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Bloodstream infections (BSIs) are a significant cause of morbidity and mortality. Successful patient outcomes are diminished by a failure to rapidly diagnose these infections and initiate appropriate therapy. A rapid and reliable diagnostic platform of high sensitivity is needed for the management of patients with BSIs. The combination of an RNA-dependent nucleic acid sequence-based amplification and molecular beacon (NASBA-MB) detection system in multiplex format was developed to rapidly detect medically important BSI organisms. Probes and primers representing pan-gram-negative, pan-gram-positive, pan-fungal, pan- Candida , and pan- Aspergillus organisms were established utilizing 16S and 28S rRNA targets for bacteria and fungi, respectively. Two multiplex panels were developed to rapidly discriminate bacterial or fungal infections at the subkingdom/genus level with a sensitivity of 1 to 50 genomes. A clinical study was performed to evaluate the accuracy of this platform by evaluating 570 clinical samples from a tertiary-care hospital group using blood bottle samples. The sensitivity, specificity, and Youden's index values for pan-gram-positive detection and pan-gram-negative detection were 99.7%, 100%, 0.997 and 98.6%, 95.9%, 0.945, respectively. The positive predictive values (PPV) and the negative predictive values (NPV) for these two probes were 100, 90.7, and 99.4, 99.4, respectively. Pan-fungal and pan- Candida probes showed 100% sensitivity, specificity, PPV, and NPV, and the pan- Aspergillus probe showed 100% NPV. Robust signals were observed for all probes in the multiplex panels, with signal detection in

Isatoic anhydride derivatives, including a biotin and a disulfide linker were specifically designed for nucleic acid separation. 2'-OH selective RNA acylation, capture of biotinylated RNA adducts by streptavidin-coated magnetic beads and disulfide chemical cleavage led to isolation of highly enriched RNA samples from an initial 9/1 DNA-RNA mixture. Starting from the parent compound N-methylisatoic anhydride A which was used at 65 °C, we improved the extraction process by designing a new generation of isatoic anhydrides that are able to react under smoother conditions. Among them, a pyridine-based isatoic anhydride derivative 15f was found to be reactive at room temperature, leading to enhance the efficiency and selectivity of the extraction process by significantly reducing DNA side extraction. The extracted and purified RNAs can then be detected by RT-PCR.

A new and efficient strategy for labeling of nucleic acids prior to their hybridization on high density DNA chip has been developed. Our approach which combines the fragmentation and the labeling is based on the reactivity of the terminal phosphates of cleaved DNA and RNA fragments with a reporter molecule bearing aryldiazomethane group.

An isatoic anhydride derivative conjugated to a biotin and a disulfide linker was specifically designed for the separation of nucleic acids. Starting from a DNA–RNA mixture, a selective 2′-hydroxyl acylation of RNAs followed by capture with streptavidin-coated magnetic beads and cleavage of the disulfide led to elution of RNAs.

Single-strand conformers (SSCs) from the C-rich strand of the triplet repeat at the FMR-1 locus are rapidly and selectively methylated by the human DNA (cytosine-5) methyltransferase. The apparent affinity of the enzyme for the FMR-1 SSC is about tenfold higher than it is for a control Watson-Crick paired duplex. The de novo methylation rate for the SSC is over 150-fold higher than the de novo rate for the control duplex. Methylation of what is generally called a hemi-methylated duplex occurs with a rate enhancement of over 100-fold, while methylation of what can be viewed as a hemi-methylated FMR-1 SSC is actually slower than the de novo rate. The pronounced inhibition of the methyltransferase by the methylated SSC suggests that the enzyme has a higher affinity for the methylated product of its reaction with the SSC than it has for the unmethylated SSC substrate. Gel retardation studies show that the methyltransferase binds selectively to SSCs from the C-rich strand of the FMR-1 triplet repeat. This suggests a two-step stalling process in which the human methyltransferase first selectively methlyates and subsequently stalls at the C-rich strand SSC. Stalling may reflect the inability of the enzyme to release a DNA product that is fixed in a conformation resembling its transition state by the unusual structure of the substrate. In particular, the data suggest that DNA methyltransferase may physically participate in biological processes that lead to dynamic mutation at FMR-1. In general, the data raise the possibility that a two-step stalling process occurs at secondary structures associated with chromosome instability, chromosome remodelling, viral replication or viral integration and may account for the local hypermethylation and global hypomethylation associated with viral and non-viral tumorigenesis.

Oligodeoxyribonucleotide (ODN)/polymer conjugates were obtained by covalent immobilization of various nucleic acid sequences to three different polymers. Two of them bore active ester groups for the covalent linkage via the formation of amide bonds and the third one featured aldehyde moieties for immobilization via reductive amination. The factors controlling the conjugation reaction were found to be the reactivities of the polymers and their abilities at forming hydrogen bonds with the ODNs to be tethered. It was found, as well, that the observed aggregation of the grafting reaction products was essentially due to hydrogen bonding with the nucleic bases of the tethered oligonucleotides.

