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PubMed1986

The contribution of alkylation to the activity of quinone antitumor agents.

Studies have shown that the quinone group can produce tumor cell kill by a mechanism involving active oxygen species. This cytotoxic activity can be correlated with the induction of DNA double strand breaks and is enhanced by the ability of the quinone compound to bind to DNA by alkylation. The cytotoxic activity and the production of DNA damage by model quinone antitumor agents were compared in L5178Y cells, sensitive and resistant to alkylating agents, to assess the contribution of alkylation to the activity of these agents. The resistant L5178Y/HN2 cells were found to be two fold and six fold more resistant to the alkylating quinones, benzoquinone mustard and benzoquinone dimustard, respectively, than parent L5178Y cells. In contrast, the L5178Y/HN2 cells showed no resistance to the nonalkylating quinones, hydrolyzed benzoquinone mustard and bis(dimethylamino)benzoquinone. The alkylating quinones produced approximately two fold less cross-linking in L5178Y/HN2 cells compared with L5178Y sensitive cells. DNA double strand break formation by hydrolyzed benzoquinone mustard and bis(dimethylamino)benzoquinone was not significantly different in sensitive and resistant cells. However, the induction of double strand breaks by the alkylating quinones benzoquinone mustard and benzoquinone dimustard was reduced by 5-fold and 15-fold, respectively, in L5178Y/HN2 cells. These results show that the alkylating activity of the alkylating quinones cannot directly explain all of the enhanced cytotoxic activity of these agents. Furthermore, they provide strong evidence that the enhanced formation of DNA double strand breaks by alkylating quinone agents is directly related to the ability of these agents to bind to DNA. This increased formation of strand breaks may account for the enhanced cytotoxic activity of the alkylating quinones.

Alkylating Agents↗
PubMed1996

Alkyl-PAF and acyl-PAF human neutrophil priming for enhanced fMLP- and rC5a-induced superoxide anion production.

Alkyl-PAF induced two components of polymorphonuclear leukocyte (PMN) priming for enhanced fMLP- and rC5a-induced superoxide anion (O2-) production. Component A priming had a shallow, linear alkyl-PAF concentration-response slope (10 pM-1 nM), and component B priming had a significantly steeper concentration-response slope (1-100 nM alkyl-PAF). Whereas the extent of component B priming decayed significantly within 5-10 min after pretreatment of PMNs with alkyl-PAF, component A priming was completely stable. WEB 2086, a specific and potent PAF receptor antagonist, abolished component A priming when PMNs were simultaneously stimulated with alkyl-PAF and either fMLP or rC5a but only partially reduced component B priming. However, whereas WEB 2086 also obliterated component A priming when PMNs were pretreated with alkyl-PAF for 2.5, 5, or 10 min prior to fMLP stimulation, WEB 2086 had little or no inhibitory effect on component B priming. Paradoxically, WEB 2086 significantly augmented alkyl-PAF-induced component B priming for enhanced rC5a-induced PMN O2. production yet concomitantly obliterated component A priming. PMN priming by acyl-PAF (1 nm-1 micron) had characteristics identical to those of alkyl-PAF-induced component A priming. These studies suggest that there are at least two effector pathways modulating alkyl-PAF-induced PMN respiratory burst priming. They are also consistent with the notion that component A priming is initiated via high-affinity PAF receptors and component B priming is mediated through low-affinity PAF receptors; and whereas alkyl-PAF interacts with both high- and low-affinity PAF receptors, both acyl-PAF and WEB 2086 preferentially bind to the high-affinity PAF receptors.

Adrenergic beta-Antagonists↗
PubMed1984

Conversion of 1-alkyl-2-acetyl-sn-glycerols to platelet activating factor and related phospholipids by rabbit platelets.

