Surface plasmon resonance imaging studies of protein-carbohydrate interactions

Carbohydrate arrays fabricated on gold films were used to study carbohydrate-protein interactions with surface plasmon resonance (SPR) imaging. An immobilization scheme consisting of the formation of a surface disulfide bond was used to attach thiol-modified carbohydrates onto gold films and to fabricate carbohydrate arrays. The carbohydrate attachment steps were characterized using polarization modulation Fourier transform infrared reflection absorption spectroscopy; and poly(dimethylsiloxane) microchannels were used to immobilize probe compounds at discrete locations on a gold film. The binding of the carbohydrate-binding proteins concanavalin A (ConA) and jacalin to arrays composed of the monosaccharides mannose and galactose was monitored with SPR imaging. SPR imaging measurements were employed to accomplish the following: (i) construct adsorption isotherms for the interactions of ConA and jacalin to the carbohydrate surfaces, (ii) monitor protein binding to surfaces presenting different compositions of the immobilized carbohydrates, and (iii) measure the solution equilibrium dissociation constants for ConA and jacalin toward mannose and galactose, respectively. Adsorption coefficients (K(ADS)) of 2.2 +/- 0.8 x 10(7) M(-)(1) and 5.6 +/- 1.7 x 10(6) M(-)(1) were obtained for jacalin adsorbing to a galactose surface and ConA adsorbing to a mannose surface, respectively. The solution equilibrium dissociation (K(D)) constant for the interaction of jacalin and galactose was found to be 16 +/- 5 microM, and for ConA and mannose was found to be 200 +/- 50 microM.     

Surface modification of polypropylene with CF4, CF3H,CF3Cl,and CF3Br plasmas

ESCA and contact angle measurements were used to characterize the surfaces of polypropylene and glass substrates exposed to CF₄, CF₃H, CF₃Cl, and CF₃Br plasmas. The use of both organic and inorganic substrates allowed clear distinction between treatments which led to plasma polymerization and treatments which caused grafting of functional groups directly to the substrate surfaces. CF₄ plasmas were the only treatments studied which fluorinated polypropylene surfaces directly, without the deposition of a thin, plasma-polymerized film. CF₃H polymerized in a plasma, while CF₃Cl and CF₃Br plasmas caused chlorination and bromination of polypropylene surfaces, respectively. Correlations were made between the active species present in the plasmas and the surface chemistry observed on the treated polypropylene substrates.     

Surface enzyme kinetics for biopolymer microarrays: a combination of Langmuir and Michaelis-Menten concepts

Real-time surface plasmon resonance (SPR) imaging measurements of surface enzymatic reactions on DNA microarrays are analyzed using a kinetics model that couples the contributions of both enzyme adsorption and surface enzyme reaction kinetics. For the case of a 1:1 binding of an enzyme molecule (E) to a surface-immobilized substrate (S), the overall enzymatic reaction can be described in terms of classical Langmuir adsorption and Michaelis-Menten concepts and three rate constants: enzyme adsorption (k(a)), enzyme desorption (k(d)) and enzyme catalysis (k(cat)). In contrast to solution enzyme kinetics, the amount of enzyme in solution is in excess as compared to the amount of substrate on the surface. Moreover, the surface concentration of the intermediary enzyme-substrate complex (ES) is not constant with time, but goes to zero as the reaction is completed. However, kinetic simulations show that the fractional surface coverage of ES on the remaining unreacted sites does reach a steady-state value throughout the course of the surface reaction. This steady-state value approaches the Langmuir equilibrium value for cases where k(a)[E] > k(cat). Experiments using the 3' --> 5' exodeoxyribonuclease activity of Exonuclease III on double-stranded DNA microarrays as a function of temperature and enzyme concentration are used to demonstrate how this model can be applied to quantitatively analyze the SPR imaging data.     

Microarray methods for protein biomarker detection

The application of protein biomarkers as an aid for the detection and treatment of diseases has been subject to intensified interest in recent years. The quantitative assaying of protein biomarkers in easily obtainable biological fluids such as serum and urine offers the opportunity to improve patient care via earlier and more accurate diagnoses in a convenient, non-invasive manner as well as providing a potential route towards more individually targeted treatment. Essential to achieving progress in biomarker technology is the ability to screen large numbers of proteins simultaneously in a single experiment with high sensitivity and selectivity. In this article, we highlight recent progress in the use of microarrays for high-throughput biomarker profiling and discuss some of the challenges associated with these efforts.     

Cleavage of thioacetals by clay-supported metal nitrates

Thioacetals are cleaved into aldehydes and ketones, under very mild conditions, K-10 clay-supported ferric or cupric nitrate.     

Chemically induced hairpin formation in DNA monolayers

A naphthyridine dimer that binds specifically to G-G mismatches has been used to induce hairpin formation in oligonucleotides immobilized onto chemically modified gold surfaces. Surface plasmon resonance (SPR) imaging measurements of DNA microarrays were used to demonstrate that binding of the naphthyridine dimer to G-G mismatches within the stem portion of an immobilized 42-mer oligonucleotide could be used to induce hairpin formation that prevented hybridization of DNA complementary to the loop sequence. In addition, the selectivity of the naphthyridine dimer for G-G mismatches was verified through SPR imaging measurements of the hybridization adsorption of an 11-mer oligonucleotide to a four-component DNA array of zero- and single-base mismatch sequences.     

Direct detection of genomic DNA by enzymatically amplified SPR imaging measurements of RNA microarrays

A novel surface enzymatic reaction scheme that amplifies the optical response of RNA microarrays to the binding of complementary DNA is developed for the direct detection and analysis of genomic DNA. The enzyme RNase H is shown to selectively and repeatedly destroy RNA from DNA-RNA heteroduplexes on gold surfaces; when used in conjunction with the label-free technique of surface plasmon resonance (SPR) imaging, DNA oligonucleotides can be detected at a concentration of 1 fM. This enzymatically amplified SPR imaging methodology is then utilized to detect and identify the presence of the TSPY gene in human genomic DNA without PCR amplification.     

A new mass spectrometric method for determining the degree of labeling with heavy isotopes: The study of deuterated toluenes

A new method of general applicability for determining the percentage deuterium labeling in organic compounds is described. It uses the heights of ‘metastable peaks’ in the mass spectrum to determine the relative amounts of deuterated and undeuterated species. The method is illustrated by describing the analysis of mixtures of toluene-o-d₁ and toluene, of toluene α-d₁ and toluene, and of toluene-2,6-d₂, toluene-o-d₁ and toluene.