Aptamers come of age - at last

Aptamers in the virologists' toolkit

Aptamers are artificial nucleic acid ligands that can be generated in vitro against a wide range of molecules, including the gene products of viruses. Aptamers are isolated from complex libraries of synthetic nucleic acids by an iterative, cell-free process that involves repetitively reducing the complexity of the library by partitioning on the basis of selective binding to the target molecule, followed by reamplification. For virologists, aptamers have potential uses as tools to help to analyse the molecular biology of virus replication, as a complement to the more familiar monoclonal antibodies. They also have potential applications as diagnostic biosensors and in the development of antiviral agents. In recent years, these two promising avenues have been explored increasingly by virologists; here, the progress that has been made is reviewed.

SELEX experiments: new prospects, applications and data analysis in inferring regulatory pathways

Systematic Evolution of Ligands by EXponential enrichment (SELEX) is an experimental procedure that allows extraction, from an initially random pool of oligonucleotides, of the oligomers with a desired binding affinity for a given molecular target. The procedure can be used to infer the strongest binders for a given DNA or RNA binding protein, and the highest affinity binding sequences isolated through SELEX can have numerous research, diagnostic and therapeutic applications. Recently, important new modifications of the SELEX protocol have been proposed. In particular, a modification of the standard SELEX procedure allows generating a dataset from which protein-DNA interaction parameters can be determined with unprecedented accuracy. Another variant of SELEX allows investigating interactions of a protein with nucleic-acid fragments derived from the entire genome of an organism. We review here different SELEX-based methods, with particular emphasis on the experimental design and on the applications aimed at inferring protein-DNA interactions. In addition to the experimental issues, we also review relevant methods of data analysis, as well as theoretical modeling of SELEX.

Dynamics of genomic-library enrichment and identification of solvent tolerance genes for Clostridium acetobutylicum

A Clostridium acetobutylicum ATCC 824 genomic library was constructed using randomly sheared DNA. Library inserts conferring increased tolerance to 1-butanol were isolated using two protocols. Protocol I utilized a single round of butanol challenges in batch culture, while protocol II, which gave clearly superior outcomes, was based on the serial transfer of stationary-phase cultures into progressively higher butanol concentrations. DNA microarray analysis made a high-resolution assessment of the dynamic process of library enrichment possible for the first time. Protocol I yielded a library insert containing the entire coding region of the gene CAC0003 (which codes for a protein of unknown function) but also several DNA fragments containing promoter regions. Protocol II enabled the successful identification of DNA fragments containing several intact genes conferring preferential growth under conditions of butanol stress. Since expression using the employed library is possible only from natural promoters, among the enriched genes, we identified 16 genes that constitute the first cistron of a transcriptional unit. These genes include four transcriptional regulators (CAC0977, CAC1463, CAC1869, and CAC2495). After subcloning plasmids carrying the CAC0003 and CAC1869 genes, strains 824(pCAC0003) and 824(pCAC1869) exhibited 13% and an 81% increases, respectively, in butanol tolerance relative to the plasmid control strain. 824(pCAC1869) consistently grew to higher cell densities in challenged and unchallenged cultures and exhibited prolonged metabolism. Our serial enrichment approach provided a more detailed understanding of the dynamic process of library enrichment under conditions of selective growth. Further characterization of the genes identified in this study will likely enhance our understanding of the complex phenotype of solvent tolerance.

Novel neuroproteomic approaches to studying traumatic brain injury

Neuroproteomics entails wide-scope study of the nervous system proteome in both its content and dynamics. The field employs high-end analytical mass spectrometry and novel high-throughput antibody approaches to characterize as many proteins as possible. The most common application has been differential analysis to identify a limited set of highly dynamic proteins associated with injury, disease, or other altered states of the nervous system. Traumatic brain injury (TBI) is an important neurological condition where neuroproteomics has revolutionized the characterization of protein dynamics, leading to a greater understanding of post-injury biochemistry. Further, proteins of altered abundance or post-translational modifications identified by neuroproteomic studies are candidate biochemical markers of TBI. This chapter explores the use of neuroproteomics in the study of TBI and the validation of identified putative biomarkers for subsequent clinical translation into novel injury diagnostics.

Fabrication and characterization of RNA aptamer microarrays for the study of protein-aptamer interactions with SPR imaging

RNA microarrays were created on chemically modified gold surfaces using a novel surface ligation methodology and employed in a series of surface plasmon resonance imaging (SPRI) measurements of DNA-RNA hybridization and RNA aptamer-protein binding. Various unmodified single-stranded RNA (ssRNA) oligonucleotides were ligated onto identical 5'-phosphate-terminated ssDNA microarray elements with a T4 RNA ligase surface reaction. A combination of ex situ polarization modulation FTIR measurements of the RNA monolayer and in situ SPRI measurements of DNA hybridization adsorption onto the surface were used to determine an ssRNA surface density of 4.0 x 10(12) molecules/cm2 and a surface ligation efficiency of 85 +/- 10%. The surface ligation methodology was then used to create a five-component RNA microarray of potential aptamers for the protein factor IXa (fIXa). The relative surface coverages of the different aptamers were determined through a novel enzymatic method that employed SPRI measurements of a surface RNase H hydrolysis reaction. SPRI measurements were then used to correctly identify the best aptamer to fIXa, which was previously determined from SELEX measurements. A Langmuir adsorption coefficient of 1.6 x 10(7) M(-1) was determined for fIXa adsorption to this aptamer. Single-base variations from this sequence were shown to completely destroy the aptamer-fIXa binding interaction.