the oxidation of the α‐C? H bond. Amines lower the activation energy of the C? C bond cleavage, and thus promote the reaction. New insight into the C? C bond cleavage mechanism is presented.     

Cuprous Oxide Catalyzed Oxidative C?C Bond Cleavage for C?N Bond Formation: Synthesis of Cyclic Imides from Ketones and Amines

Selective oxidative cleavage of a C C bond offers a straightforward method to functionalize organic skeletons. Reported herein is the oxidative C C bond cleavage of ketone for C N bond formation over a cuprous oxide catalyst with molecular oxygen as the oxidant. A wide range of ketones and amines are converted into cyclic imides with moderate to excellent yields. In‐depth studies show that both α‐C H and β‐C H bonds adjacent to the carbonyl groups are indispensable for the C C bond cleavage. DFT calculations indicate the reaction is initiated with the oxidation of the α‐C H bond. Amines lower the activation energy of the C C bond cleavage, and thus promote the reaction. New insight into the C C bond cleavage mechanism is presented.     

Mobile and localized protons: a framework for understanding peptide dissociation

Protein identification and peptide sequencing by tandem mass spectrometry requires knowledge of how peptides fragment in the gas phase, specifically which bonds are broken and where the charge(s) resides in the products. For many peptides, cleavage at the amide bonds dominate, producing a series of ions that are designated b and y. For other peptides, enhanced cleavage occurs at just one or two amino acid residues. Surface-induced dissociation, along with gas-phase collision-induced dissociation performed under a variety of conditions, has been used to refine the general 'mobile proton' model and to determine how and why enhanced cleavages occur at aspartic acid residues and protonated histidine residues. Enhanced cleavage at acidic residues occurs when the charge is unavailable to the peptide backbone or the acidic side-chain. The acidic H of the side-chain then serves to initiate cleavage at the amide bond immediately C-terminal to Asp (or Glu), producing an anhydride. In contrast, enhanced cleavage occurs at His when the His side-chain is protonated, turning His into a weak acid that can initiate backbone cleavage by transferring a proton to the backbone. This allows the nucleophilic nitrogen of the His side-chain to attack and form a cyclic structure that is different from the 'typical' backbone cleavage structures.     

Improved in-gel approaches to generate peptide maps of integral membrane proteins with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

This paper reports studies of in-gel digestion procedures to generate MALDI-MS peptide maps of integral membrane proteins. The methods were developed for the membrane domain of the mannitol permease of E. coli. In-gel digestion of this domain with trypsin, followed by extraction of the peptides from the gel, yields only 44% sequence coverage. Since lysines and arginines are seldomly found in the membrane-spanning regions, complete tryptic cleavage will generate large hydrophobic fragments, many of which are poorly soluble and most likely contribute to the low sequence coverage. Addition of the detergent octyl-beta-glucopyranoside (OBG), at 0.1% concentration, to the extraction solvent increases the total number of peptides detected to at least 85% of the total protein sequence. OBG facilitates the recovery of hydrophobic peptides when they are SpeedVac dried during the extraction procedure. Many of the newly recovered peptides are partial cleavage products. This seems to be advantageous since it generates hydrophobic fragments with a hydrophilic solubilizing part. In-gel CNBr cleavage resulted in 5-10-fold more intense spectra, 83% sequence coverage, fully cleaved fragments and no effect of OBG. In contrast to tryptic cleavage sites, the CNBr cleavage sites are found in transmembrane segments; cleavage at these sites generates smaller hydrophobic fragments, which are more soluble and do not need OBG. With the results of both cleavages, a complete sequence coverage of the membrane domain of the mannitol permease of E. coli is obtained without the necessity of using HPLC separation. The protocols were applied to two other integral membrane proteins, which confirmed the general applicability of CNBr cleavage and the observed effects of OBG in peptide recovery after tryptic digestion.     

