Synthesis of Oligonucleotides containing the cis-Interstrand Crosslink Produced by Mitomycins in their Reaction with DNA.

Mitomycin C (MC) an antitumor drug and decarbamoylmitomycin C (DMC), a derivative of MC lacking the carbamoyl moiety, are DNA alkylating agents which can form DNA interstrand crosslinks (ICLs) between deoxyguanosine residues located on opposing DNA strands. MC forms primarily deoxyguanosine adducts with a 1"-R stereochemistry at the guanine-mitosene bond (1"-α, trans) whereas DMC forms mainly adducts with a 1"-S stereochemistry (1"-ß, cis). The crosslinking reaction is diastereospecific: trans-crosslinks are formed exclusively at CpG sequences, while cis-crosslinks are formed only at GpC sequences. Until now, oligonucleotides containing 1"-ß-deoxyguanosine adducts or ICL at a specific site could not be synthesized, thus limiting the investigation of the role played by the stereochemical configuration at C1'' in the toxicity of these compounds. Here, a novel biomimetic synthesis to access these substrates is presented. Structural proof of the adducted oligonucleotides and ICL were provided by enzymatic digestion to nucleosides, high resolution mass spectral analysis, CD spectroscopy and UV melting temperature studies. Finally, a virtual model of the 25-mer 1"-ß ICL synthesized was created to explore the conformational space and structural features of the crosslinked duplex.

Synthesis of Mitomycin C and decarbamoylmitomycin C N6 deoxyadenosine-adducts.

Mitomycin C (MC), an anti-cancer drug, and its analog, decarbamoylmitomycin C (DMC), are DNA-alkylating agents. MC is currently used in the clinics and its cytotoxicity is mainly due to its ability to form Interstrand Crosslinks (ICLs) which impede DNA replication and, thereby, block cancer cells proliferation. However, both MC and DMC are also able to generate monoadducts with DNA. In particular, we recently discovered that DMC, like MC, can form deoxyadenosine (dA) monoadducts with DNA. The biological role played by these monoadducts is worthy of investigation. To probe the role of these adducts and to detect them in enzymatic digests of DNA extracted from culture cells treated by both drugs, we need access to reference compounds i.e. MC and DMC dA-mononucleoside adducts. Previous biomimetic methods used to generate MC and DMC mononucleoside adducts are cumbersome and very low yielding. Here, we describe the diastereospecific chemical synthesis of both C-1 epimers of MC and DMC deoxyadenosine adducts. The key step of the synthesis involves an aromatic substitution reaction between a 6-fluoropurine 2'-deoxyribonucleoside and appropriately protected stereoisomeric triaminomitosenes to form protected-MC-dA adducts with either an S or R stereochemical configuration at the adenine-mitosene linkage. Fluoride-based deprotection methods generated the final four reference compounds: the two stereoisomeric MC-dA adducts and the two stereoisomeric DMC-dA adducts. The MC and DMC-dA adducts synthesized here will serve as standards for the detection and identification of such adducts formed in the DNA of culture cells treated with both drugs.

A Versatile Bis-Allylboron Reagent for the Stereoselective Synthesis of Chiral Diols.

Allylboron reagents are popular in synthesis owing to their versatility and the predictable stereochemical outcomes of their reactions with carbonyl compounds. Herein, we describe the synthesis of (Z,Z)-hexadienyl bis-boronate 1, a configurationally stable, crystalline, and easy to handle compound, which represents a class of bis-allylic boron reagents with heretofore untapped synthetic potential. In combination with a chiral phosphoric acid catalyst, the reagent can be employed for the enantioselective allyl transfer reaction to a variety of one-pot transformations, enabling swift access to functionalized 1,n-diols. The in situ conversion of the reagent into the corresponding bis-borinic ester allows for the direct and diastereoselective two-fold allyl transfer to aldehydes. This affords C2 - or Ci -symmetric stereotetrads containing a 1,4-diol moiety for natural product synthesis. The usefulness of our method was demonstrated with a short synthesis of the lignan (±)-neo-olivil.

