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A novel strategy for generating platelet-like fragments from megakaryocytic cell lines and human progenitor cells.

Transfusion of allogeneic platelets is the mainstay of therapy for patients with thrombocytopenic hemorrhage. However, donated platelets can only be stored for 5 days and are maintained at room temperature, increasing the risk of bacterial growth. Developing a method to produce functional platelets in vitro would greatly advance transfusion therapy. During our studies to understand megakaryocyte development, we discovered that a Src kinase inhibitor, SU6656, induces cellular enlargement, polyploidization, and cytoplasmic fragmentation of several hematopoietic cell lines. Therefore, we tested the hypothesis that these fragments possess platelet-like activity. We studied a megakaryocytic cell-line, UT-7/TPO, and immature human primary megakaryocytes. After 6 days in the presence of thrombopoietin and SU6656, the majority of cells became polyploid and started shedding platelet-like fragments. These fragments were tested for aggregation and analyzed by electron microscopy. The platelet-like fragments did not undergo spontaneous activation but did show rapid and sustained aggregation in response to each of the standard agonists collagen, arachidonic acid, adenosine diphosphate, and epinephrine. Platelet-like fragments generated in SU6656 had higher amplitude and more prolonged aggregation in each of three experiments. Primary progenitors developed demarcation membranes within 72 h and evidence of dense granules and platelet-like fragments after 6 days. These cell fragments demonstrated properties consistent with platelet aggregation in response to multiple agonists without spontaneous aggregation. These studies provide evidence that SU6656 promotes megakaryocytic differentiation and thrombopoiesis in vitro.

Blood Platelets↗

Fibrinogen catabolism within the procoagulant VX-2 tumor of rabbit lung in vivo: Effluxing fibrin(ogen) fragments contain antiangiogenic activity.

Many types of solid tumors are known to be procoagulant environments. This is partly because a hyperpermeable vascular system within the tumor allows plasma hemostatic factors to accumulate in relatively high concentrations in the stroma, and many solid-tumor cells express tissue factor or a procoagulant factor. These circumstances appear to exist in the VX-2 lung tumor of the New Zealand White (NZW) rabbit, and they sustain a measurable turnover of stromal deposits of fibrin(ogen). We have measured the turnover of fibrinogen within tumors of the VX-2 tumor-burdened rabbit and analysed the catabolic products of fibrin(ogen) and the status of fibrinolysis in tumor-derived interpleural effusate. Using intravenously injected (125)I-labeled rabbit fibrinogen as a marker, we found that fibrinogen (approximate blood concentration 1740 microg/mL) passed from blood to VX-2 tumor stroma, saturating the tumor at a concentration of approximately 348 microg fibrinogen/g in approximately 12 hours. We measured fibrin(ogen) fragments, at a concentration of approximately 292 microg/mL, in interpleural effusates that we recovered from 13% of the VX-2-burdened rabbits. Unreduced fibrin(ogen) fragments consisted of 4 major components with a relative molecular mass of approximately 250,000 (assumed to be fragment X; approximately 9% of total fragments from densitometry of immunoblots), 200,000 (d-dimer; 41%), 110,000 (fragment D; 49%), and 50,000 to 55,000 (fragment E; 1%-2%) kD. Total fibrin(ogen) fragments immunopurified from effusates exhibited an antiangiogenic effect when subjected to a chick embryo chorioallantoic membrane procedure. Interpleural effusates were devoid of plasmin activity or active plasminogen activator inhibitor-1 but contained plasmin complexes and active urokinase-like plasminogen activator (uPA), alpha(2)-antiplasmin, and thrombin-activatable fibrinolysis inhibitor. We speculate that VX-2 cells release uPA to activate fibrinolysis within the tumor stroma. Catabolic products of hemostasis (eg, fibrinolytic fragments, angiostatin) flux from the stroma into the interpleural space, thereby providing a net antiangiogenic property to the effusate and ultimately to the lymphatic and circulatory systems.