The metabolic pathway for 1-alkyl-2-acetyl-sn-glycerols, a recently discovered biologically active neutral lipid class, was elucidated in experiments conducted with rabbit platelets. The total lipid extract obtained from platelets incubated with 1-[1,2-(3)H]alkyl-2-acetyl-sn-glycerols or 1-alkyl-2-[3H]acetyl-sn-glycerols contained at least six metabolic products. The six metabolites, identified on the basis of chemical and enzymatic reactions combined with thin-layer or high-performance liquid chromatographic analyses, corresponded to 1-alkyl-sn-glycerols, 1-alkyl-2-acetyl-sn-glycero-3-phosphates, 1-alkyl-2-acyl (long-chain)-sn-glycero-3-phosphoethanolamines, 1-alkyl-2-acetyl-sn-glycero-3-phosphoethanolamines, 1-alkyl-2-acetyl-sn-glycero-3-phosphoethanolamines, 1-alkyl-2-acyl(long-chain)-sn-glycero-3-phosphocholines, and 1-alkyl-2-acetyl-sn-glycero-3-phosphocholines (platelet activating factor). These results indicate that the metabolic pathway for enzymatic activities: choline- and ethanolamine- phosphotransferases, acetyl-hydrolase, an acyltransferase, and a phosphotransferase. The step responsible for the biosynthesis of platelet activating factor would appear to be the most important reaction in this pathway and this product could explain the hypotensive activities previously described for alkylacetyl-(or propionyl)-glycerols. Of particular interest was the preference exhibited for the utilization of the 1-hexadecyl-2-acetyl-sn-glycerol species in the formation of platelet activating factor.

Animals↗
PubMed1984

A new class of antihypertensive neutral lipid: 1-alkyl-2-acetyl-sn-glycerols, a precursor of platelet activating factor.

A new type of neutral lipid is described that possesses hypotensive activity in genetic hypertensive (SHR) and normotensive (WKY) rats. 1-Alkyl-2-acetyl-sn-glycerols and 1-alkyl-2-propionyl-sn-glycerols are both equally effective in eliciting the hypotensive response. Requirement for the 1-alkyl and 2-acetyl or 2-propionyl structure of the active isomer was documented by the negative responses obtained with closely related neutral lipid analogs (1-alkyl-2-acyl-, 1-alkyl-3-acetyl-, 1-acyl-2-acetyl-, 1-alkyl-2,3-diacetyl-, and 1-alkyl-glycerols). Although less potent than PAF (1-alkyl-2-acetyl-sn-glycero-3-phosphocholine), the 1-alkyl-2-acetyl-sn-glycerols produce a response of significantly longer duration and may have fewer immediate side effects than PAF. The mechanism for the biological activity is unknown; however, we have demonstrated previously that the enzymatic synthesis of 1-alkyl-2-acetyl-sn-glycerols to PAF occurs via a specific cholinephosphotransferase and therefore the observed blood pressure response might be due to the conversion of the neutral lipid precursor to PAF in vivo.

Animals↗
PubMed2005

Thermodynamic study of N-trifluoroacetyl-O-alkyl nipecotic acid ester enantiomers on diluted permethylated beta-cyclodextrin stationary phase.

Thermodynamic studies were performed on 12 pairs of N-trifluoroacetyl-O-alkyl nipecotic acid ester enantiomers on diluted permethylated beta-cyclodextrin stationary phase (CP Chirasil-Dex CB). The influence of ester alkyl group structure on interaction with permethylated beta-cyclodextrin (Me-CD) and enantioselectivity was studied. The types of alkyl groups studied included n-alkyl (C1-C5) and groups containing branching at differing locations relative to the chiral center of the molecule. The results show that for a given molecular weight, the n-alkyl esters have stronger interactions with Me-CD than esters containing branched alkyl groups. However, although having weaker interactions with Me-CD, esters containing alpha-branched alkyl groups exhibit higher enantioselectivity than the corresponding n-alkyl or beta-branched isobutyl esters. From the retention data, thermodynamic parameters were estimated using the retention increment method and enthalpy-entropy compensation plots (ln R' versus deltaH) were constructed. The results suggest that ester enantiomers with branching at the alpha-carbon of the ester alkyl group have additional and/or different types of enantioselective interactions with Me-CD than the C1-C5 n-alkyl esters or beta-branched isobutyl ester. In order to obtain a qualitative sense of the interaction with Me-CD, structures of the diastereomeric complexes formed between Me-CD and some of the ester enantiomers were modeled using simulated annealing molecular dynamics.

