Dual affinity method for plasmid DNA purification in aqueous two-phase systems

The DNA binding fusion protein, LacI–His₆–GFP, together with the conjugate PEG–IDA–Cu(II) (10 kDa) was evaluated as a dual affinity system for the pUC19 plasmid extraction from an alkaline bacterial cell lysate in poly(ethylene glycol) (PEG)/dextran (DEX) aqueous two-phase systems (ATPS). In a PEG 600–DEX 40 ATPS containing 0.273 nmol of LacI fusion protein and 0.14% (w/w) of the functionalised PEG–IDA–Cu(II), more than 72% of the plasmid DNA partitioned to the PEG phase, without RNA or genomic DNA contamination as evaluated by agarose gel electrophoresis. In a second extraction stage, the elution of pDNA from the LacI binding complex proved difficult using either dextran or phosphate buffer as second phase, though more than 75% of the overall protein was removed in both systems. A maximum recovery of approximately 27% of the pCU19 plasmid was achieved using the PEG–dextran system as a second extraction system, with 80–90% of pDNA partitioning to the bottom phase. This represents about 7.4 μg of pDNA extracted per 1 mL of pUC19 desalted lysate.     

Detrapping particles in gel electrophoresis: a numerical study of different pulsed field sequences

Large particles tend to get trapped in dead-ends more often than small particles when electrophoresed in random cross-linked gels. It is known that pulsed electric fields can be used to free particles from these traps, leading to an increase in velocity and improved size separation. Although numerical and theoretical models have been proposed for the mobility of smaller particles in the so-called Ogston sieving limit, the effect of pulsed fields on trapping has not been previously modeled. We present a numerical study of detrapping and we compare our results with those of To and Boyde (To, K.-Y., Boyde, T. R., Electrophoresis 1993, 14, 597). We use an exact numerical method to examine detrapping in various two-dimensional systems of obstacles. We also propose and investigate new ways to optimize the pulse sequence in order to separate particles of different sizes.     

Formation of a Dimer of Trinuclear Helicates which Encapsulates an Array of Six Hydrogen‐Bonded Anions

The amine‐containing ligand L, composed of two bidentate pyridyl‐thiazole moieties linked by a 1,3‐diaminophenylene unit, reacts with copper(II) ions to form a dinuclear double helicate [Cu₂L₂]⁴⁺. Reaction of [Cu₂L₂]⁴⁺ with dihydrogen phosphate (0.5 equivalents) gives the unsaturated dinuclear double helicate [Cu₂L₂(OPO₃H₂)]³⁺. [Cu₂L₂(OPO₃H₂)]³⁺ further reacts with another 0.5 equivalents of dihydrogen phosphate to give a trinuclear circular helicate which then self‐assembles into a hexameric cluster [{Cu₃L₃(OPO₃H₂)₃}]²⁶⁺.     

Separating DNA sequencing fragments without a sieving matrix.

The possibility of separating appropriately labeled DNA fragments using free-flow capillary electrophoresis was predicted a few years ago based on simple theoretical arguments. Free-flow separation of double-stranded DNA (dsDNA) fragments in the 100-1000 base range was later demonstrated using a streptavidin label. In this article, we now report that end-labeled free-flow electrophoresis (ELFSE) can also be used to sequence single-stranded DNA (ssDNA). The first 100 bases of a DNA sequencing reaction were read without any sieving matrix when fractionated streptavidin was added to the 5'-end of the ssDNA fragments. These separations required only 18 min and did not require coated capillaries. An analysis of the results indicates that sample injection, analyte-wall interactions and thermal diffusion are the limiting factors at this time. Extrapolating from our data, we predict that several hundred bases could be sequenced in less than 30 min with the proper conditions. ELFSE thus offers an attractive potential alternative to polymer solutions for DNA sequencing in capillaries and microchips.     

Construction of approximate entropic forces for finitely extensible nonlinear elastic (FENE) polymers

When the stress applied to a Rouse-like polymer chain is large enough, one must use anharmonic entropic spring forces in order to keep the chain contour length from increasing to unphysical values. Although one can derive “exact” equations relating the spring extension to the entropic force produced by a finitely extensible non-linear elastic (FENE) random-walk polymer, such expressions are usually of little interest because their complexity would entail large evaluation times in numerical studies by computer. Moreover, these expressions can rarely be used directly in analytical studies. In this article, we describe a systematic method to construct analytically simple yet numerically accurate expressions to relate the entropic force to the extension of an entropic spring for a random-walk polymer chain in arbitrary dimension d ≥ 2. These expressions are modified Pade approximants which yield the correct asymptotic behaviours in both the small and large extension limits. It is shown that the well-known Warner empirical approximation is but a limiting case (for infinite dimensions).