Animals↗

Retained nuclear fragments in the anterior chamber after phacoemulsification with an intact posterior capsule.

OBJECTIVE: To review the clinical features and treatment of patients with retained nuclear fragments in the anterior chamber (AC). DESIGN: Single-center, retrospective, noncomparative, consecutive case series. PARTICIPANTS: Sixteen patients with a diagnosis of retained nuclear fragments in the AC. METHODS: Retrospective review of the medical records at Bascom Palmer Eye Institute in Miami, Florida, to identify all patients with a diagnosis of retained nuclear fragments in the AC after phacoemulsification surgery without rupture of the posterior capsule. Charts were reviewed and patient characteristics, ocular history, clinical findings, treatment (medical and surgical), and visual outcomes were recorded. MAIN OUTCOME MEASURES: Visual outcome and visual acuity at last follow-up visit. RESULTS: Most patients presented with corneal edema and anterior segment inflammation. All patients proved refractory to medical management, and surgical extraction of the retained lens fragment was required. Ten patients were myopic or had long axial lengths and/or steep keratometry readings. Three patients underwent penetrating keratoplasty for intractable corneal edema. One patient required a second surgery for fragment removal after a previous unsuccessful attempt at removal. Visual outcomes for the patients without macular disease who had lens fragment removal alone ranged from 20/20 to 20/40. Of the 2 patients without macular disease who underwent penetrating keratoplasty, the visual outcomes were 20/50 and 20/30. CONCLUSIONS: Retention of nuclear fragments in the AC may occur after phacoemulsification. This complication was associated with myopia in a majority of patients in this series, and we hypothesize that small fragments may hide in the posterior chamber in these larger eyes. Surgical removal was associated with a good visual outcome in patients without macular disease.

Aged↗

Multimerization-cyclization of DNA fragments as a method of conformational analysis.

Ligation of short DNA fragments results in the formation of linear and circular multimers of various lengths. The distribution of products in such a reaction is often used to evaluate fragment bending caused by specific chemical modification, by bound ligands or by the presence of irregular structural elements. We have developed a more rigorous quantitative approach to the analysis of such experimental data based on determination of j-factors for different multimers from the distribution of the reaction products. j-Factors define the effective concentration of one end of a linear chain in the vicinity of the other end. To extract j-factors we assumed that kinetics of the reaction is described by a system of differential equations where j-factors appear as coefficients. The assumption was confirmed by comparison with experimental data obtained here for DNA fragments containing A-tracts. At the second step of the analysis j-factors are used to determine conformational parameters of DNA fragments: the equilibrium bend angle, the bending rigidity of the fragment axis, and the total twist of the fragments. This procedure is based on empirical equations that connect the conformational parameters with the set of j-factors. To obtain the equations, we computed j-factors for a large array of conformational parameters that describe model fragments. The approach was tested on both simulated and actual experimental data for DNA fragments containing A-tracts. A-tract DNA bend angle determined here is in good agreement with previously published data. We have established a set of experimental conditions necessary for the data analysis to be successful.

Base Sequence↗

Mechanical percussion inversion can result in relocation of lower pole stone fragments after shock wave lithotripsy.

OBJECTIVES: To determine whether mechanical percussion combined with inversion (MPI) therapy and forced diuresis can move stone fragments out of the lower pole of the kidney. METHODS: Twelve patients with lower pole residual stone fragments at least 2 weeks after shock wave lithotripsy were treated using the following protocol. Eleven patients received 20 mg of furosemide before MPI therapy. Patients were treated in the prone Trendelenberg position on a pivoting stretcher and given 10 minutes of percussion over the flank using a mechanical chest physiotherapy percussor. Stone location was documented with plain abdominal radiographs before, immediately after, and 2 weeks following MPI therapy. Voided urine was strained immediately after MPI therapy and throughout the study period. RESULTS: Abdominal radiographs before and after treatment demonstrated movement of fragments out of the lower pole in 11 patients. In 8 patients, the lower pole appeared entirely clear of fragments on the immediate post-treatment film. Four patients passed stone fragments in their first voided urine. Ten patients passed stone fragments during the 2-week follow-up period. CONCLUSIONS: MPI therapy combined with diuresis can effectively mobilize stone fragments out of the lower pole calyces and appears to aid in the passage of fragments.