Indicators and Reagents↗
PubMed1999

The percutaneous penetration of prostaglandin E1 and its alkyl esters.

The percutaneous delivery of PGE1 and its alkyl esters in alcoholic saline solution through hairless mouse skin was compared. The quantification of alkyl esters was based on the same principle as that for PGE1, which was converted to PGB1 to enhance the sensitivity and minimize the interference. Results showed that it was PGE1 that appeared in the receiver compartment for all alkyl esters examined. The flux of all alkyl esters of PGE1 in the same concentration was higher than PGE1 itself at most of saline vehicle with various fractions of alcohol. The maximal flux for a fixed concentration of each alkyl ester appeared at different fractions of alcohol. When the fractions of alcohol was kept constant, the alkyl ester that showed the maximal flux at this concentration appeared to have a longer chain length with increasing the fraction of alcohol. But isopropyl ester deviated from this order. It was concluded that the alkyl ester derivatives promoted the penetration of PGE1 mainly as a result of enhancing the drug partitioning into the stratum corneum. The alcohol fraction that needed to achieve the maximal flux at the same concentration increased with the increase of alkyl chain length, which resulted in the decrease of solubility parameter. It is necessary to optimize the fraction of alcohol in the saline solution in order to achieve the maximal flux at a fixed concentration for these alkyl esters with different alkyl chain length.

Alprostadil↗
PubMed2005

Solvation dynamics in aqueous anionic and cationic micelle solutions: sodium alkyl sulfate and alkyltrimethylammonium bromide.

Solvation dynamics of the fluorescence probe, coumarin 102, in anionic surfactant, sodium alkyl sulfate (C(n)H(2n+1)SO(4)Na; n = 8, 10, 12, and 14), and cationic surfactant, alkyltrimethylammonium bromide (C(n)H(2n+1)N(CH(3))(3)Br; n = 10, 12, 14, and 16), micelle solutions have been investigated by a picosecond streak camera system. The solvation dynamics in the time range of 10(-10)-10(-8) s is characterized by a biexponential function. The faster solvation time constants are about 110-160 ps for both anionic and cationic micelle solutions, and the slower solvation time constants for sodium alkyl sulfate and alkyltrimethylammonium bromide micelle solutions are about 1.2-2.6 ns and 450-740 ps, respectively. Both the faster and the slower solvation times become slower with longer alkyl chain surfactant micelles. The alkyl-chain-length dependence of the solvation dynamics in both sodium alkyl sulfate and alkyltrimethylammonium bromide micelles can be attributed to the variation of the micellar surface density of the polar headgroup by the change of the alkyl chain length. The slower solvation time constants of sodium alkyl sulfate micelle solutions are about 3.5 times slower than those of alkyltrimethylammonium bromide micelle solutions for the same alkyl-chain-length surfactants. The interaction energies of the geometry optimized mimic clusters (H(2)O-C(2)H(5)SO(4)(-) and H(2)O-C(2)H(5)N(CH(3))(3)(+)) have been estimated by the density functional theory calculations to understand the interaction strengths between water and alkyl sulfate and alkyltrimethylammonium headgroups. The difference of the slower solvation time constants between sodium alkyl sulfate and alkyltrimethylammonium bromide micelle solutions arises likely from their different specific interactions.

Anions↗
PubMed1980

Comparison of alkylation rates and mutagenicity of directly acting industrial and laboratory chemicals: epoxides, glycidyl ethers, methylating and ethylating agents, halogenated hydrocarbons, hydrazine derivatives, aldehydes, thiuram and dithiocarbamate derivatives.