Inordinate expansion and hypermethylation of the fragile X DNA triplet repeat, (GGC)n.(GCC)n, are correlated with the ability of the individual G- and C-rich single strands to form hairpin structures. Two-dimensional NMR and gel electrophoresis studies show that both the G- and C-rich single strands form hairpins under physiological conditions. This propensity of hairpin formation is more pronounced for the C-rich strand than for the G-rich strand. This observation suggests that the C-rich strand is more likely to form hairpin or "slippage" structure and show asymmetric strand expansion during replication. NMR data also show that the hairpins formed by the C-rich strands fold in such a way that the cytosine at the CpG step of the stem is C.C paired. The presence of a C.C mismatch at the CpG site generates local flexibility, thereby providing analogs of the transition to the methyltransferase. In other words, the hairpins of the C-rich strand act as better substrates for the human methyltransferase than the Watson-Crick duplex or the G-rich strand. Therefore, hairpin formation could account for the specific methylation of the CpG island in the fragile X repeat that occurs during inactivation of the FMR1 gene during the onset of the disease.

2′-Deoxyadenosine substituted at C-8 by a propylthio group was introduced into oligodeoxyribonucleotides by solid phase synthesis. Oxidation by potassium persulfate (oxone) occurred selectively on the sulfur containing nucleoside causing a weakening of the glycosidic bond. Subsequent hydrolytic treatment led to selective removal of the modified base and generation of an abasic site. This constitutes a novel and convenient route for the chemical synthesis of oligodeoxyribonucleotides containing an abasic site at a preselected position in the sequence.

Molecules 2-5 that include in their structure a biotin moiety as detectable unit and differently substituted phenyl diazo functions as reactive group were prepared as reagents for labeling the phosphate group in mono and polynucleotides. These molecules were shown to react selectively and quantitatively with the model nucleotide 3'-UMP. They were used successfully in the labeling step of DNA and RNA analysis using high-density DNA-chips (or microarrays) technology.

An efficient strategy for nucleic acid labeling and analysis on deoxyribonucleic acid (DNA) chips has been developed. This approach, which combines the fragmentation and the labeling steps, is based on the reactivity of the phosphates of DNA and ribonucleic acid (RNA) fragments and is using reporter molecules bearing a bromomethyl- or aryldiazomethane-reactive group. In this chapter, we describe the preparation of the reactive label and protocols for efficient labeling of any nucleic acid sequence, DNA or RNA, prior to their hybridization, detection, and analysis on DNA chips.

An efficient strategy for nucleic acid labeling and analysis on deoxyribonucleic acid (DNA) chips has been developed. This approach, which combines the fragmentation and the labeling steps, is based on the reactivity of the phosphates of DNA and ribonucleic acid (RNA) fragments and is using reporter molecules bearing a bromomethyl- or aryldiazomethane-reactive group. In this chapter, we describe the preparation of the reactive label and protocols for efficient labeling of any nucleic acid sequence, DNA or RNA, prior to their hybridization, detection, and analysis on DNA chips.

Pyrenyldiazomethane was shown to react quantitatively and selectively at phosphate with 2'-, 3'-, and 5'-nucleotide phosphates incorporating the different nucleic bases.

DNA and RNA labeling and detection are key steps in nucleic acid-based technologies, used in medical research and molecular diagnostics. We report here the synthesis, reactivity, and potential of a new type of labeling molecule, m-(N-Biotinoylamino)phenylmethyldiazomethane (m-BioPMDAM), that reacts selectively and efficiently with phosphates in nucleotide monomers, oligonucleotides, DNA, and RNA. This molecule contains a biotin as detectable unit and a diazomethyl function as reactive moiety. We demonstrate that this label fulfills the requirements of stability, solubility, reactivity, and selectivity for hybridization-based analysis and especially for detection on high-density DNA chips.

We show here a new and efficient aqueous chemistry for labeling of any class of nucleic acids for their detection on DNA chip. The labels contain a diazo function as reactive moiety and biotin as detectable unit. The highly selective reaction of diazo group on the phosphate does not disrupt base pairing recognition and hybridization specificity.

An efficient and direct labeling method based on direct alkylation of nucleic acids at phosphates by aryldiazomethane derivatives is described.

