End-labeled free-solution electrophoresis of DNA

DNA is a free-draining polymer. This subtle but "unfortunate" property of highly charged polyelectrolytes makes it impossible to separate nucleic acids by free-flow electrophoresis. This is why one must typically use a sieving matrix, such as a gel or an entangled polymer solution, in order to obtain some electrophoretic size separation. An alternative approach consists of breaking the charge to friction balance of free-draining DNA molecules. This can be achieved by labeling the DNA with a large, uncharged molecule (essentially a hydrodynamic parachute, which we also call a drag-tag) prior to electrophoresis; the resulting methodology is called end-labeled free-solution electrophoresis (ELFSE). In this article, we review the development of ELFSE over the last decade. In particular, we examine the theoretical concepts used to predict the ultimate performance of ELFSE for single-stranded (ssDNA) sequencing, the experimental results showing that ELFSE can indeed overcome the free-draining issue raised above, and the technological advances that are needed to speed the development of competitive ELFSE-based sequencing and separation technologies. Finally, we also review the reverse process, called free-solution conjugate electrophoresis (FSCE), wherein uncharged polymers of different sizes can be analyzed using a short DNA molecule as an electrophoretic engine.     

Kinetics of Dissociation of Iron(III) Complexes of Tiron in Aqueous Acid

The kinetics of dissociation of the mono, bis, and tris complexes of Tiron (1,2-dihydroxy-3,5-benzenedisulfonate) have been studied in acidic aqueous solutions in 1.0 M HClO(4)/NaClO(4), as a function of [H(+)] and temperature. In general, the kinetics can be explained by two reactions, (H(2)O)Fe(L)(n)(-1) + H(2)L right arrow over left arrow (H(2)O)Fe(L(n)H) + H(+) (k(n), k(-n)) and (HO)Fe(L)(n)(-1) + H(2)L right arrow over left arrow (H(2)O)Fe(L(n)H) (k(n)', k(-n)'), a rapid equilibrium, (H(2)O)Fe(L(n)H) right arrow over left arrow (H(2)O)Fe(L)(n) + H(+) (K(cn)), and the formation constant (H(2)O)Fe(L)(n)(-1) + H(2)L right arrow over left arrow (H(2)O)Fe(L)(n) + 2H(+). For n = 1, the reaction was observed at 670 nm, and at [H(+)] of 0.05-0.5 M at temperatures of 2.0, 14.0, 25.0, and 36.7 degrees C. For n = 2, the analogous conditions are 562 nm, at [H(+)] of 1.5 x 10(-3) to 1.4 x 10(-2) M at temperatures of 2.0, 9.0, and 14.0 degrees C. For n = 3, the conditions are 482 nm, at pH 4.5-5.7 in 0.02 M acetate buffer at temperatures of 1.8, 8.0, and 14.5 degrees C. The rate or equilibrium constants (25 degrees C) with DeltaH or DeltaH degrees (kcal mol(-1)) and DeltaS or DeltaS degrees (cal mol(-1) K(-1)) in brackets are as follows: for n = 1, k(1) = 2.3 M(-1) s(-1) (8.9, -27.1), k(-1) = 1.18 M(-1) s(-1) (4.04, -44.8), K(c1) = 0.96 M (-9.99, -33.6), K(f1) = 2.01 M (-5.14, -15.85); for n = 2, k(-2)/K(c2) = 1.9 x 10(7) (19.9, 41.5) and k(-2)'/K(c2) = 1.85 x 10(3) (1.4, -38.8) and a lower limit of K(c2) > 0.015 M; for n = 3, k(3) = 7.7 x 10(3) (15.8, 12.3), k(-3) = 1.7 x 10(7) (16.2, 28.9), K(c3) = 7.4 x 10(-5) M (4.1, -5.1), and K(f3) = 3.35 x 10(-8) (3.7, -21.7). From the variations in rate constants and activation parameters, it is suggested that the Fe(L)(2) and Fe(L)(3) complexes undergo substitution by dissociative activation, promoted by the catecholate ligands.     