Groups of industrial and laboratory chemicals were tested for their alkylation activity using 4-(p-nitrobenzyl)-pyridine and deoxyguanosine as nucleophiles. The alkylation activity was compared with mutagenicity of the chemicals to E. coli WP2 uvrA without metabolic activation. All the epoxide-containing compounds including simple epoxides and glycidyl ethers elicited alkylation activity and mutagenicity. Furthermore there was a reasonable correlation between the rate of alkylation and the mutagenic potency. All the methylating and ethylating compounds tested were active but no correlation was observed between the rate of alkylation and the mutagenic potency, apparently due to the different types of alkylation products formed. The other compounds tested including halogenated hydrocarbons, hydrazine derivatives, aldehydes, thiuram and dithiocarbamate derivatives elicited a slow or no alkylation activity while many of the compounds were mutagenic. There was no evidence among the chemicals tested of an alkylating non-mutagen. Thus evidence of alkylation activity appears to indicate mutagenic risk.

Aldehydes↗
PubMed2005

Alkylating potential of potassium sorbate.

A kinetic study of the alkylating potential of potassium sorbate (S)-a food preservative used worldwide-in 7:3 water/dioxane medium was performed. The following conclusions were drawn: (i) Potassium sorbate shows alkylating activity on the nucleophile 4-(p-nitrobenzyl)pyridine (NBP), a trap for alkylating agents with nucleophilic characteristics similar to those of DNA bases, (ii) The NBP alkylation reaction complies with the rate equation r = k(alk)[H+][S][NBP]/(K(a) + [H+]), K(a) being the sorbic acid dissociation constant and k(alk) the rate constant of NBP alkylation by the undissociated acid. In the range of pH 5-6, the alkylation time ranges between 18 days (pH 5.2) and >1 month (pH > or = 6). (iii) NBP alkylation occurs through a reaction with deltaH# = 78 kJ mol(-1), which is much higher than those of NBP alkylation by stronger alkylating agents. (iv) The absorption coefficient of the sorbate-NBP adduct was determined to be epsilon = 204 M(-1) cm(-1) (lambda = 580 nm), this value being rationalized in terms of the adduct structure. (v) The results can help to establish suitable expiration times for products preserved with potassium sorbate.

Alkylating Agents↗
PubMedDate not supplied

Alkylation of Escherichia coli thioredoxin by S-(2-chloroethyl)glutathione and identification of the adduct on the active site cysteine-32 by mass spectrometry.

Alkylation of reduced Escherichia coli thioredoxin by the episulfonium ion derived from S-(2-chloroethyl)glutathione (CEG) at physiologic pH resulted in at least three different alkylation products. These adducts were separated by reverse phase chromatography, digested with trypsin, and peptide-mapped. The peptide containing the active site cysteines was collected and sequenced by tandem mass spectrometry. Results indicate that the site of alkylation was at Cys-32 exclusively with no alkylation at Cys-35. Raising the pH above the pKa of Cys-35 to ionize the thiol before reacting with the episulfonium ion of CEG did not lead to alkylation at Cys-35, suggesting that a steric factor prevents the alkylating moiety of CEG from accessing this cysteine. A tryptic digest of a minor bis-adduct yielded an alkylated peptide which contained tyrosine, an amino acid known to be alkylated at its hydroxyl group by CEG. Sequencing by tandem mass spectrometry, however, was unsuccessful due to fragmentation of the alkylating moiety from the peptide. Results of this study confirm that the episulfonium ion of CEG can adduct thioredoxin at the active site and may have important toxicologic significance regarding the mechanism of 1,2-dichloroethane toxicity.

Alkylating Agents↗
PubMed1983

Significance of electrophilic reactivity and especially DNA alkylation in carcinogenesis and mutagenesis.

Alkylating agents have proved useful as models, especially for low molecular weight mutagens and carcinogens, to probe molecular mechanisms of genotoxicity. Results of many studies have indicated that not all DNA substitutions cause mutagenic or carcinogenic responses. Often, quantitatively minor alkylation products are responsible for initiating these biological processes. The factors that influence the distribution of DNA substitution products include: the SN1 reactivity of the electrophilic species; the nucleophilicity and steric accessability of the DNA site; van der Waals or electrostatic interactions that attract the agent to specific DNA sites; and post-alkylation rearrangements. With low molecular weight alkylating agents, a primary determinant of product distribution in DNA, and of genotoxic potential, is the electrophilic reactivity. Agents with high SN1 reactivity (low Swain -Scott s factors) generally have high mutagenic and carcinogenic activity, at equal levels of total DNA alkylkation . This appears to be due to the ability of such agents to cause relatively more alkylation at oxygen sites in DNA, especially at O6 of guanine and at O4 of thymine. Alkylation of DNA alone is insufficient to induce cancer or mutations. Post-alkylation factors such as DNA repair, rate of cell turnover, or presence of tumor promoters can have a profound effect on the biological response to DNA damage (1,5,6,24,42). In this sense, the persistence of a specific miscoding of altered DNA base is significant in carcinogenesis or mutagenesis only to the extent that it remains in DNA long enough to be fixed into the code. This concept necessarily assumes that the altered base has promutagenic potential. Persistence of an alkylated DNA constituent does not, by itself, indicate that the alkylated constituent has biological significance.