Comparative analysis of condom lubricants on pre & post-coital vaginal swabs using AccuTOF-DART.

In this study we demonstrate the use of Direct Analysis in Real Time Mass Spectrometry (DART) as a powerful tool for detection of nonoxynol in vaginal fluid post contact with a condom, enabling rapid tracing and added evidences in sexual assault crimes. Vaginal fluid was sampled using cotton swabs and glass rods and measured directly with DART. Sample preparation using water, hexane, methanol, and dichloromethane extraction, was explored for comparison and optimization of signals. Nonoxynol was detected up to eight hours after sampling. Optimal sampling conditions and mass spectrometry parameters are reported and discussed.

Circular dichroism analysis of the calicheamicin-DNA interaction revisited.

Calicheamicin, γ1I, is a remarkable DNA binding-cleaving, enediyne-containing, natural product that exhibits potent antitumor activity. In this study, we used electronic circular dichroism spectroscopy to monitor potential drug-induced DNA conformational changes and DNA induced conformational changes in the calicheamicin aglycone. Three DNA dodecamer sequences were examined: one containing a primary TCCT binding/cleavage site and two dodecamers containing less prominent CTCT and TCTC sites. The binding was monitored by taking advantage of the drug's unique negative exciton couplet (-313nm/+275nm) in phosphate buffer/ethanol 10%. Specifically the CD analysis focused at the longest wavelength region around 313nm where there is no interference by the positive CD contributions of the DNA. Upon binding at a DNA/drug ratio of 1/1.2 and 1/2.7 a slight red shift from 313nm to 319nm was observed. At a ratio of 1/1.2, the CE intensity remained practically unchanged from that of free drug, which indicates no conformational changes in the bound aglycone itself. A larger amount of drug, at a molar ratio of DNA/drug of 1/2.7 but especially at 1/6 and up to 1/10, however, caused a surprisingly distinct decrease in the intensity at this negative CD band and a further small red-shift to 322nm, evidence for non-specific binding.

Chiral tetranuclear and dinuclear copper(ii) complexes for TEMPO-mediated aerobic oxidation of alcohols: are four metal centres better than two?

The one-pot reaction of 3,5-di-tert-butyl-2-hydroxybenzaldehyde, (R)-2-aminoglycinol and Cu(OAc)2·2H2O in a 1 : 1 : 1 ratio in the presence of triethylamine led to the isolation of X-ray quality crystals of the chiral complex (R)- in high yield. The single crystal structure of (R)- reveals a tetranuclear copper(ii) complex that contains a {Cu4(µ-O)2(µ3-O)2N4O4} core. A reaction using (1S,2R)-2-amino-1,2-diphenylethanol as precursor under the same conditions generated the chiral complex (S,R)-; its structure was determined by single crystal X-ray crystallography and was found to contain a {Cu2(µ-O)2N2O2} core. Both (R)- and (S,R)- have been used for catalytic aerobic oxidation of benzylic alcohols in combination with the TEMPO (2,2,6,6-tetramethylpiperidinyl-1-oxyl) radical. (R)- selectively catalyses the conversion of various aromatic primary alcohols to the corresponding aldehydes with high yields (99%) and TONs (770) in the air, while (S,R)- exhibits less promising catalytic performance under the same reaction conditions. The role of the cluster structures in (R)- and (S,R)- in controlling the reactivity towards aerobic oxidation reactions is discussed.

A direct stereoselective preparation of a fish pheromone and application of the zinc porphyrin tweezer chiroptical protocol in its stereochemical assignment.

