Super-resolution imaging of PDMS nanochannels by single-molecule micelle-assisted blink microscopy.

Single-molecule super-resolution microscopy is an emerging technique for nanometer-scale fluorescence imaging, but in vitro single-molecule imaging protocols typically require a constant supply of reagents, and such transport is restricted in constrained geometries. In this article, we develop single-molecule micelle-assisted blink (MAB) microcopy to enable subdiffraction-limit imaging of nanochannels with better than 40 nm accuracy. The method, based on micelles and thiol-related photoswitching, is used to measure nanochannels formed in polydimethylsiloxane through tensile cracking. These conduits are reversibly size-adjustable from a few nanometers up to a micrometer and enable filtering of small particles and linearization of DNA. Unfortunately, conventional techniques cannot be used to measure widths, characterize heterogeneities, or discover porosity in situ. We overcome the access barriers by using sodium dodecyl sulfate (SDS), an ionic surfactant, to facilitate delivery of Cy5 dye and ß-mercaptoethanol reducing agent in the confined geometry. These SDS micelles and admicelles have the further benefit of slowing diffusion of Cy5 to improve localization accuracy. We use MAB microscopy to measure nanochannel widths, to reveal heterogeneity along channel lengths and between different channels in the same device, and to probe biologically relevant information about the nanoenvironment, such as solvent accessibility.

Evidence for coupled motion and hydrogen tunneling of the reaction catalyzed by glutamate mutase.

Glutamate mutase is one of a group of adenosylcobalamin-dependent enzymes that catalyze unusual isomerizations that proceed through organic radical intermediates generated by homolytic fission of the coenzyme's unique cobalt-carbon bond. These enzymes are part of a larger family of enzymes that catalyze radical chemistry in which a key step is the abstraction of a hydrogen atom from an otherwise inert substrate. To gain insight into the mechanism of hydrogen transfer, we previously used pre-steady-state, rapid-quench techniques to measure the alpha-secondary tritium kinetic and equilibrium isotope effects associated with the formation of 5'-deoxyadenosine when glutamate mutase was reacted with [5'-(3)H]adenosylcobalamin and L-glutamate. We showed that both the kinetic and equilibrium isotope effects are large and inverse, 0.76 and 0.72, respectively. We have now repeated these measurements using glutamate deuterated in the position of hydrogen abstraction. The effect of introducing a primary deuterium kinetic isotope effect on the hydrogen transfer step is to reduce the magnitude of the secondary kinetic isotope effect to a value close to unity, 1.05 +/- 0.08, whereas the equilibrium isotope effect is unchanged. The significant reduction in the secondary kinetic isotope effect is consistent with motions of the 5'-hydrogen atoms being coupled in the transition state to the motion of the hydrogen undergoing transfer, in a reaction that involves a large degree of quantum tunneling.

High-performance CE: an effective method to study lactonization of alpha2,8-linked oligosialic acid.

A sensitive and efficient method using high-performance CE (HPCE) and neuraminidase hydrolysis was developed to study the lactonization and hydrolysis of alpha2,8-pentasialic acid. Eleven lactone species of pentasialic acid formed in glacial acetic acid were detected and classified into three groups based on the number of carboxylic acids: monolactones with four carboxylic acids, dilactones with three carboxylic acids, and trilactones with two carboxylic acids. These lactones eluted between the original pentamer (with five carboxylic acids) and the fully lactonized species (with one carboxylic acid) in HPCE. Eight of the isomers were identified by hydrolysis with neuraminodase. Results obtained from previous reports and from this study together reveal a general rule for predicting the subtle difference in the acidity of each carboxylic acid in oligosialic acids: the closer the carboxylic acid is to the nonreducing end, the more acidic it is. Therefore, the elution order of lactone isomers having the same number of carboxylic groups can be predicted from the position of the free carboxylic groups in pentasialic acid. We used this principle and the results of hydrolysis with neuraminidase to identify hexamer lactone isomers separated by HPCE.

Isotope effects for deuterium transfer between substrate and coenzyme in adenosylcobalamin-dependent glutamate mutase.

