A Simple Route for Synthesis of 4-Phospho-D-Erythronate.

4-Phospho-D-erythronate is an intermediate in synthesis of pyridoxal 5'-phosphate in some bacteria and an inhibitor of ribose 5-phosphate isomerase. Previous synthetic schemes for the preparation of 4-phospho-D-erythronate required expensive precursors and typically gave low yields. We report a straightforward synthesis of 4-phospho-D-erythronate from the inexpensive precursor D-erythronolactone in 5 steps with a preparatively useful yield of 22%.

Aptamer-based multiplexed proteomic technology for biomarker discovery.

Background: The interrogation of proteomes ("proteomics") in a highly multiplexed and efficient manner remains a coveted and challenging goal in biology and medicine.

Methodology/principal Findings: We present a new aptamer-based proteomic technology for biomarker discovery capable of simultaneously measuring thousands of proteins from small sample volumes (15 µL of serum or plasma). Our current assay measures 813 proteins with low limits of detection (1 pM median), 7 logs of overall dynamic range (~100 fM-1 µM), and 5% median coefficient of variation.

Expanding the chemistry of DNA for in vitro selection.

Six new 5-position modified dUTP derivatives connected by a unique amide linkage were synthesized and tested for compatibility with the enzymatic steps of in vitro selection. Six commercially available DNA polymerases were tested for their ability to efficiently incorporate each of these dUTP derivatives during PCR. It was not possible to perform PCR under standard conditions using any of the modified dUTP derivatives studied.

Scanning probe-based fabrication of 3D nanostructures via affinity templates, functional RNA, and meniscus-mediated surface remodeling.

Developing generic platforms to organize discrete molecular elements and nanostructures into deterministic patterns on surfaces is one of the central challenges in the field of nanotechnology. Here we review three applications of the atomic force microscope (AFM) that address this challenge. In the first, we use two-step nanografting to create patterns of self-assembled monolayers (SAMs) to drive the organization of virus particles that have been either genetically or chemically modified to bind to the SAMs.

Selection of biomolecules capable of mediating the formation of nanocrystals.

Biopolymers in the biosphere are well known to mediate the formation of a wide array of inorganic materials, such as bone, shells, lenses, and magnetic particles to name a few. Recently, in vitro experiments with biopolymers such as peptides, RNA, and DNA have shown that templating by these macromolecules can yield a variety of materials under mild reaction conditions. The primary sequence of the biopolymer can be viewed as a proteomic or genomic signature for the templating of an inorganic material from defined metal precursors and reaction conditions.

Charge-transfer excited state dynamics in DNA hairpins substituted with an ethylenylpyrenyl-dU electron source and halo-dU traps.

In this work nine DNA hairpins (HPs) are studied at room temperature to observe their pyrene(*+)/dU(*-) CT excited-state dynamics following photoexcitation at 355 nm with a 25 ps laser pulse. The HPs are 18-24 bases long, have a central tetra-T loop, and have a single U(PE) (5-(2-pyren-1-yl-ethylenyl)-2'-deoxyuridine) substitution in the central region of their stems. Three of the HPs are also substituted with 5-XdU traps, where X = Br or F, to learn about the effects of these traps on CT excited-state lifetimes and emission quantum yields in U(PE) substituted HPs.

RNA-mediated synthesis of palladium nanoparticles on Au surfaces.

RNA catalysts for the shape-controlled synthesis of Pd particles from the precursor complex trisdibenzylideneacetone dipalladium ([Pd2(DBA)3] were recently discovered in our laboratory (J. Am. Chem.

RNA-mediated control of metal nanoparticle shape.

RNA sequences previously isolated by in vitro selection were further characterized for their ability to control palladium particle growth. Five pyridyl-modified RNA sequences (Pdases) representing each of the different evolved families were found to form hexagonal plates with a high degree of shape specificity. However, a sixth nonrelated pyridyl-modified RNA sequence was found to form exclusively cubic particles under identical conditions.

The effect of mutation on RNA Diels-Alderases.

Chemical mutagenesis of a previously reported RNA Diels-Alderase (DA22) was followed by in vitro selection based on [4 + 2] catalysis. New mutated families of RNA Diels-Alderases closely related in sequence space were obtained. The mutated Diels-Alderases selected showed significant improvements in catalytic efficiency (k(cat)/K(m)) as compared to the original DA22.

T7 RNA polymerase transcription with 5-position modified UTP derivatives.

Seven UTP derivatives modified at the 5-position through an amide linkage were tested as substrates for T7 RNA polymerase (T7 RNAP) transcription. All UTP derivatives gave good yields of full-length transcript even from DNA templates that showed a significant number of abortive transcripts using unmodified UTP. A kinetic assay to determine the relative K(m) and V(max) for T7 RNAP transcription gave surprisingly similar values for UTP and the 5-position hydrophobic modifications phenyl, 4-pyridyl, 2-pyridyl, indolyl, and isobutyl.

RNA-mediated metal-metal bond formation in the synthesis of hexagonal palladium nanoparticles.

RNA sequences have been discovered that mediate the growth of hexagonal palladium nanoparticles. In vitro selection techniques were used to evolve an initial library of approximately 10(14) unique RNA sequences through eight cycles of selection to yield several active sequence families. Of the five families, all representative members could form crystalline hexagonal palladium platelets.

Synthesis of 5-(2,2'-bipyridinyl and 2,2'-bipyridinediiumyl)-2'-deoxyuridine nucleosides: precursors to metallo-DNA conjugates.

The synthesis of 2,2'-bipyridinyl-2'-deoxyuridine metal-chelator nucleosides (Bipy-dU) with either ethynyl or ethylenyl linkers was now been accomplished. These new nucleosides will permit the construction of a number of corresponding metallo-DNA conjugates where many types of metals can be complexed to the 2,2'-bipyridinyl chelator group and the resulting metallo-dU conjugates incorporated into DNA oligonucleotides. Additionally this paper also reports the synthesis of a di-N-alkylated bipyridinediiumyl-2'-deoxyuridine nucleoside (Bipy(2+)-dU) with an ethylenyl linker.