Energetics and dynamics of the fragmentation reactions of protonated peptides containing methionine sulfoxide or aspartic acid via energy- and time-resolved surface induced dissociation

The surface-induced dissociation (SID) of six model peptides containing either methionine sulfoxide or aspartic acid (GAILM(O)GAILR, GAILM(O)GAILK, GAILM(O)GAILA, GAILDGAILR, GAILDGAILK, and GAILDGAILA) have been studied using a specially configured Fourier transform ion-cyclotron resonance mass spectrometer (FT-ICR MS). In particular, we have investigated the energetics and dynamics associated with (i) preferential cleavage of the methionine sulfoxide side chain via the loss of CH3SOH (64 Da), and (ii) preferential cleavage of the amide bond C-terminal to aspartic acid. The role of proton mobility in these selective bond cleavage reactions was examined by changing the C-terminal residue of the peptide from arginine (nonmobile proton conditions) to lysine (partially mobile proton conditions) to alanine (mobile proton conditions). Time- and energy-resolved fragmentation efficiency curves (TFECs) reveal that selective cleavages due to the methionine sulfoxide and aspartic acid residues are characterized by slow fragmentation kinetics. RRKM modeling of the experimental data suggests that the slow kinetics is associated with large negative entropy effects and these may be due to the presence of rearrangements prior to fragmentation. It was found that the Arrhenius pre-exponential factor (A) for peptide fragmentations occurring via selective bond cleavages are 1-2 orders of magnitude lower than nonselective peptide fragmentation reactions, while the dissociation threshold (E0) is relatively invariant. This means that selective bond cleavage is kinetically disfavored compared to nonselective amide bond cleavage. It was also found that the energetics and dynamics for the preferential loss of CH3SOH from peptide ions containing methionine sulfoxide are very similar to selective C-terminal amide bond cleavage at the aspartic acid residue. These results suggest that while preferential cleavage can compete with amide bond cleavage energetically, dynamically, these processes are much slower compared to amide bond cleavage, explaining why these selective bond cleavages are not observed if fragmentation is performed under mobile proton conditions. This study further affirms that fragmentation of peptide ions in the gas phase are predominantly governed by entropic effects.     

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.     

Ring Cleavage of N-Alkylisothiazolilm Salts by Complex Metal Hydrides. Synthesis of β-Enaminothioketones

N-Alkylisothiazolium salts undergo ring cleavage when treated with complex metal hydrides to give β-enami-nothioketones in high yields.

The isothiazole nucleus is remarkably stable to chemical attack by reducing agents.¹ In fact, little work has been published on reactions involving reductive cleavage of the isothiazole ring. Thus, other azole systems as isoxazole are readily cleaved by catalytic hydrogenolysis whereas the isothiazole nucleus, in the same conditions, remains unchanged.² However there are instances in which ring cleavage occurs. For example, cleavage of isothiazole during lithiation at the 5-position gives a small proportion of a β-mercaptoenone resulting from the cleavage of the N-S bond.^3,4 Isothiazoles are reductively desulfu-rized by Raney nickel and this method has been used by Woodward in a remarkable synthesis of colchicine.⁵     

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.     

A novel salt bridge mechanism highlights the need for nonmobile proton conditions to promote disulfide bond cleavage in protonated peptides under low-energy collisional activation

The gas-phase fragmentation mechanisms of small models for peptides containing intermolecular disulfide links have been studied using a combination of tandem mass spectrometry experiments, isotopic labeling, structural labeling, accurate mass measurements of product ions, and theoretical calculations (at the MP2/6-311 + G(2d,p)//B3LYP/3-21G(d) level of theory). Cystine and its C-terminal derivatives were observed to fragment via a range of pathways, including loss of neutral molecules, amide bond cleavage, and S-S and C-S bond cleavages. Various mechanisms were considered to rationalize S-S and C-S bond cleavage processes, including charge directed neighboring group processes and nonmobile proton salt bridge mechanism. Three low-energy fragmentation pathways were identified from theoretical calculations on cystine N-methyl amide: (1) S-S bond cleavage dominated by a neighboring group process involving the C-terminal amide N to form either a protonated cysteine derivative or protonated sulfenyl amide product ion (44.3 kcal mol(-1)); (2) C-S bond cleavage via a salt bridge mechanism, involving abstraction of the alpha-hydrogen by the N-terminal amino group to form a protonated thiocysteine derivative (35.0 kcal mol(-1)); and (3) C-S bond cleavage via a Grob-like fragmentation process in which the nucleophilic N-terminal amino group forms a protonated dithiazolidine (57.9 kcal mol(-1)). Interestingly, C-S bond cleavage by neighboring group processes have high activation barriers (63.1 kcal mol(-1)) and are thus not expected to be accessible during low-energy CID experiments. In comparison to the energetics of simple amide bond cleavage, these S-S and C-S bond cleavage reactions are higher in energy, which helps rationalize why bond cleavage processes involving the disulfide bond are rarely observed for low-energy CID of peptides with mobile proton(s) containing intermolecular disulfide bonds. On the other hand, the absence of a mobile proton appears to "switch on" disulfide bond cleavage reactions, which can be rationalized by the salt bridge mechanism. This potentially has important ramifications in explaining the prevalence of disulfide bond cleavage in singly protonated peptides under MALDI conditions.     