A two-step stereoselective preparation of a goldfish pheromone, 17α,20ß-dihydroxy-4-pregnen-3-one, is reported from the readily available cortexolone in 64% overall yield. The (20S)-epimer was also synthesized in three steps from cortexolone with an overall yield of 47%. A microscale chiroptical technique based on a host/guest complexation mechanism between the substrate and a dimeric metalloporphyrin host (tweezer) was used to confirm the stereochemical assignment, while Density Functional Theory (DFT) calculations were employed to explain the high stereoselectivity induced by the 17α-hydroxyl and C18-methyl groups.

Bulky melamine-based Zn-porphyrin tweezer as a CD probe of molecular chirality.

The transfer of chirality from a guest molecule to an achiral host is the subject of significant interest especially when, upon chiral induction, the chiroptical response of the host/guest complex can effectively report the absolute configuration (AC) of the guest. For more than a decade, dimeric metalloporphyrin hosts (tweezers) have been successfully applied as chirality probes for determination of the AC for a wide variety of chiral synthetic compounds and natural products. The objective of this study is to investigate the utility of a new class of melamine-bridged Zn-porphyrin tweezers as sensitive AC reporters. A combined approach based on an experimental CD analysis and a theoretical prediction of the prevailing interporphyrin helicity demonstrates that these tweezers display favorable properties for chiral recognition. Herein, we discuss the application of the melamine-bridged tweezer to the chiral recognition of a diverse set of chiral guests, such as 1,2-diamines, α-amino-esters and amides, secondary alcohols, and 1,2-amino-alcohols. The bulky periphery and the presence of a rigid porphyrin linkage lead, in some cases, to a more enhanced CD sensitivity than that reported earlier with other tweezers.

Bioactive A-type proanthocyanidins from Cinnamomum cassia.

Two trimeric proanthocyanidins, cinnamtannin B-1 (1) and cinnamtannin D-1 (2), have been isolated from the bark of Cinnamomum cassia along with the known tetramer parameritannin A-1 (3) and a previously unreported tetramer, named cassiatannin A (4). The structures of 1-4 were elucidated on the basis of 1D and 2D NMR, MS, and CD analyses and compared to the reported data. Proanthocyanidins (1-4) possess significant in vitro inhibitory activity against cyclooxygenase-2 (COX-2) at micromolar concentrations.

Epiafzelechin from the root bark of Cassia sieberiana: detection by DART mass spectrometry, spectroscopic characterization, and antioxidant properties.

The root bark of Cassia sieberiana was analyzed using direct analysis in real time mass spectrometry, and a main flavonoid component with an [M + H](+) mass of 275 was identified. The flavonoid, epiafzelechin, was isolated and fully characterized with the concerted use of NMR spectroscopy, circular dichroism, and optical rotation. Electronic circular dichroism and optical rotation TDDFT calculations were also performed, and their agreement with the experimental results confirmed the enantiomeric identity of the isolated natural product. The antioxidant activity of the compound was also investigated.

A review of forensic science higher education programs in the United States: bachelor's and master's degrees.

As the number of forensic science programs offered at higher education institutions rises, and more students express an interest in them, it is important to gain information regarding the offerings in terms of courses, equipment available to students, degree requirements, and other important aspects of the programs. A survey was conducted examining the existing bachelor's and master's forensic science programs in the U.S. Of the responding institutions, relatively few were, at the time of the survey, accredited by the forensic science Education Programs Accreditation Commission (FEPAC). In general, the standards of the responding programs vary considerably primarily in terms of their size and subjects coverage. While it is clear that the standards for the forensic science programs investigated are not homogeneous, the majority of the programs provide a strong science curriculum, faculties with advanced degrees, and interesting forensic-oriented courses.

Identification and quantitation of 3,4-methylenedioxy-N-methylamphetamine (MDMA, ecstasy) in human urine by 1H NMR spectroscopy. Application to five cases of intoxication.

