An Interscholastic Network To Generate LexA Enhancer Trap Lines in .

Binary expression systems like the LexA-LexAop system provide a powerful experimental tool kit to study gene and tissue function in developmental biology, neurobiology, and physiology. However, the number of well-defined LexA enhancer trap insertions remains limited. In this study, we present the molecular characterization and initial tissue expression analysis of nearly 100 novel StanEx LexA enhancer traps, derived from the index line.

Microchannel plate detector detection efficiency to monoenergetic electrons between 3 and 28 keV.

An unshielded microchannel plate (MCP) detector with an ultrafine pore diameter of 2 μm was irradiated by an electron beam to determine the detection efficiency of electrons for creating detector signals, or counts. Tested electron energies spanned a range of 3 kiloelectron volts (keV) to 28 keV. Higher detection efficiencies were measured at the lower end of this energy range, 0.

Double displacement: An improved bioorthogonal reaction strategy for templated nucleic acid detection.

Quenched autoligation probes have been employed previously in a target-templated nonenzymatic ligation strategy for detecting nucleic acids in cells by fluorescence. A common source of background signal in such probes is the undesired reaction with water and other cellular nucleophiles. Here, we describe a new class of self-ligating probes, double displacement (DD) probes, that rely on two displacement reactions to fully unquench a nearby fluorophore.

5'-Iodination of solid-phase-linked oligodeoxyribonucleotides.

5'-Iodinated oligodeoxyribonucleotides readily react with 3'-phosphorothioated DNA in the presence of a complementary template to yield a conjugate that is identical to natural DNA in every respect except that one oxygen atom in the phosphodiester backbone is replaced by a sulfur atom. The 5'-iodo group is easily converted to a variety of other functional groups and will quickly react with thiol-containing labels to yield stable thioether conjugates. This unit presents manual and automated procedures for converting the 5'-hydroxyl of protected CPG-bound oligodeoxyribonucleotides to an iodo group and for releasing and purifying the products.

New, stronger nucleophiles for nucleic acid-templated chemistry: Synthesis and application in fluorescence detection of cellular RNA.

Nucleic acid-templated chemistry is a promising strategy for imaging genetic sequences in living cells. Here we describe the synthesis of two new nucleophiles for use in templated nucleophilic displacements with DNA probes. The nucleophilic groups are phosphorodithioate and phosphorotrithioate; we report on synthetic methods for introducing these groups at the 3'-terminus of oligonucleotides.

Chemoselective covalent coupling of oligonucleotide probes to self-assembled monolayers.

A chemoselective route to routinely and rapidly attach oligonucleotide probes to well-defined surfaces is presented. Cu(I) tris(benzyltriazolylmethyl)amine-catalyzed coupling of terminal acetylenes to azides on a self-assembled monolayer is used instead of traditional nucleophilic-electrophilic coupling reactions. The reaction proceeds well even in the presence of purposely introduced nucleophilic and electrophilic impurities.

General method for modification of liposomes for encoded assembly on supported bilayers.

An amphiphilic oligonucleotide species ((C18)2-DNA) is presented as a generally useful reagent to display encoded tether sequences on the surface of phospholipid assemblies. (C18)2-DNA inserts into preformed vesicles and proteoliposomes of arbitrary composition, content, and origin using a simple and gentle procedure and is a significant improvement over the previously described method particularly since it allows postmodification of any phospholipid assembly without the need for special lipids carrying reactive headgroups. DNA-modified vesicles can then be tethered, via DNA hybridization, onto a supported phospholipid bilayer displaying the complementary sequence.

Versatile 5'-functionalization of oligonucleotides on solid support: amines, azides, thiols, and thioethers via phosphorus chemistry.

Although the preparation of conjugates of oligonucleotides is by now commonplace, existing methods (usually utilizing thiols or primary amines) are generally expensive, and often require postsynthetic reaction with the DNA followed by a separate purification. Here we describe simple procedures for a broad set of direct 5'-end (5'-terminal carbon) functionalizations of DNA oligonucleotides while they remain on the synthesizer column. 5'-Iodinated oligonucleotides (prepared by an automated cycle as previously reported) are converted directly to 5'-azides, 5'-thiocarbamates, and alkyl and aryl 5'-thioethers in high yields.

Prodrugs of dynemicin analogs for selective chemotherapy mediated by an aldolase catalytic Ab.

Prodrugs of dynemicin analogs were synthesized, and their activation by aldolase antibody (Ab) 38C2 was evaluated by DNA-cleaving activity, as well as tumor cell growth inhibition. Further, we provide evidence that the activated enediynes underwent covalent crosscoupling with the aldolase Ab, which appears to be a limiting factor of their tumor cell growth-inhibiting activity and should be of general interest in the field of enediyne chemotherapy. These findings might open new avenues for defined conjugations of small molecule drugs to mAbs in general and aldolase Abs in particular.

Artificial human telomeres from DNA nanocircle templates.

Human telomerase is a reverse-transcriptase enzyme that synthesizes the multikilobase repeating hexamer telomere sequence (TTAGGG)n at the ends of chromosomes. Here we describe a designed approach to mimicry of telomerase, in which synthetic DNA nanocircles act as essentially infinite catalytic templates for efficient synthesis of long telomeres by DNA polymerase enzymes. Results show that the combination of a nanocircle and a DNA polymerase gives a positive telomere-repeat amplification protocol assay result for telomerase activity, and similar to the natural enzyme, it is inhibited by a known telomerase inhibitor.

A simple method for electrophilic functionalization of DNA.

[reaction: see text] An extremely simple and versatile method for placing an electrophilic functional group (iodide) at the 5' end of oligodeoxyribonucleotides is described. The reaction is carried out while the protected oligodeoxyribonucleotide remains on a solid support and utilizes inexpensive iodination chemistry. We demonstrate that this reaction can be automated on a DNA synthesizer as the last step of DNA synthesis.