Diuretics↗

Endophthalmitis in patients with retained lens fragments after phacoemulsification.

PURPOSE: To review the treatment and outcomes of patients presenting with concurrent endophthalmitis and retained lens fragments after phacoemulsification. METHODS: A retrospective chart review was conducted on patients presenting with culture-proven endophthalmitis and retained lens fragments after phacoemulsification between 1990 and 1994. RESULTS: Five patients were identified with culture-proven endophthalmitis and retained lens fragments after phacoemulsification. In all patients, coagulase-negative staphylococci were cultured from the vitreous fluid. One patient also had positive cultures for Proteus mirabilis and Escherichia coli. The interval between cataract surgery and treatment ranged from 5 days to 6 months. Echography was beneficial in showing retained lens fragments in five of five patients when media opacities obscured the view of the fundus. Four patients had vitrectomy and removal of retained lens fragments during their initial treatment. The fifth patient was treated with intravitreal antibiotics alone and continued to have marked inflammation, eventually requiring vitrectomy for removal of the retained lens fragments. A final visual acuity of 20/400 or better was achieved in four of the five patients. CONCLUSIONS: Patients may present with endophthalmitis in the setting of retained lens fragments after phacoemulsification. In such cases, the preferred initial management may be pars plana vitrectomy, removal of retained lens fragments, and injection of intraocular antibiotics. In eyes with endophthalmitis and opaque media, echography is a useful screening modality.

Aged↗

Trace labeling of proteins with stable isotopes to identify fragments in complex mixtures.

We describe a novel nonradioactive protein-labeling technique that permits mass spectrometric identification of fragments of labeled proteins. Proteins are labeled by modulating their content of carbon-13 and labeled fragments identified from the distinctive isotope pattern observed on MALDI-TOF mass spectrometry. We show that carbon-13 enrichment to just 2.3% of total carbon (about twice the natural abundance of 1.1%) is sufficient for all fragments to be distinguishable from fragments of natural carbon-13-content proteins. Distinguishing labeled fragments is easily accomplished by visual inspection of spectra, but importantly, we show that labeled fragments can also be identified by computer analysis of spectra using novel parameters we have derived. The technique is demonstrated for identification of fragments of carbon-13-enriched glutathione transferase within a complex mixture of unlabeled peptides by visual and computer analysis of MALDI-TOF mass spectra, but it could be developed to mass spectrometrically identify and characterize fragments of labeled proteins recovered from biological systems.

Automation↗

Predictions of micelle-water partition coefficients and retention in micellar electrokinetic chromatography from solute structure. 2. Fragmental constant approach.

The fragmental constant approach (FCA) was used to calculate water-sodium dodecyl sulfate (SDS) micelle partition coefficients, K(mw), for uncharged solutes from their structure. Subsequently, the availability of K(mw) values allows prediction of retention factor, k, in micellar electrokinetic chromatography (MEKC) using the simple relationship k = K(mw)phi, where phi is the phase ratio. The FCA model describes a micelle-water partition coefficient as the sum of the partition coefficients of the constituent atomic/molecular fragments, measured by fragmental constant values, f (i), as well as correction factors to account for various "intramolecular effects" that cause deviations from the predicted partition coefficients as, log K(mw) = sum(n)(i=1)aif i+sum(m)(i=1)kiCm. The fragmental constants for a set of 41 fragments were determined using a training set of 229 aromatic solutes and 198 aliphatic compounds. The K(mw) of the aromatic compounds in the training set were determined by MEKC, while the K(mw) of the aliphatic solutes were estimated using the linear solvation energy relationship (LSER) for the SDS micelles. The fragments consisted of both aromatic fragments (i.e., directly attached to an aromatic ring) and aliphatic fragments. The FCA predictions agree nicely with the observed and LSER partition coefficient values, even for complex molecular structures such as beta-blocker drugs. The results show the great potential of the FCA for a priori prediction of retention behavior in MEKC from solute structure.