Identification of 3,4-methylenedioxy-N-methylamphetamine (MDMA, ecstasy) in five cases of intoxication using nuclear magnetic resonance (NMR) spectroscopy of human urine is reported. A new water suppression technique PURGE (Presaturation Utilizing Relaxation Gradients and Echoes) was used. A calibration curve was obtained using spiked samples. The method gave a linear response (correlation coefficient of 0.992) over the range 0.01-1mg/mL. Subsequently, quantitation of the amount of MDMA present in the samples was performed. The benefit and reliability of NMR investigations of human urine for cases of intoxication with MDMA are discussed.

CD-sensitive Zn-porphyrin tweezer host-guest complexes, part 1: MC/OPLS-2005 computational approach for predicting preferred interporphyrin helicity.

This article describes a computational study on dimeric zinc porphyrin tweezer complexes with primary/secondary amines and secondary alcohols that validates the use of Optimized Potential for Liquid Simulations (OPLS-2005) as the lead computational choice for assisting the tweezer methodology in the absolute configurational assignment of organic compounds. A supramolecular, microscale approach known as the tweezer method has been widely applied in the past decade for determining the absolute configuration of chiral substrates that are difficult to study by other readily available methods. The method relies on a host/guest complexation mechanism between a porphyrin tweezer moiety and a substrate, after its conversion into a bidentate conjugate. The formation of 1:1 complexes is a stereodifferentiating process: upon complexation, the originally achiral tweezer adopts a preferential interporphyrin helicity, dictated by the absolute configuration of the chiral substrate. By correctly predicting the sign of the interporphyrin helicity in the complex, OPLS-2005 provides a correlation between the observed circular dichroism (CD) signal and the absolute configuration of the substrate. It also offers a great degree of insight into the structural factors responsible for chiral recognition and the amplitude of exciton couplets. Moreover, the preferential binding sites between the Zn-tweezer and secondary amine conjugates were revealed by using the new computational approach.

CD-sensitive Zn-porphyrin tweezer host-guest complexes, part 2: cis- and trans-3-hydroxy-4-aryl/alkyl-beta-lactams. A case study.

This article describes an application of the host-guest chiral recognition approach called tweezer methodology for the determination of the absolute configuration of 3-hydroxy-beta-lactams. These substrates represent challenging cases due to their chemical reactivity, the presence of multiple stereogenic centers and several functional groups which offer various possibilities of binding to the Zn-porphyrin host. OPLS-2005, the force field used in this work to predict the interporphyrin twist, modeled correctly the host-guest complexation mechanism and revealed conformational details of the bound substrates. The computational study also suggested that in cases where an increase in the magnitude of the stereodifferentiation and an intense experimental CD are observed, the bound conformation of the conjugates are hydrogen bonded. The present investigation provides evidence that when the tweezer method is assisted by the OPLS-2005 based computational approach, it can be successfully applied to the configurational and conformational elucidation of multi-functional compounds with multiple stereogenic centers.

Probing molecular chirality by CD-sensitive dimeric metalloporphyrin hosts.

This feature article reviews dimeric metalloporphyrin hosts employed as chirality probes in chiral recognition processes involving synthetic compounds and natural products. Upon formation of a chiral host-guest supramolecular complex between an achiral bis-metalloporphyrin derivative and a chiral non-racemic guest, a CD response occurs in the porphyrin spectral region, which is diagnostic of the guest's absolute configuration. Several bis-porphyrin hosts used in the stereochemical investigation of organic compounds are described and the scope of their application as chirality probes critically assessed. The review encompasses the description of structural features of the host-guest complexes, the nature of the chirality transfer mechanism and the practical application in solving stereochemical problems. In particular, with reference to the method based on bis-porphyrin tweezers, we describe recent advances based on the use of molecular modeling, which have broadened the applicability of the tweezer methodology and allowed extraction of deeper structural information contained in the experimental CD data.

Ab initio studies of receptor interactions with AMPA ((S)-2-amino-3-(3-hydroxy-5-methyl-4-isoxazolyl) propionic acid) and kainic acid (2S-(2 alpha, 3 beta, 4 beta))-2-carboxy-4-(1-methylethenyl)-3-pyrrolidineacetic acid.