Site-specific DNA photocleavage by rhodium intercalators analyzed by MALDI-TOF mass spectrometry

The DNA photocleavage reaction of mismatch-selective Rh complexes has been analyzed by MALDI-TOF mass spectrometry as well as gel electrophoresis analysis of radioactively tagged oligonucleotides. Analogous results are obtained with these two techniques showing site-specific cleavage neighboring the mismatch to yield primarily 5'- and 3'-phosphate termini. Additional intermediates and products are observed, however, using MALDI-TOF analysis. MALDI-TOF mass spectrometry is seen to be particularly powerful in the analysis of DNA cleavage by site-specific molecules. The method requires no radioactive labeling, only little material, and analysis can be accomplished within minutes. Moreover, this mass spectral analysis of DNA cleavage yields direct information regarding products rather than simply the base pair site of cleavage.     

Thioethers as Dichotomous Electrophiles for Site-Selective Silylation via C−S Bond Cleavage

The development of aryl alkyl sulfides as dichotomous electrophiles for site-selective silylation via C−S bond cleavage has been achieved. Iron-catalyzed selective cleavage of C(aryl)−S bonds can occur in the presence of β-diketimine ligands, and the cleavage of C(alkyl)−S bonds can be achieved by t-BuONa without the use of transition metals, resulting in the corresponding silylated products in moderate to excellent yields. Mechanistic studies suggest that Fe−Si species may undergo metathesis reactions during the cleavage of C(aryl)−S bonds, while silyl radicals are involved during the cleavage of C(alkyl)−S bonds.     

Backbone and side-chain cleavages in electron detachment dissociation (EDD)

Ab-initio electronic structure methods are used to explore potential energy profiles pertinent to the fragmentations of gas-phase radicals thought to be formed in the new negative-ion mode EDD mass spectroscopic studies of peptides. Barriers to fragmentation as well as the associated overall energy differences are computed for the observed Calpha-C backbone bond cleavage as well as for side-chain loss for a variety of side chains (valine, arginine, glutamic acid, and tyrosine). It is found that Calpha-C bond cleavage is favored over side-chain loss, although loss of a tyrosine side chain may compete with Calpha-C cleavage because the tyrosine radical formed can delocalize its unpaired electron over its aromatic ring. In addition, it is found that fragmentation of the nitrogen-centered radicals formed in EDD results in cleavage to produce so-called a*/x fragments rather than a/x* fragments both because producing the former involves a significantly smaller barrier and is nearly thermoneutral, while cleavage to yield a/x* is significantly endothermic.     

Identification of strong DNA binding motifs for bleomycin

The bleomycins (BLMs) are clinically used antitumor antibiotics. Their mechanism of action is believed to involve oxidative cleavage of DNA and possibly also RNA degradation. DNA degradation has been studied extensively and shown to involve binding of an activated metallobleomycin to DNA, followed by abstraction of C4'-H from deoxyribose in the rate-limiting step for DNA degradation. It is interesting that while DNA and RNA degradation by activated Fe.BLM has been studied extensively, much less is known about the actual binding selectivity of BLM, that is, the obligatory step that precedes cleavage. Thus it is unclear whether cleavage specificity is defined by the binding event or whether cleavage occurs at a subset of preferred binding sites. With only a few exceptions, NMR binding studies have employed metalloBLMs such as Co.BLM and Zn.BLM whose therapeutic relevance is uncertain. A single biochemical study that compared DNA binding and cleavage directly also employed Co.BLM. It is logical to anticipate that preferred sites of DNA cleavage will occur at sites that are (a subset of) preferred DNA binding sites, but there are currently no data available relevant to this issue. Herein, we describe the development and implementation of a novel strategy to identify DNA motifs that bind BLM strongly.     