A key step in the mechanism of all adenosylcobalamin-dependent enzymes is the abstraction of a hydrogen atom from the substrate by a 5'-deoxyadenosyl radical generated by homolytic fission of the coenzyme cobalt-carbon bond. We have investigated the isotope effects associated with this process for glutamate mutase reacting with deuterated glutamate. The kinetics of deuterium incorporation into 5'-deoxyadenosine (5'-dA) during the reaction were followed by rapid chemical quench, using HPLC and electrospray mass spectrometry to analyze the 5'-dA formed. The kinetics of 5'-dA formation are biphasic, comprising a rapid phase k(app) = 37 +/- 3 s(-)(1) and a slower phase k(app) = 0.9 +/- 0.4 s(-)(1). The mass spectral data clearly show that the faster phase is associated with the formation of monodeuterated 5'-dA whereas the slower phase is associated with the incorporation of a second and then a third deuterium into 5'-dA. This observation implies that a large inverse equilibrium secondary isotope effect is associated with the formation of 5'-dA from adenosylcobalamin. The primary deuterium kinetic isotope effects on V and V/K for the formation of 5'-dA were determined from time-based and competition experiments. (D)V = 2.4 +/-0.4 whereas (D)(V/K) = 10 +/- 0.4, implying that an isotopically insensitive step is partially rate-determining. The additional data provided by these experiments cause us to revise our interpretation of earlier UV-visible stopped-flow kinetic measurements of AdoCbl homolysis obtained with deuterated substrates.

Pre-steady-state measurement of intrinsic secondary tritium isotope effects associated with the homolysis of adenosylcobalamin and the formation of 5'-deoxyadensosine in glutamate mutase.

Glutamate mutase is one of a group of adenosylcobalamin-dependent enzymes that catalyze a variety of reactions that proceed through organic radical intermediates generated by homolytic fission of coenzyme's unique cobalt-carbon bond. For all the enzymes that have been examined, the homolysis step is kinetically indistinguishable from abstraction of hydrogen from the substrate (or protein), implying that deoxyadenosyl radical is formed only as a fleeting intermediate. To examine how these two steps are coupled together, we have used pre-steady-state, rapid quench techniques to measure the alpha-secondary tritium isotope effect associated with the formation of 5'-deoxyadenosine when the enzyme is reacted with [5'-(3)H]-adenosylcobalamin and L-glutamate. Surprisingly, a large inverse equilibrium isotope effect of 0.72 +/- 0.04 was found for the overall reaction, indicating that the 5'-C-H bonds become significantly stiffer on going from adenosylcobalamin to 5'-deoxyadenosine, even though the 5'-carbon remains formally sp(3) hybridized. The kinetic isotope effect for the formation of 5'-deoxyadenosine was 0.76 +/- 0.02, which suggests a late transition state for the reaction.

Hydrolysis, lactonization, and identification of alpha(2 --> 8)/alpha(2 --> 9) alternatively linked tri-, tetra-, and polysialic acids.

Alpha-(2 --> 8)/alpha(2 --> 9) alternatively linked polysialic acid (PSA) can be identified by controlled hydrolysis followed by the analysis with capillary electrophoresis (CE). Due to the different stability of alpha(2 --> 8) and alpha(2 --> 9) linkages in acidic hydrolysis, oligosialic acids (OSAs) from the hydrolysis of alpha(2 --> 8)/alpha(2 --> 9) OSA/PSA could be classified into two groups in the CE profile. The group with an odd numerical degree of polymerization (DP) had two peaks in the CE profile, and the other group, with even number of DP, showed one peak. Each alternating alpha(2 --> 8)/alpha(2 --> 9) linked OSA contains two isomers: one starts with the alpha(2 --> 8) linkage from the nonreducing end and the other starts with the alpha(2 --> 9) linkage from the nonreducing end. Trimers and tetramers were isolated by using a Mono Q column with an HPLC system. The two trimer isomers are alpha(2 --> 8)/alpha(2 --> 9) and alpha(2 --> 9)/alpha(2 --> 8) linkages and only showed partial separation by CE. After lactonization, sialidase hydrolysis, and alkaline treatment, the two trimer isomers could be separated and identified by CE analysis, but only the alpha(2 --> 8)/alpha(2 --> 9) trimer could be converted to the dilactone in glacial acetic acid. The two tetramer isomers could be converted to four monolactones and three dilactones. These lactonized species could be identified on the basis of several principles in sialidase hydrolysis and lactonization. In conclusion, regioselectivity on the lactonization of oligosialic acids proceeds under several principles: (1) Lactonization takes place more easily in the alpha(2 --> 8) linkage than in the alpha(2 --> 9) linkage; (2) all of the positions of alpha(2 --> 8) linkages in alpha(2 --> 8)/alpha(2 --> 9) alternatively linked OSA can be lactonized regardless of external or internal carboxyl groups involved; and (3) for the site of alpha(2 --> 9) linkage, only internal carboxyl groups can be lactonized.

Regioselective Lactonization of α-(2→8)-Trisialic Acid.

A simple and selective method has been developed to obtain both monolactones of the title compound, a model compound for biologically important polyneuraminic acid derivatives: acidic lactonization and alkaline hydrolysis of dilactone 1. The two monolactonized trimers can be separated by capillary electrophoresis, and then distinguished by enzymatic hydrolysis with neuraminidase; only the 2-monolactone undergoes reaction.