Unusual reactivity of tris(pyrazolyl)borate zirconium benzyl complexes

The synthesis and reactivity of [Tp*Zr(CH2Ph)2][B(C6F5)4] (2, Tp* = HB(3,5-Me2pz)3, pz = pyrazolyl) have been explored to probe the possible role of Tp'MR2+ species in group 4 metal Tp'MCl3/MAO olefin polymerization catalysts (Tp' = generic tris(pyrazolyl)borate). The reaction of Tp*Zr(CH2Ph)3 (1) with [Ph3C][B(C6F5)4] in CD2Cl2 at -60 degrees C yields 2. 2 rearranges rapidly to [{(PhCH2)(H)B(mu-Me2pz)2}Zr(eta2-Me2pz)(CH2Ph)][B(C6F5)4] (3) at 0 degrees C. Both 2 and 3 are highly active for ethylene polymerization and alkyne insertion. Reaction of 2 with excess 2-butyne yields the double insertion product [Tp*Zr(CH2Ph)(CMe=CMeCMe=CMeCH2Ph)][B(C6F5)4] (4). Reaction of 3 with excess 2-butyne yields [{(PhCH2)(H)B(mu-Me2pz)2}Zr(Cp*)(eta2-Me2pz)][B(C6F5)4] (6, Cp* = C5Me5) via three successive 2-butyne insertions, intramolecular insertion, chain walking, and beta-Cp* elimination.     

Model systems for flavoenzyme activity: a tuneable intramolecularly hydrogen bonded flavin-diamidopyridine complex

We report the electrochemically tuneable intramolecular hydrogen bonding interactions between a covalently linked flavin-diamidopyridine unit.     

Electrical conductivity and phase transitions of the solid electrolyte system (Cs1−yRby)Cu4Cl3(I2−xClx)

Results of electrical conductivity measurements, thermal analysis, and X-ray diffraction studies indicate the existence of four phases, between 295 K and the melting points, in the system (Cs_1?yRb_y)Cu₄Cl₃I₂. These phases are designated α, á β, γ in order of decreasing temperature. The α phase is isostructural with α-RbAg₄I₅; the á phase is also cubic and very likely belongs to space groupP2₁3, a subgroup ofP4₁32 andP4₃32 to which the α phase belongs. There is a high probability that the á → α transition is continuous. The á → α transition is not discernible in the conductivity measurements or thermal analysis; therefore the line of á-α transitions is presently unknown. The β phase transforms to the á and the γ phase transforms to the β phase wheny ≤ 0.36; the γ phase transforms to the α phase wheny ≥ 0.36. That is, there is a triple point aty = 0.36, T = 399K. The γ-β, β-α′, and γ-α transitions are all hysteretic and are therefore first order. The conductivities of the β phases are relatively low and the enthalpies of activation relatively high. The conductivity of the β phase decreases with increasingy. The β phase probably belongs to space groupR3, in which the Cu⁺ ions can be ordered. The α and á phases are the true solid electrolytes; the conductivities are high, >0.73 Ω^?1cm^?1 at 419 K, and the enthalpies of activation of motion of the Cu⁺ ions low, 0.11 eV.In the system CsCu₄Cl₃(I_2?xCl_x), 0 ≤ x ≤ 0.25, the Cl^? for I^? substitutions affect the transitions to only a small extent relative to the stoichiometric compound. The β phase occurs for allx and transforms to á.     

OH stretch IR spectra of (H2O)3 and benzene-(H2O)3

The OH stretch IR spectrum of (H₂O)₃ is significantly altered upon complexation of the cluster with a benzene molecule. Theoretical calculations show that the differences in the OH stretch spectra of (H₂O)₃ and benzene-(H₂O)₃ are primarily due to mode localization induced by the benzene molecule. Received: 27 January 1997 / Accepted: 28 January 1997     

Efficient conversion of substituted aryl thioureas to 2-aminobenzothiazoles using benzyltrimethylammonium tribromide

The reaction of molecular bromine (Br2) with arylthioureas is known to produce 2-aminobenzothiazoles (Hugerschoff reaction). We show here that benzyltrimethylammonium tribromide (1, PhCH2NMe3Br3), a stable, crystalline organic ammonium tribromide (OATB), can be readily utilized as an alternative electrophilic bromine source. It is easier to control the stoichiometry of addition with an OATB, which minimizes aromatic bromination caused by excess reagent. We have developed a direct procedure from isothiocyanates and amines using tetrabutylammonium thiocyanate (Bu4NSCN) and PhCH2NMe3Br3 to afford functionalized 2-aminobenzothiazoles.     