The optimum geometries and binding energies of the complexes formed by AMPA and Kainic acid, as well as their anions with tyrosine, proline and some tripeptides are investigated with quantum chemical calculations (HF/6-31G**). It was found that receptors featuring the Tyr-Ala-Pro sequence exhibit stronger binding energies to the substrates than the Tyr-Ser-Pro and Tyr-Ser-Ser. As expected, the anions are more bound than the neutral species. This work can lead to investigations on the effect of AMPA receptors mutations on the brain functions, possibly related to criminal tendencies.

Amino acid alanine reactivity with the fingerprint reagent ninhydrin. A detailed ab initio computational study.

Ninhydrin is one of the most widely used reagents for chemical development of fingerprints on porous surfaces. The detection is based on the reaction of ninhydrin with a monoacidic component of the fingerprint to form an intensively colored compound named Ruhemann's Purple. A computational study of the mechanisms and reaction energetics of the formation of Ruhemann's Purple from ninhydrin and alanine is presented. Such a study is significant from a forensic science point of view because of the strong interest in the forensic chemistry and law enforcement communities in developing alternatives to the current generation of ninhydrin like chemicals for the detection and development of latent fingerprints. Information about the mechanism of reaction between ninhydrin and amino acids can ultimately help to design compounds with stronger chromo-fluorogenic properties in aid of detecting fingerprints at crime scenes. The three most accepted mechanisms of formation have been considered using ab initio quantum mechanical calculations. At relatively high temperature ( approximately 100 degrees C) all three mechanisms are energetically feasible. However since it is recommended that forensic analyses be performed at room temperature, a revised mechanism is proposed for the formation of Ruhemann's Purple under this condition.

Synthesis and circular dichroism of tetraarylporphyrin-oligonucleotide conjugates.

The preparation and circular dichroic (CD) studies of self-complimentary 8-mer DNA sequences with a porphyrin at the 3' end are presented. Electronic interaction between the two porphyrins (the interchromophoric distance is in the range of 28-40 A), attached to both ends of the double-stranded helix, gives rise to a long-range exciton-coupled CD in the visible region (400-450 nm). The porphyrin chromophores act as sensitive probes of geometrical changes in the DNA backbone and sensitively reflect the double-strand to single-strand transition. This study demonstrates the possibility of using exciton-coupled porphyrin CDs for conformational studies of DNA.

Porphyrin substituted phosphoramidites: new building blocks for porphyrin-oligonucleotide syntheses.

Thymidine phosphoramidites containing trispyridylphenyl and tetraphenylporphyrin chromophores attached via a short amide linker in the 3'-position have been synthesized and used as building blocks in solid-phase synthesis of self-complementary 8-mer oligonucleotides 3'-T-5'-GCGCGCA-3' and 5'-ACGCGCGT-3'. To our knowledge, these are the first porphyrin-oligonucleotide conjugates carrying the porphyrin chromophores in the 3'-position. Chain assembly was achieved by automated solid-phase synthesis and by inexpensive straightforward 'in flask' modification of commercially available solid supported oligonucleotides. This approach allows the synthesis of modified oligonucleotides without using costly instrumentation for automated DNA synthesis. Porphyrin-containing self-complementary oligonucleotides are expected to be a valuable model for drug binding studies and determination of conformational changes in DNA sequences using circular dichroism.

Detection of zinc ions by differential circularly polarized fluorescence excitation.

A new chiroptical spectroscopic approach, differential circularly polarized fluorescence excitation (CPE), can be used to provide a selective method for detecting the presence of zinc ions. The approach utilizes the same instrumentation as fluorescence-detected circular dichroism and provides strong contrast in metal detection due to response to both chelation-enhanced fluorescence and circular dichroism upon metal ion binding. The observed contrast is therefore better than either of the parent spectroscopic detection methods. CPE also provides a strategy to reduce interference from background such as protein-based tryptophan fluorescence.