Alkylating Agents↗
PubMed1983

Alkylating agent interactions with the nuclear matrix.

The interrelationship of DNA to the nuclear matrix is integral to the organization of chromatin within the nucleus and to the DNA replication process. The influence of nitrosourea and nitrogen mustard interactions with the nuclear matrix were studied in log phase HeLa cells. Alkylation of the nuclear matrix by chlorozotocin (CLZ) or 1-(2-chloroethyl-3-cyclohexyl)-1-nitrosourea (CCNU) was 1.58 and 1.27 pmoles drug/micrograms protein, respectively, whereas carbamoylation by CCNU was 32.5 pmoles/micrograms. These constituted approximately 30% of the total (nuclear) drug modifications. The structural matricin fibrillar components of the matrix were alkylated and carbamoylated twice as much as the ribonuclear protein elements (RNP). However, when alkylations are measured per microgram of protein, the ratio of covalently bound drug to RNP:matricin was 1.2 for both CLZ and CCNU. The RNP:matricin carbamoylation ratio for CCNU was 0.9. The importance of DNA and matrix protein alkylations to the process of reassociation was studied. Under control conditions, in vitro, approximately 80% of the DNA was associated with the matrix at a protein:DNA ratio (micrograms for micrograms) of 50:1. Direct alkylation or carbamoylation of the matrix proteins did not affect these DNA-protein interactions. However, using in vitro alkylated DNA (1 alkylation/10(2) base pairs), there was a 60% reduction of the alkylated nucleic acid bound to the matrix at the same protein: DNA ratio. The reduced binding of DNA to matrix may be a function of interference with the DNA recognition sites by alkylation of specific bases. The interference of DNA-matrix association by DNA alkylation may contribute to the cytotoxic activity of these antineoplastic agents.

Alkylating Agents↗
PubMed1990

Differences in sequence selectivity of DNA alkylation by isomeric intercalating aniline mustards.

Two DNA-targeted mustard derivatives, N,N-bis(2-chloroethyl)-4-(5-[9-acridinylamino]-pentamido)aniline and 4-(9-[acridinylamino]butyl 4-(N,N-bis[2-chloroethyl]-aminobenzamide, which are isomeric compounds where the mustard is linked to the DNA-binding 9-aminoacridine moiety by either a -CONH- or a -NHCO- group, show significant differences in the sequence selectivity of their alkylation of DNA. The CONH isomer is a more efficient alxylating agent than the NHCO compound by an order of magnitude, consistent with the larger electron release of the CONH group to the aniline ring. However, the pattern of alkylation by the two compounds is also very different, with the CONH isomer preferring alkylation of guanines adjacent to 3'- or 5'-adenines and cytosines (for example those in sequences 5'-CGC, 5'-AGC, 5'-CGG and 5'-AGA) while the isomeric NHCO compound shows preference for guanines in runs of Gs. In addition, both isomers alkylate 3'-adenines in runs of adenines. Both compounds also show completely different patterns of alkylation to their untargeted mustard counterparts, since 4-MeCONH-aniline mustard alkylates all guanines and adenines in runs of adenines, while 4-Me2NCO-aniline mustard fails to alkylate DNA at all. These differences in alkylation patterns between the CONH- and its isomeric NHCO- compounds and their relationships between the alkylation patterns of the isomers and their biological activities are discussed.