The activation of various synthetic oligodeoxyribonucleotides (ODNs), bearing a hexamethylamine arm at their 5′-end, with the 2,4-phenylenediisothiocyanate (PDC) was studied. The activation reaction had to be performed within 40 min, because of competitive hydrolysis of the isothiocyanate functions. ODN modifications were then characterized by different analytical methods i.e. gel capillary electrophoresis, Matrix-Assisted Laser Desorption-Ionization-Time of Flight (MALDI-TOF) mass spectrometry. Moreover, activation of the amine groups of the nucleic bases was evidenced through the chemical analysis of the enzymatic-digested conjugate (PDC-ODN) by reverse phase HPLC. Preliminary results on the covalent grafting of activated ODN molecules onto the aminated latex particles showed that the amount of grafted ODNs was directly related to the number of potential grafting sites on the nucleic acid probe (primary amine group of hexamethyl arm and amine functions of the nucleic bases).

The three nucleoside triphosphates 1, 2 and 3 bearing a linker with a terminal methylketone group were prepared for incorporation into RNA fragments and post-labelling by the fluorescein derivative 4 containing an aminooxy group.

DNA and RNA labeling and detection are key steps in nucleic acid testing, particularly for molecular diagnostics applications. Here, we report a new class of aryldiazomethyl labels that include in their structure a biotin moiety as a detectable unit and a nitro substituted phenyl diazomethyl as a reactive group. The greatest reactivity towards phosphates of nucleic acids, the water solubility and the stability of these new molecules were demonstrated. These very important properties, which are the main requirements for nucleic acid labeling in aqueous conditions using automated protocols within integrated diagnostic devices, make them the perfect labeling tools for hybridization-based analysis, especially for high-density DNA chips.

In this study, the adsorption of single-stranded oligodeoxyribonucleotides (ODN) onto well-characterized polymer latex particles has been investigated. At first, the case of poly(thymidylic acid) (dT35) was thoroughly examined as a function of pH and ionic strength in the presence of cationic polystyrene colloids prepared by emulsifier-free copolymerization of styrene and vinylbenzylamine hydrochloride. Due to the polyelectrolyte character of the oligodeoxyribonucleotides (which are negatively charged) and the positive charges of the particles, strong adsorption was clearly noticed together with a high affinity; in addition, a decrease in the maximal adsorption was observed upon raising the pH. These adsorption phenomena corroborate that electrostatic forces play a major role in the adsorption process; however the contribution of hydrophobic forces was also evidenced using the various adsorption isotherms at various pHs and extrapolating these results to zero surface charge density (σ = 0) and to zero zet...

8-Hydroxyl-2'-deoxyguanosine (also referred to as 8-hydroxyguanine [8-OH-dG] or 7,8-dihydro-8-oxoguanine), a common DNA adduct resulting from injury to DNA via reactive oxygen species, affects the in vitro methylation of nearby cytosine moieties by the human DNA methyltransferase. The exact position of 8-OH-deoxyguanosine relative to a CpG dinucleotide appears important to this effect. Our data indicate that 8-OH-deoxyguanosine diminishes the ability of the methyltransferase to methylate a target cytosine when the 8-OH-deoxyguanosine is one or two nucleotides 3' from the cytosine, on the same strand. On the other hand 8-OH-deoxyguanosine does not diminish the ability of the enzyme to respond to a methyl director (5-methylcytosine) when the 8-OH-deoxyguanosine is on the same strand but one or two nucleotides 3' from the methyl director. Differences in methylation rates as great as 13-fold have been detected using various 8-OH-deoxyguanosine-containing oligonucleotides as substrates in methylation assays. Our findings suggest that oxidative damage of parental strand guanines would permit normal copying of methylation patterns through maintenance methylation, while oxidative damage of guanines in the nascent strand DNA would inhibit such methylation.

Synthetic oligodeoxyribonucleotide duplexes have been used to study the methylation specificity of M · Hpa II, a bacterial DNA methyltransferase. Substrates of four types were compared. A 30-mer containing a Watson-Crick paired CCGG recognition sequence was rapidly methylated at the central cytosine on each strand in the recognition sequence. A 30-mer containing an asymmetrically methylated recognition sequence, of the type transiently produced by DNA replication, was rapidly methylated at the central cytosine on the unmethylated strand. A heteroduplex containing an A-C mispair in the recognition sequence (CCGG/CCAG) was rapidly methylated at the cytosine in the mispair. A heteroduplex containing an A-C and an adjacent C-C mispair in the recognition sequence (CCGG/CCCA) was not methylated at a significant rate. The results show that M · Hpa II can tolerate a single mispair at its recognition site in a heteroduplex without loss of activity pr specificity.