Chromatography, Micellar Electrokinetic Capillary↗

Thermal unfolding of a llama antibody fragment: a two-state reversible process.

Camelids produce functional "heavy chain" antibodies which are devoid of light chains and CH1 domains [Hamers-Casterman, C., et al. (1993) Nature 363, 446-448]. It has been shown that the variable domains of these heavy chain antibodies (the V(HH) fragments) are functional at or after exposure to high temperatures, in contrast to conventional antibodies [Linden van der, R. H. J., et al. (1999) Biochim. Biophys. Acta 1431, 37-44]. For a detailed understanding of the higher thermostability of these V(HH) fragments, knowledge of their structure and conformational dynamics is required. As a first step toward this goal, we report here the essentially complete (1)H and (15)N NMR backbone resonance assignments of a llama V(HH) antibody fragment, and an extensive analysis of the structure at higher temperatures. The H-D exchange NMR data at 300 K indicate that the framework of the llama V(HH) fragment is highly protected with a DeltaG(ex) of >5.4 kcal/mol, while more flexibility is observed for surface residues, particularly in the loops and the two outer strands (residues 4-7, 10-13, and 58-60) of the beta-sheet. The CD data indicate a reversible, two-state unfolding mechanism with a melting transition at 333 K and a DeltaH(m) of 56 kcal/mol. H-D exchange studies using NMR and ESI-MS show that below 313 K exchange occurs through local unfolding events whereas above 333 K exchange mainly occurs through global unfolding. The lack of a stable core at high temperatures, observed for V(HH) fragments, has also been observed for conventional antibody fragments. The main distinction between the llama V(HH) fragment and conventional antibody fragments is the reversibility of the thermal unfolding process, explaining its retained functionality after exposure to high temperatures.

Amides↗

1H NMR spectroscopic studies on the interactions between human plasma antithrombin III and defined low molecular weight heparin fragments.

The effects of length and composition upon the antithrombin-binding properties of heparin have been investigated for two series of structurally related heparin oligosaccharides. Each series consists of a tetrasaccharide, hexasaccharide, and octasaccharide heparin fragment composed of alternating hexuronic acid (either iduronate 2-sulfate or glucuronate) and glucosamine 6,N-disulfate residues. These two series represent dominant structural motifs in intact heparin and differ from each other by the presence of a glucuronic acid in one series in place of an iduronate 2-sulfate residue penultimate to the reducing end of the fragment. Perturbations to the 1H resonances in the NMR spectrum of antithrombin upon binding of the two series of heparin fragments are compared to those generated by intact heparin binding, as well as to the effects of binding of a synthetic high-affinity pentasaccharide. All of the heparin fragments examined appear to bind to antithrombin at the same site. Three of the heparin fragments (hexasaccharide-2, octasaccharide-2, and octasaccharide-1) produce almost identical perturbations in the antithrombin 1H NMR spectrum compared to binding of intact heparin, including perturbations of resonances from tryptophan 49. This indicates that neither the glucuronic acid nor the trisulfated glucosamine residue (structural elements known to be part of the high-affinity heparin motif) are necessary for the majority of the conformational changes induced upon heparin fragment binding to antithrombin. However, the low anticoagulant activity of these fragments indicates that the changes in protein conformation upon fragment binding, as manifested by these 1H resonance perturbations, are not sufficient for catalytic activation of the inhibitor.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

Fragment E-2 from fibrin substantially enhances pro-urokinase-induced Glu-plasminogen activation. A kinetic study using the plasmin-resistant mutant pro-urokinase Ala-158-rpro-UK.

