The elastic theory of a single DNA molecule

We study the elastic responses of double-(ds) and single-stranded (ss) DNA at external force fields. A double-strand-polymer elastic model is constructed and solved by path integral methods and Monte Carlo simulations to understand the entropic elasticity, cooperative extensibility, and supercoiling property of dsDNA. The good agreement with experiments indicates that short-ranged base-pair stacking interaction is crucial for the stability and the high deformability of dsDNA. Hairpin-coil transition in ssDNA is studied with generating function method. A threshold force is needed to pull the ssDNA hairpin patterns, stabilized by base pairing and base-pair stacking, into random coils. This phase transition is predicted to be of first order for stacking potential higher than some critical level, in accordance with experimental observations.     

Precise synthesis of porphyrin array scaffolding polyisocyanides

Aryl isocyanides bearing free‐base and metallo‐porphyrins were prepared and polymerized with a Pd–Pt μ‐ethynediyl complex as the initiator to give polymers with narrow polydispersity indices. The molecular weights of the resulting polymers were precisely controlled by the initial feed ratio of the porphyrin monomer to the initiator. The UV–VIS spectra suggested that the porphyrin pendants are regularly arranged to form stacked columns. Metallo‐porphyrin polymers were also prepared by reacting free‐base porphyrin polymers with metal salts. The successive reactions of free‐base and zinc‐porphyrin monomers resulted in the formation of diblock polymers. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 585–595, 2006     

Intramolecular dimers: a new design strategy for fluorescence-quenched probes

Fluorogenic probes dual-labeled with reporter and quencher dyes use a change in fluorescence to monitor biochemical events (e.g., substrate binding or enzyme digestion). Such events change the reporter-quencher distance, which affects fluorescence. Recently, it is has been shown that static quenching through intramolecular dimers is an important mechanism that can sometimes be more efficient than F?rster resonance energy transfer (FRET).     

Carbocyclic and nitrogen-containing fused CH-acids with an annelated indenyl fragment. Thermogravimetric and X-ray structural analysis of 6H-indeno[1,2-b]quinoline

Based on thermogravimetric characteristics first obtained for the model 6H-indeno [1,2-b]quinoline, the scheme of thermal conversions of this compound in the temperature range 20–700 °C has been proposed, and the limit of its thermal stability (300 °C) has been determined. This temperature is recommended as the optimum for synthesizing fused benzoaza(diaza)fluorenes. Based on the results of X-ray structural analysis, the molecules of the studied indenoquinoline form centrosymmetric pairs, which are arranged in (110) layers. The molecules are orientationally disordered. The observed self-association of these molecules is similar to the - association of fused heterocyclic systems with-excessive and ****- deficient fragments. It has been suggested that interferon-inducing and antitumor compounds with an annelated indenyl fragment have a common mechanism of action according to the intercalation model of stacking structures.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 703–709, April, 1995.     

Synthesis and Crystal Structure of a New Copper(II) Complex with 4-Cyanobenzoic Acid

1 INTRODUCTION Exploration on the syntheses and properties of car- boxylate complexes, especially aromatic carboxylate complexes, has always been a fascinating and chal- lenging research field for decades either in coor- dination chemistry or in functional materials[1, 2]. Cy- anobenzoic acid (Hcba) possessing two functional coordination groups should display structural diver- sities on the formation of complexes[3～15]. In particu- lar, the copper(II) carboxylate complexes bearing spe- …     

Effect of conformational control of chiral oxazaborolidine by π-π stacking interaction of a pentafluorophenyl group toward asymmetric borane reduction

A pentafluorophenyl group can act as a stereo-controlling group in oxazaborolidine-catalyzed asymmetric borane reduction through intramolecular π-π stacking interaction with a phenyl group. The intramolecular π-π interaction in oxazaborolidine bearing pentafluorophenyl group is confirmed by calculations and ¹H NMR study. The interaction affects the enantioselectivity of the asymmetric reduction of acetophenone while the extent is small.     

Synthesis of an ethidium nucleoside and its acyclic analog

The protected ethidium nucleosides 8-(3′,5′-di-O-benzoyl-2′-deoxy-d-ribofuranosyl)-3-acetamido-5-ethyl-6-phenyl-phenanthridinium (5), 8-(3′,5′-di-O-acetyl-2′-deoxy-d-ribofuranosyl)-3-acetamido-5-ethyl-6-phenyl-phenanthridinium (6), and the acyclic analog 8-[(3R)-1,3-dihydroxy-4-yl]-acetamido-3-amino-5-ethyl-6-phenyl-phenanthridinium (3) were prepared. Based on to their different stability, only the acyclic derivative 3 seems to be suitable for oligonucleotide synthesis. Furthermore, the acyclic ethidium nucleoside analog 3 exhibits comparable absorption and emission properties of the underivatized ethidium (1).     

Synthesis and Crystal Structure of [Co(H<Subscript>2</Subscript>O)<Subscript>6</Subscript>](C<Subscript>19</Subscript>H<Subscript>17</Subscript>O<Subscript>4</Subscript>SO<Subscript>3</Subscript>)<Subscript>2</Subscript>⋅8H<Subscript>2</Subscript>O

The title compound, cobalt 4′,7-diethoxylisoflavone-3′-sulfonate([Co(H₂O)₆](X)₂⋅8H₂O, X = C₁₉H₁₇O₄SO₃) was synthesized and its structure was determined by single-crystal X-ray diffraction analysis. It crystallizes in the triclinic space group P-1 with cell parameters a = 9.026(3) Å, b = 16.431(5) Å, c = 18.195(6) Å, α = 72.289(4)^∘, β = 87.498(4)^∘, γ = 82.775(5)^∘, V = 2550.1(13) Å⁻³, D_c = 1.419 Mg m⁻³, and Z = 2. The results show that the title compound consists of one cobalt cation, six coordinated water molecules, eight lattice water molecules, and two 4′,7-diethoxylisoflavone-3′-sulfonate anions, C₁₉H₁₇O₄SO⁻₃. Two anions have different conformations. Twelve H atoms of six coordinated water molecules, as donors, form hydrogen bonds with four oxygen atoms of sulfo-groups of two anions and eight oxygen atoms of eight lattice water molecules. In addition, π < eqid1 > ⋅ < eqid2 > π stacking interactions exist in the crystal structure, which together with hydrogen bonds lead to supramolecular formation with a three-dimensional network.     

On-channel base stacking in microchip capillary gel electrophoresis for high-sensitivity DNA fragment analysis

We evaluated a novel strategy for high-sensitivity DNA fragment analysis in a conventional glass double-T microfluidic chip. The microchip allows for a DNA on-channel concentration based on base stacking (BS) with a microchip capillary gel electrophoretic (MCGE) separation step in a poly(vinylpyrrolidone) (PVP) sieving matrix. Depending if low conductivity caused a neutralization reaction between the hydroxide ions and the run buffer component Tris+, the stacking of DNA fragments were processed in the microchip. Compared to a conventional MCGE separation with a normal electrokinetic injection, the peak heights of 50-2650-base pair (bp) DNA fragments on the MCGE-BS separation were increased 3.9-8.0-fold. When we applied the MCGE-BS method to the analysis of a clinical sample of bovine theileria after PCR reaction, the peak height intensity of the amplified 816-bp DNA fragment from the 18S rRNA of T. buffeli was enhanced 7.0-fold compared to that of the normal injection method.