Computational study on nonenzymatic peptide bond cleavage at asparagine and aspartic acid

Nonenzymatic peptide bond cleavage at asparagine (Asn) and glutamine (Gln) residues has been observed during peptide deamidation experiments; cleavage has also been reported at aspartic acid (Asp) and glutamic acid (Glu) residues. Although peptide backbone cleavage at Asn is known to be slower than deamidation, fragmentation products are often observed during peptide deamidation experiments. In this study, mechanisms leading to the cleavage of the carboxyl-side peptide bond of Asn and Asp residues were investigated using computational methods (B3LYP/6-31+G**). Single-point solvent calculations at the B3LYP/6-31++G** level were carried out in water, utilizing the integral equation formalism-polarizable continuum (IEF-PCM) model. Mechanism and energetics of peptide fragmentation at Asn were comparatively analyzed with previous calculations on deamidation of Asn. When deamidation proceeds through direct hydrolysis of the Asn side chain or through cyclic imide formationvia a tautomerization routeit exhibits lower activation barriers than peptide bond cleavage at Asn. The fundamental distinction between the mechanisms leading to deamidationvia a succinimideand backbone cleavage was found to be the difference in nucleophilic entities involved in the cyclization process (backbone versus side-chain amide nitrogen). If deamidation is prevented by protein three-dimensional structure, cleavage may become a competing pathway. Fragmentation of the peptide backbone at Asp was also computationally studied to understand the likelihood of Asn deamidation preceding backbone cleavage. The activation barrier for backbone cleavage at Asp residues is much lower (approximately 10 kcal/mol) than that at Asn. This suggests that peptide bond cleavage at Asn residues is more likely to take place after it has deamidated into Asp.     

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.     

Semiempirical Analysis of the Homolytic Decomposition of Peresters with the Concerted Cleavage of Two Bonds

The parabolic model of a bimolecular reaction is modified to study the monomolecular decomposition of molecules into radicals by the cleavage of several bonds. Together with the oscillation model of molecule decomposition with the concerted cleavage of several bonds, this model is used to analyze the kinetic data on the decomposition of 16 peresters with the simultaneous cleavage of C–C and O–O bonds. Parameters characterizing this decomposition are obtained and multiple variants in representing such decomposition in terms of the parabolic model are discussed.     

Ether Cleavage with Organo-Alkali-Metal Compounds and Alkali Metals

Reactions with organo-alkali-metal compounds are mostly carried out in ether-type solvents. It has long been known that ether cleavage takes place at the same time. The mechanism of the cleavage, in particular the fact that dialkyl ethers can be decomposed by a variety of mechanisms acting simultaneously, has only become clear in the most recent investigations. The observation that even with purely aliphatic ethers a considerable amount of Wittig ether rearrangement can occur is remarkable. Unusual secondary reactions can also occur by means of which alkyl- and aryllithium compounds in ether or tetrahydrofuran yield new organolithium compounds—sometimes with rearrangement. The reactions of alkyl aryl ethers with alkali metals are also varied and five different mechanisms for them have been discussed in the literature. It is interesting, for example, that the cleavage of anisole can be directed simply by changing the solvent so that in one case only cleavage of the aryl-oxygen bond occurs and in the other almost 100% cleavage of the alkyl-oxygen bond results. The formation of biphenyl as a by-product upon cleavage of the alkyl-oxygen bond in anisole was also puzzling. This was later shown to occur not through the dimerization of phenyl radicals but via 2-methoxybiphenyl. The number of cleavage mechanisms reduces to two if one assumes two different σ^*-radical anions as being intermediates in the kinetically controlled reaction. Comparison of the reactivity of thioethers and ethers reveals not only gradual but also fundamental differences—the cleavage of the thioethers is thermodynamically controlled.