Alkylation↗
PubMed1977

Three alkylation methods for the determination of indometacin in plasma by electron capture gas chromatography.

The following alkylation methods for the determination of indometacin in plasma by electron capture gas chromatography are compared: 1, alkylation with diazopropane; 2, extractive alkylation; 3, alkylation by a solid-liquid phase transfer catalysed process. The drug in plasma at pH 4.0 is initially extracted with heptane containing 5% n-pentanol. The methyl ester of indometacin is based as internal standard. After alkylation to the propyl ester according to one of the three alkylation methods, indometacin can be determined down to 5 ng per sample by electron capture gas chromatography. The relative standard deviations (n = 10) at the 200 ng level are 5.1% for the alkylation with diazopropane, 7.5% for the extractive alkylation technique and 3.5% for the alkylation by the solid-liquid phase transfer catalysed process. The comparatively low value obtained by the last method indicates that decomposition of indometacin can be avoided under such mild conditions.

Alkylation↗
PubMed1992

Use of [8-3H]guanine-labeled deoxyribonucleic acid to study alkylating agent reaction kinetics and stability.

Alkylation at the N7 position of guanine in DNA renders the C8-hydrogen acidic. This serves as the basis for an assay of guanine N7 alkylation using [8-3H]-guanine-labeled DNA. I modified the assay by preparing a high specific activity substrate in vitro and by replacing the distillation step with charcoal adsorption of substrate. Using the appearance of noncharcoal-adsorbable label as a measure of guanine-N7 alkylation I examined the reaction of DNA with dimethyl sulfate and mechlorethamine. The rate of reaction of dimethyl sulfate with the N7 position of guanine in DNA was constant over time, i.e., loss of label from DNA proceeded linearly with time. On the other hand, the rate of reaction of mechlorethamine with DNA increased with time, consistent with the initial formation of the reactive aziridinium ion. The assay can also be used to compare the reaction rates of various alkylating agents with DNA. Thus, the acridine mustards ICR-170 and quinacrine mustard were far more potent alkylating agents than mechlorethamine. Furthermore the assay may be used to determine the alkylating potency and stability of various alkylating agent preparations: while frozen solutions of acridine mustards in organic solvents retained alkylating activity for several months, different commercial preparations of quinacrine mustard had little or no alkylating activity.

Alkylating Agents↗
PubMed1985

Effect of alkyl side chain variation on the electron-transfer activity of ubiquinone derivatives.

The effect of the alkyl side chain of the ubiquinone molecule on the electron-transfer activity of ubiquinone in mitochondrial succinate-cytochrome c reductase is studied by using synthetic ubiquinone derivatives that possess the basic ubiquinone structure of 2,3-dimethoxy-5-methyl-1,4-benzoquinone with different alkyl side chains at the 6-position. The alkyl side chains vary in chain length, degree of saturation, and location of double bonds. When a ubiquinone derivative is used as an electron acceptor for succinate-ubiquinone reductase, an alkyl side chain of six carbons is needed to obtain the maximum activity. However, when it serves as an electron donor for ubiquinol-cytochrome c reductase or as a mediator in succinate-cytochrome c reductase, an alkyl side chain of 10 carbons gives maximal efficiency. Introduction of one or two isolated double bonds into the alkyl side chain of the ubiquinone molecule has little effect on electron-transfer activity. However, a conjugated double bond system in the alkyl side chain drastically reduces electron-transfer efficiency. The effect of the conjugated double bond system on the electron-transferring efficiency of ubiquinone depends on its location in the alkyl side chain. When location is far from the benzoquinone ring, the effect is minimal. These observations together with the results obtained from photoaffinity-labeling studies lead us to conclude that flexibility in the portion of the alkyl side chain immediately adjacent to the benzoquinone ring is required for the electron-transfer activity of ubiquinone.

Alkylation↗
PubMed1976

Detection of the sites of alkylation in DNA and polynucleotides by laser Raman spectroscopy.