In a previous study, it was shown that fibrin fragment E-2 selectively promotes the activation of plasminogen by pro-urokinase (pro-UK) [Liu, J., & Gurewich, V. (1991) J. Clin. Invest. 88, 2012-2017]. In this study, the kinetics of this promotion by fragment E-2 was studied. Alanine-158-rpro-UK (A-pro-UK), a recombinant plasmin-resistant mutant, was used in order to avoid interference by UK generation during the reaction. In some experiments, pro-UK was substituted in order to validate the mutant as a surrogate. In the presence of a range of concentrations (0-20 microM) of fragment E-2, a linear promotion of the catalytic efficiency of A-pro-UK against native Glu-plasminogen was seen which was 245.5-fold at the highest concentration of fragment E-2 and 450-fold at the highest ratio of E-2/plasminogen used. The promotion was largely a function of an increase in kcat, since fragment E-2 induced a less than 10-fold reduction in KM (8.50-1.40 microM). In contrast to this ligand, epsilon-aminocaproic acid (EACA) induced a biphasic promotion of the activation of Glu-plasminogen which was only 18-fold at maximum. Fragment E-2 did not promote the activation of Lys-plasminogen, but the catalytic efficiency of A-pro-UK was 19.7-fold greater against the open Lys-form than against the closed Glu- form of plasminogen. Fragment E-2 had no effect on the amidolytic activity of A-pro-UK or pro-UK, suggesting that the promotion of their activities was indirect and related to a fragment E-2-induced conformational change in Glu-plasminogen.(ABSTRACT TRUNCATED AT 250 WORDS)

Alanine↗

Effects of ammonium sulfate on the unfolding and refolding of the variable and constant fragments of an immunoglobulin light chain.

The equilibria and kinetics of unfolding and refolding by guanidine hydrochloride of the VL and CL fragments of a type kappa immunoglobulin light chain were studied in the presence of ammonium sulfate using circular dichroism and tryptophyl fluorescence at pH 7.5 and 25 degrees C. The unfolding equilibria of the VL and CL fragments were described in terms of the two-state transition. The midpoints of unfolding in the absence of ammonium sulfate were at 0.9 and 1.2 M guanidine hydrochloride for the CL and VL fragments respectively. The transition curves were shifted to higher concentrations of guanidine hydrochloride by 1.4 and 1.6 M for the CL and VL fragments, respectively, per mole of ammonium sulfate. Unfolding reactions of the VL and CL fragments in 3 M guanidine hydrochloride followed first-order kinetics, and the rate constants for the two proteins were both greatly decreased by the presence of ammonium sulfate. The refolding reaction of the CL fragment in 0.3 M guanidine hydrochloride consisted of two phases, and the rate constants were increased a little by the presence of ammonium sulfate. The refolding reaction of the VL fragment in 0.3 M guanidine hydrochloride followed first-order kinetics, and the rate was not affected by the presence of ammonium sulfate. These results showed that ammonium sulfate stabilizes the CL and VL fragments mainly by decreasing the unfolding rate.

Ammonium Sulfate↗

Characterization of human glucocorticoid receptor complexes formed with DNA fragments containing or lacking glucocorticoid response elements.

Sucrose density gradient shift assays were used to study the interactions of human glucocorticoid receptors (GR) with small DNA fragments either containing or lacking glucocorticoid response element (GRE) DNA consensus sequences. When crude cytoplasmic extracts containing [3H]triamcinolone acetonide [( 3H]TA) labeled GR were incubated with unlabeled DNA under conditions of DNA excess, a GRE-containing DNA fragment obtained from the 5' long terminal repeat of mouse mammary tumor virus (MMTV LTR) formed a stable 12-16S complex with activated, but not nonactivated, [3H]TA receptor. By contrast, if the cytosols were treated with calf thymus DNA-cellulose to deplete non-GR-DNA-binding proteins prior to heat activation, a smaller 7-10S complex was formed with the MMTV LTR DNA fragment. When similar experiments were conducted under conditions of large receptor excess, using 3' [32P]-MMTV LTR DNA, the trace quantity of DNA formed a stable 10-14S complex with DNA-cellulose pretreated cytosols or with untreated cytosols in the presence of excess Escherichia coli competitor DNA. If trace quantities of the 3' [32P]-MMTV LTR DNA were incubated with untreated crude cytosols, much larger complexes were formed, indicating the association of other cytosolic proteins with the MMTV LTR DNA fragment. Activated [3H]TA receptor from DNA-cellulose pretreated cytosols also interacted with two similarly sized fragments from pBR322 DNA, but with lower apparent affinities in the order MMTV LTR DNA fragment much greater than pBR322 fragment containing a single GRE DNA consensus sequence greater than non-GRE-containing pBR322 fragment.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗

Preparation of milligram amounts of 21 deoxyribonucleic acid restriction fragments.

Twenty-one DNA restriction fragments ranging in size from 12 to 880 base pairs (bp) were purified to homogeneity in milligram amounts. The developments which facilitated this work were (a) procedures for the rapid preparation of gram quantities of pure recombinant plasmid DNAs, (b) selective poly(ethylene glycol) (PEG) precipitation of DNAs according to broad classes of lengths, and (c) large-scale high-pressure liquid chromatography on RPC-5 for the purification of fragments to homogeneity. The 95- and 301-bp sequences from the lactose control region of Escherichia coli were cloned into the single EcoRI site of pVH51 in up to four copies per plasmid. These tandem inserts are separated by EcoRI sites and have a head to tail orientation in all cases. A total of 50 and 90 mg of th 95- and 301-bp fragments, respectively, were prepared from 300-L fermentations of E. coli cells transformed with these plasmids. A rapid and improved method, which can easily be scaled up, for the purification of plasmids and DNA restriction fragments was developed. Also, the linear pVH51 vector DNA was digested with HaeIII to yield fragments ranging in size from 12 to 880 bp. The five smaller fragments (from 12 to 180 bp) were purified quantitatively by a selective PEG precipitation enrichment step followed by RPC-5 column fractionation. The larger fragments (245-880 bp) were prepared in milligram amounts. Ten subfragments from the 301-bp lac fragment were prepared by HpaII, HinfI, or HaeIII/AluI digestions followed by separation of the reaction products on RPC-5.

Chemical Phenomena↗

Hybridization of nuclear matrix attached deoxyribonucleic acid fragments.

Annealing studies were performed on DNA fragments associated with rat and mouse liver interphase nuclear matrix and the metaphase scaffold of Chinese hamster DON cells. Matrix and scaffold bound DNA fragments, reassociated with an excess of total genomic DNA, displayed kinetics virtually identical with total nuclear DNA probes. Moreover, both the extent and kinetics of these hybridizations were independent of the matrix DNA fragment size (less than 350--5000 base pairs) and the method of nuclease digestion used in their preparation (DNase I, micrococcal nuclease or endogenous digestion). The repetitive DNA component of the matrix DNA was examined by reacting discrete sizes of matrix DNA fragments (less than 350--5000 base pairs) from mouse liver with a library of cloned repetitive sequence DNA fragments which included mouse major satellite sequences. Our results demonstrate that short DNA fragments anchored to the nuclear matrix contain these cloned sequences is similar proportion of total nuclear DNA and, when viewed in light of the annealing results, indicate that matrix DNA is not enriched in either repetitive or unique sequences. Furthermore, the matrix DNA fragments appear to contain the entire sequence complexity of the genome. Finally, we hybridized both matrix and total nuclear DNA fragments with cDNA to total nuclear polyadenylated RNA. The kinetics and extent of hybridization indicate that most, if not all, of the actively transcribed DNA sequences are present in similar concentrations. We conclude that in the overall organization of eukaryotic DNA within the nucleus, the repeating domains or loops which have been demonstrated by a number of investigators are not anchored at specific attachment sequences in interphase cells or during mitosis. These findings are discussed with regard to current concepts of eukaryotic DNA loop organization.

