Digital imaging considerations for gel electrophoresis analysis systems

Gel analysis system purchasers have a large variety of digital imaging products to choose from today. Understanding the specifications presented by the manufacturers is important to ensure that the system fits the needs ofthe researcher using the system. The background information contained in this paper explains the terminology and many of the specifications along with their significance.     

The pure rotational Raman spectra of cyanogen, C2N2 and C2N2

The pure rotational Raman spectra of C₂¹⁴N₂ and C₂¹⁵N₂ have been recorded photographically using a 3-metre spectrograph with a reciprocal linear dispersion of 1.4 cm⁻¹ mm⁻¹ at 488.0 nm and analysed to give the rotational and centrifugal distortion constants for both species. Corrections were applied to compensate for the effect of molecules in excited vibrational states on the pure rotational spectra. Comparisons are made with previous infrared vibration—rotational studies on these species and with previous Raman studies on C₂¹⁴N₂. The following bond lengths were calculated: r₀(C---N) = 116 ± 1 pm; r₀(C---C) = 138 ± 2 pm.     

A simple DNase model system comprising a dinuclear Zn(II) complex in methanol accelerates the cleavage of a series of methyl aryl phosphate diesters by 10(11)-10(13)

The di-Zn(II) complex of 1,3-bis[ N1, N1'-(1,5,9-triazacyclododecyl)]propane with an associated methoxide ( 3:Zn(II) 2: (-)OCH 3) was prepared and its catalysis of the methanolysis of a series of fourteen methyl aryl phosphate diesters ( 6) was studied at s (s)pH 9.8 in methanol at 25.0 +/- 0.1 degrees C. Plots of k obs vs [ 3:Zn(II) 2: (-)OCH 3] free for all members of 6 show saturation behavior from which K(M) and kcat (max) were determined. The second order rate constants for the catalyzed reactions (kcat (max)/K(M)) for each substrate are larger than the corresponding methoxide catalyzed reaction (k 2 (-OMe)) by 1.4 x 10(8) to 3 x 10 (9)-fold. The values of k cat (max) for all members of 6 are between 4 x 10(11) and 3 x 10(13) times larger than the solution reaction at s (s)pH 9.8, with the largest accelerations being given for substrates where the departing aryloxy unit contains ortho-NO 2 or C(O)OCH 3 groups. Based on the linear Br?nsted plots of k cat (max) vs s (s)pKa of the phenol, beta lg values of -0.57 and -0.34 are determined respectively for the catalyzed methanolysis of "regular" substrates that do not contain the ortho-NO 2 or C(O)OCH 3 groups, and those substrates that do. The data are consistent with a two step mechanism for the catalyzed reaction with rate limiting formation of a catalyst-coordinated phosphorane intermediate, followed by fast loss of the aryloxy leaving group. A detailed energetics calculation indicates that the catalyst binds the transition state comprising [CH 3O (-): 6], giving a hypothetical [ 3:Zn(II) 2:CH 3O (-): 6] complex, by -21.4 to -24.5 kcal/mol, with the strongest binding being for those substrates having the ortho-NO 2 or C(O)OCH 3 groups.     

Study on the transesterification of methyl aryl phosphorothioates in methanol promoted by Cd(II), Mn(II), and a synthetic Pd(II) complex

Methanol solutions containing Cd(II), Mn(II), and a palladacycle, (dimethanol bis(N,N-dimethylbenzylamine-2C,N)palladium(II) (3), are shown to promote the methanolytic transesterification of O-methyl O-4-nitrophenyl phosphorothioate (2b) at 25 °C with impressive rate accelerations of 10(6)-10(11) over the background methoxide promoted reaction. A detailed mechanistic investigation of the methanolytic cleavage of 2a-d having various leaving group aryl substitutions, and particularly the 4-nitrophenyl derivative (2b), catalyzed by Pd-complex 3 is presented. Plots of k(obs) versus palladacycle [3] demonstrate strong saturation binding to form 2b:3. Numerical fits of the kinetic data to a universal binding equation provide binding constants, K(b), and first order catalytic rate constants for the methanolysis reaction of the 2b:3 complex (k(cat)) which, when corrected for buffer effects, give corrected (k(cat)(corr)) rate constants. A sigmoidal shaped plot of log(k(cat)(corr)) versus (s)(s)pH (in methanol) for the cleavage of 2b displays a broad (s)(s)pH independent region from 5.6 ≤ (s)(s)pH ≤ 10 with a k(minimum) = (1.45 ± 0.24) × 10(-2) s(-1) and a [lyoxide] dependent wing plateauing above a kinetically determined (s)(s)pK(a) of 12.71 ± 0.17 to give a k(maximum) = 7.1 ± 1.7 s(-1). Br?nsted plots were constructed for reaction of 2a-d at (s)(s)pH 8.7 and 14.1, corresponding to reaction in the midpoints of the low and high (s)(s)pH plateaus. The Br?nsted coefficients (β(LG)) are computed as -0.01 ± 0.03 and -0.86 ± 0.004 at low and high (s)(s)pH, respectively. In the low (s)(s)pH plateau, and under conditions of saturating 3, a solvent deuterium kinetic isotope effect of k(H)/k(D) = 1.17 ± 0.08 is observed; activation parameters (ΔH(Pd)(++) = 14.0 ± 0.6 kcal/mol and ΔS(Pd)(++)= -20 ± 2 cal/mol·K) were obtained for the 3-catalyzed cleavage reaction of 2b. Possible mechanisms are discussed for the reactions catalyzed by 3 at low and high sspH. This catalytic system is shown to promote the methanolytic cleavage of O,O-dimethyl phosphorothioate in CD3OD, producing (CD3O)2P═O(S(-)) with a half time for reaction of 34 min.     