Runs of G residues on the G-rich strands of 30mers from the region spanning codon 12 of c-Ha- ras appear to be protected against chemical modification by dimethylsulfate. This suggests that the G-rich strand might spontaneously form a Hoogsteen-paired quadruplex, which is characteristic of telomere-like DNA sequences. In this report we show that the predominant species in 1:1 mixtures of complementary 30mers from this region are duplex DNA and a smaller amount of unimolecular foldback formed by the C-rich strand. Foldbacks of this type resemble structures first observed in the C-rich strand of telomeric DNA and also occur at, the CCG triplet repeat present in the FMR-1 gene of human fragile X syndrome. Foldbacks from the C-rich strand of c-Ha- ras and the FMR-1 triplet repeat are exceptional substrates for the human methyltransferase in isolation. Substituting inosine for guanosine alters the secondary structure of the folded oligomers and dramatically reduces their ability to serve as substrates for the human methyltransferase, suggesting that secondary structure is required for recognition by the enzyme. These findings suggest that one mechanism by which methyl groups accumulate in the c-Ha- ras region of chromosome 11 during carcinogenesis and at the FMR-1 locus during repeat expansion at fragile X may be structurally induced de novo methylation at sites undergoing local conformational change. Such methylation might serve to mark unusual structures for repair. In the absence of repair, asymmetrically methylated duplexes produced by resolution of the unusual structures would be rapidly converted to symmetrically methylated duplexes through the methyl-directed activity also carried by the human methyltransferase.

In a search for more active radioprotective compounds, we have prepared and examined a series of model molecules in which the radioprotective beta-aminothiol unit (free or derivatized as acetate or phosphorothioate) is tethered to the DNA-binding chromophores quinoline and acridine through links of variable length. The modifying activity of these 'hybrid' molecules was estimated by measuring the formation of 8-oxo-2'-deoxyguanosine (8-oxodGuo) in double-strand DNA upon exposure to gamma-rays in oxygen-free solution in the presence of the drugs. We show that all hybrid molecules protect the guanine moiety from oxidation more efficiently than the parent beta-aminothiol units. The degree of protection is the highest for the molecules in which the thiol is linked to the strong binding intercalator acridine through a long polyaminochain.

We have prepared a series of tailor-made molecules that recognize and cleave DNA at apurinic sites in vitro. These molecules incorporate in their structure different units designed for specific function: an intercalator for DNA binding, a nucleic base for abasic site recognition and a linking chain of variable length and nature (including amino and/or amido functions). The cleavage efficiency of the molecules can be modulated by varying successively the nature of the intercalating agent, the nucleic base and the chain. All molecules bind to native calf thymus DNA with binding constants ranging from 10(4) to 10(6) M-1. Their cleavage activity was determined on plasmid DNA (pBR 322) containing 1.8 AP-sites per DNA-molecule. The minimum requirements for cleavage are the presence of the three units, the intercalator, the nucleic base and at least one amino function in the chain. The most efficient molecules cleave plasmid DNA at nanomolar concentrations. Enzymatic experiments on the termini generated after cleavage of AP-DNA suggest a strand break induced by a beta-elimination reaction. In order to get insight into the mode of action (efficiency, selectivity, interaction), we have used synthetic oligonucleotides containing either a true abasic site at a determined position to analyse the cleavage parameters of the synthetic molecules by HPLC or a chemically stable analog (tetrahydrofuran) of the abasic site for high field 1H NMR spectrometry and footprinting experiments. All results are consistent with a beta-elimination mechanism in which each constituent of the molecule exerts a specific function as indicated in the scheme: DNA targeting, abasic site recognition, phosphate binding and beta-elimination catalysis.(ABSTRACT TRUNCATED AT 250 WORDS)

A new class of affinity labels has been developed for human DNA (cytosine-5) methyltransferases. These oligodeoxynucleotides contain 5-fluorodeoxycytidine at a mispair within the recognition motif of the human enzyme. They were not effectively recognized by bacterial methyltransferases. They can be viewed as analogs of the intermediates transiently produced by methyltransferases during catalysis. Affinity labelling patterns suggest that both the structurally induced activity and the methyl-directed activity of the human enzymes operate by the same mechanism and reside on the same polypeptide chains.

We report a novel strategy for Post-Amplification Labelling based upon coupling nucleotide incorporating an oxyamino function with a fluorophore bearing an aldehydic group.

The hydrolytic stability of 2′-deoxypurine nucleosides is decreased by introduction of electron-withdrawing substituents at the C-8 position in the series of compounds 2–8 , 10–14 . The sulfone group causes a 2.9 × 10 4 rate acceleration for glycosidic bond cleavage in compound 14 .

A series of bifunctional molecules in which a heterocycle is linked to an aminothiol chain were synthesized. A new synthesis of N,N′-bis-(3-aminopropyl) cystamine (WR 33278) is described. Reaction of WR 33278 or analogues with the phenoxy derivatives of quinoline or acridine yielded the desired bifunctional molecules.

Preparation of the uridine and adenosine triphosphates 1 and 2 bearing a linker with a terminal aminooxy group is described. Both 1 and 2 react readily with the aldehydic fluorescein derivative 15. They could each be incorporated into a 330-mer fragment with T7 RNA polymerase.