Animals↗

Interaction of Hoechst 33258 and echinomycin with nucleosomal DNA fragments containing isolated ligand binding sites.

We have examined the interaction of Hoechst 33258 and echinomycin with nucleosomal DNA fragments which contain isolated ligand binding sites. A 145 base pair fragment was prepared on the basis of the sequence of tyrT DNA, which contained no CpG or (A/T)(4) binding sites for these ligands. Isolated binding sites were introduced into this fragment at discrete locations where the minor groove is known to face toward or away from the protein core when reconstituted onto nucleosome core particles. The interaction of ligands with target sites on these nucleosomal DNA fragments was assessed by DNase I footprinting. We find that Hoechst 33258 can bind to single nucleosomal sites which face both toward and away from the protein core, without affecting the nucleosome structure. Hoechst binding is also observed on nucleosomal fragments which contain two or more drug binding sites, though in these cases the footprints are accompanied by the presence of new cleavage products in positions which suggest that the ligand has caused a proportion of the DNA molecules to adopt a new rotational positioning on the protein surface. Hoechst 33258 does not affect nucleosome reconstitution with any of these fragments. In contrast, the bifunctional intercalating antibiotic echinomycin is not able to bind to single nucleosomal CpG sites. Echinomycin footprints are observed on nucleosomal fragments containing two or more CpG sites, but there are no changes in the cleavage patterns in the remainder of the fragment. Echinomycin abolishes nucleosome reconstitution when included in the reconstitution mixture.

Base Sequence↗

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↗

Bridgehead carbocations via carbene fragmentation: erasing a 10(10) kinetic preference.

1-Norbornyloxychlorocarbene (1-NorOCCl), 1-bicyclo[2.2.2]octyloxychlorocarbene (1-BcoOCCl), and 1-adamantyloxychlorocarbene (1-AdOCCl) were generated in dichloroethane (DCE) by photolysis of the appropriate diazirines. The exclusive product in each case was the bridgehead alkyl chloride formed by fragmentation of the carbene to [R(+) OC Cl(-)] ion pairs, loss of CO, and cation-anion collapse. In mixtures of methanol and DCE, each carbene gave three products: RCl, ROH, and ROMe. RCl and ROMe resulted from competition between ion pair collapse and methanol capture of the cation. ROH resulted from methanol capture of the carbene (before fragmentation), followed by eventual methanolysis and hydrolysis of ROCH(Cl)OMe. The ratios of carbene capture to carbene fragmentation fell in the order 1-NorOCCl > BcoOCCl > 1-AdOCCl; 1-Nor(+) was the least stable cation and the slowest to form by fragmentation, so that this carbene was the most readily captured. This trend was accentuated in methanol-pentane mixtures, where ionic fragmentation was further slowed in the less polar solvent. Laser flash photolysis with either UV or time-resolved infrared (TRIR) monitoring permitted the determination of the absolute rate constants for fragmentations of the carbenes in DCE at 25 degrees C. The rate constants (s(-1)) were: 1-NorOCCl (3.3 x 10(4)), 1-BcoOCCl (1.5 x 10(5)), and 1-AdOCCl (5.9 x 10(5)). The rate constants decreased in the order of increasing strain in the resulting bridgehead carbocation, but the range of rate constants was compressed to a factor of only approximately 18. This constrasts with the factor of 10(10) by which the acetolysis of 1-AdOTs at 70 degrees C exceeded that of 1-NorOTs. The fragmentation of 1-NorOCCl to the ion pair was 3 x 10(15) times faster than the acetolysis of 1-NorOTs. The activation energies were measured as 9.0 kcal/mol (log A = 11.2 s(-1)) for the fragmentation of 1-NorOCCl and 4.4 kcal/mol (log A = 8.44 s(-1)) for that of 1-BcoOCCl both in DCE. B3LYP/6-31G computed activation energies in simulated DCE were 14.6 and 2.7 kcal/mol, respectively.

Journal Article↗