Amino acid end-group in commercial heparin. III. Determination of the number of amino groups of amino acid and hexosamine residues per heparin molecule

The reactions of heparin with 2,4,6-trinitrobenzenesulfonic acid (TNBS) were studied spectrometrically. Seven different commercial heparins were used in this study. The amino groups react with TNBS to form equimolar amounts of trinitrophenylated (TNP) amino groups and bisulfite ions. The TNP-amino groups further react with bisulfite ions to form the monosubstituted anionic sigma complex. The absorption spectrum with two maxima at approximately 350 nm and approximately 420 nm, characteristic of either the TNP-amino groups or the complex, was analyzed for the reaction of TNBS with heparin. It was shown that the reactivities of TNBS with amino groups from α-amino acid and hexosamine residues are greatly different. By combining the results of the reaction kinetics and the reaction of heparin with Sanger's reagent, the number of the α-amino groups and the free amino groups in hexosamine residues were determined. These data have been performed with a range of heparins from different commercial sources, of different activities and physical characteristics. No correlation was found between the free amino contents of these heparins and biological potency. © 1993 John Wiley & Sons, Inc.     

Peptide conjugated cellulose nanocrystals with sensitive human neutrophil elastase sensor activity

In chronic wounds, elevated human neutrophil elastase (HNE) is a destructive protease that has been proposed as a biomarker. Numerous wound dressing designs have been introduced in an effort to lower HNE levels. The clinical detection of HNE as a point of care biomarker or an in situ colorimetric adjuvant to chronic wound dressings presents potential advantages in the management of chronic wounds. A colorimetric approach to the detection of HNE using peptide conjugated cotton cellulose nanocrystals (CCN) is reported here. For this purpose a HNE tripeptide substrate, n-Succinyl-Alanine–Alanine-Valine-para-nitroanilide (Suc-Ala–Ala-Val-pNA), was covalently attached to glycine esterified CCN and compared with a similar tetrapeptide analog for colorimetric HNE sensor activity. Visible HNE activity was significantly higher on CCN tripeptide conjugates when compared with similar analogs synthesized on paper. Upon enzymatic release of para-nitroaniline (pNA) from the Glycine-CCN conjugate of succinyl-Ala–Ala-Val-pNA, amplification of the colorimetric response from pNA with reactive dyes enhanced visible absorption of the chromogen. Two color amplifying dyes that react with pNA were compared for their ability to enhance the visual sensor response to HNE activity. The colorimetric detection of HNE with CCN tripeptide conjugates was sensitive at HNE levels previously reported in chronic wound fluid (0.05 U/mL HNE). The HNE sensor and the chromogen amplifying dyes were interfaced with 50 and 10 kD dialysis cellulose membranes (DCM) to model filtration of HNE and chromogen (pNA) from a model wound dressing surface before and after sensor reactivity. The detection sensitivity to HNE activity was assessed with the CCN-tripeptide conjugate interfaced at the DCM surface distal and proximal to a dressing surface. The HNE sensor interfaced proximal to the dressing surface was most efficient with 10 kD membrane filtration of pNA and subsequent reaction with amplifying dyes. When interfaced with the 10 kD cellulose membrane, elastase sensor activity remained sensitive to 0.05 U/mL HNE. The nanocellulose surface properties, performance and design issues of the biosensor approach are discussed.     

Synthesis of all diastereomeric methyl 2,5-anhydro-3-deoxy-hexonates: precursors to C-2-deoxynucleosides and THF-templated γ- and δ-amino acids

Efficient syntheses of all diastereomers of methyl 2,5-anhydro-3-deoxy-hexonate from mannono- or gulono-lactones provide precursors for C-nucleosides of 2-deoxyribose and for THF-templated γ- and δ-amino acids.     

Pyrrolidinones derived from (S)-pyroglutamic acid: penmacric acid and analogues

Alkylation reactions using alpha-halolactams or lactam enolates derived from bicyclic lactam templates can proceed with high endo- or exo- diastereoselectivity respectively. In the latter case, stereochemical correction by means of enolate generation and hindered phenol quench is possible with moderate efficiency. This protocol has been applied to the synthesis of protected penmacric acid and its analogues.