A laser Raman study of the alkylation of calf thymus DNA, poly(dG)-poly(dC) and poly(dA)-(dT) has been made using two water soluble alkylating agents: an antitumor drug, the difunctional methyl nitrogen mustard (HN2), which froms interstrand cross-links, and the dimethyl nitrogen half mustard (HN1). When an excess of the alkylating agent was used, the observed Raman frequencies due to the guanine ring modes in DNA and poly(dG)-poly(dC) changed virtually quantitatively to those of 7-methylguanosine (7-Me-Guo) showing that essentially all of the guanine bases were alkylated in the N-7 position. Furthermore, this alkylated DNA formed a stable double helical complex at neutral pH in which the alkylated guanine residues are in the keto form. No changes in the Raman bands of any of the other bases were observed in alkylated DNA. The DNA double helix, completely alkylated in at the N-7 position of guanine, melts about 35 degrees C below that of the native DNA. Upon melting, the alkylated guanine changes from the keto to the zwitterionic form.

Alkylation↗
PubMed2002

Metal ion-catalyzed nucleic acid alkylation and fragmentation.

Nucleic acid microarrays are a growing technology in which high densities of known sequences are attached to a substrate in known locations (addressed). Hybridization of complementary sequences leads to a detectable signal such as an electrical impulse or fluorescence. This combination of sequence addressing, hybridization, and detection increases the efficiency of a variety of genomic disciplines including those that profile genetic expression, search for single nucleotide polymorphisms (SNPs), or diagnose infectious diseases by sequencing portions of microbial or viral genomes. Incorporation of reporter molecules into nucleic acids is essential for the sensitive detection of minute amounts of nucleic acids on most types of microarrays. Furthermore, polynucleic acid size reduction increases hybridization because of increased diffusion rates and decreased competing secondary structure of the target nucleic acids. Typically, these reactions would be performed as two separate processes. An improvement to past techniques, termed labeling-during-cleavage (LDC), is presented in which DNA or RNA is alkylated with fluorescent tags and fragmented in the same reaction mixture. In model studies with 26 nucleotide-long RNA and DNA oligomers using ultraviolet/visible and fluorescence spectroscopies as well as high-pressure liquid chromatography and mass spectrometry, addition of both alkylating agents (5-(bromomethyl)fluorescein, 5- or 6-iodoacetamidofluorescein) and select metal ions (of 21 tested) to nucleic acids in aqueous solutions was critical for significant increases in both labeling and fragmentation, with >or=100-fold increases in alkylation possible relative to metal ion-free reactions. Lanthanide series metal ions, Pb(2+), and Zn(2+) were the most reactive ions in terms of catalyzing alkylation and fragmentation. While oligonucleotides were particularly susceptible to fragmentation at sites containing phosphorothioate moieties, labeling and cleavage reactions occurred even without incorporation of phosphorothioate moieties into the RNA and DNA target molecules. In fact, LDC conditions were found in which RNA could be fragmented into its component monomers, allowing simultaneous sequencing from both the 5'- and the 3'-termini by mass spectrometry. The results can be explained by alkylation of the (thio)phosphodiester linkages to form less hydrolytically stable (thio)phosphotriesters, which then decompose into 2',3'-cyclic phosphate (or 2'-phosphate) and 5'-hydroxyl terminal products. Analysis of fragmentation and alkylation products of Mycobacterium tuberculosis (Mtb) ribosomal RNA (rRNA) transcripts by polyacrylamide gel electrophoresis was consistent with the model studies. Building upon these results, I found that products from Mtb rRNA amplification products were processed with fluorescent reporters and metal ions in a single reaction milieu for analysis on an Affymetrix GeneChip. Mild conditions were discovered which balanced the need for aggressive alkylation and the need for controlled fragmentation, advantageously yielding GeneChip results with greater than 98% of the nucleotides reported correctly relative to reference sequences, results sufficient for accurately identifying Mtb from other Mycobacterium species. Thus, LDC is a new, straightforward, and rapid aqueous chemistry that is based on metal ion-catalyzed alkylation and alkylation-catalyzed fragmentation of nucleic acids for analysis on microarrays or other hybridization assays and that, possibly, has utility in similar processing of other appropriately functionalized biomolecules.

Alkylation↗