Negative dipole potentials of uncharged langmuir monolayers due to fluorination of the hydrophilic heads

The dipole potential, affecting the structure, functions, and interactions of biomembranes, lipid bilayers, and Langmuir monolayers, is positive toward the hydrocarbon moieties. We show that uncharged Langmuir monolayers of docosyl trifluoroethyl ether (DFEE) exhibit large negative dipole potentials, while the nonfluorinated docosyl ethyl ether (DEE) forms films with positive dipole potentials. Comparison of the Delta V values for these ethers with those of the previously studied(37-39) monolayers of trifluoroethyl ester (TFEB) and ethyl ester of behenic acid (EB) shows that the reversal of the sign of Delta V causes the same change Delta(Delta V) = -706 +/- 16 mV due to fluorination of heads. The Delta V values of both TFEB and EB films differ by -122 +/- 16 mV from those of DFEE and DEE monolayers, respectively, with the same density. Such quantitative coincidence points to a common mechanism of reversal of the sign of the dipole potential for the ether and ester films despite the different structure of their heads. The mechanical properties and phase behaviors of these monolayers show that both fluorinated heads are less hydrated, suggesting that the change of the sign of Delta V could, at least partially, be related to different hydration water structure. The same negative contribution of the carbonyl bond in both TFEB and EB films contrasts with the generally accepted positive contribution of the C(delta+)=O(delta-) bond in condensed Langmuir monolayers of fatty acids, their alcohol esters, glycerides, and phospholipids but concurs with the theoretical analysis of Delta V of stearic acid monolayers. Both results question the literature values of the molecular dipole moments of these substances calculated via summation of bonds and atomic group contributions. Mixed monolayers of DFEE and DEE show smooth monotonic variation of Delta V from +450 to -235 mV, indicating a way for adjustment of the sign and magnitude of the dipole potential at the membrane-water boundary and regulation of such membrane behaviors as binding and translocation rate of hydrophobic ions and ion-carriers, adsorption and penetration of amphiphilic peptides, polarization of hydration water, and short-range repulsion. The interaction of the hydrophobic ions tetraphenylboron TPhB- and tetraphenylphosphonium TPhP+ with DFEE and DEE monolayers qualitatively follows the theory of binding of such ions to lipid bilayers, but the shifts Delta(Delta V) from the values obtained on water are much smaller than those for DPPC monolayers. This difference seems to be due to the solid (polycrystalline) character of the DFEE and DEE films that hampers the penetration of TPhB- and TPhP+ in the monolayers and reduces the attractive interaction with the hydrophobic moiety. This conclusion orients the future synthesis of amphiphiles with fluorinated heads to those which could form liquid-expanded Langmuir monolayers.     

An NMR study of hydrogen exchange in p-hydroxybenzoic acid

The compound has been used over a temperature range in dimethylsulfoxide, with trichloroacetic acid and triethylamine as catalysts. The rate constant for uncatalyzed bimolecular exchange at 25 C is k_N=131 M^–1 sec^–1; the constant for acid-catalyzed exchange is k_A=0.9 · 10⁴ M^–1 sec^–1; and that for base-catalyzed exchange is k_B=0.5 · 10⁴ M^–1 sec^–1. The activation energy for uncatalyzed exchange is 5.75 kcal/mole. The exchange rates in dimethylformamide and acetone are higher, on account of differences in the hydrogen bond. The exchange rates of the isomers fall in the sequence ortho > para > meta, which is due to conjugation and intramolecular hydrogen bonding. The exchange mechanism is discussed. Simple relationships in dimensionless parameters are given for calculating the exchange rate from the shape of the NMR signal.     

On the contribution of vibrational anharmonicity to the binding energies of water clusters

The second-order vibrational perturbation theory method has been used together with the B3LYP and MP2 electronic structure methods to investigate the effects of anharmonicity on the vibrational zero-point energy (ZPE) contributions to the binding energies of (H2O)n, n = 2-6, clusters. For the low-lying isomers of (H2O)6, the anharmonicity correction to the binding energy is calculated to range from -248 to -355 cm(-1). It is also demonstrated that although high-order electron correlation effects are important for the individual vibrational frequencies, they are relatively unimportant for the net ZPE contributions to the binding energies of water clusters.