Theoretical Principles of In Vitro Selection Using Combinatorial Nucleic Acid Libraries

Abstract

A new paradigm for drug discovery and biological research has developed from technologies that integrate combinatorial chemistry with rounds of selection and amplification, a technique called in vitro selection or systematic evolution of ligands by exponential enrichment (SELEX). This overview unit discusses nucleic acid libraries that can be used, affinity probability distributions, an equilibrium model for SELEX, and optimal conditions including concentrations and signal-to-noise ratios.

Synthesis and Characterization of Oligonucleotides Containing a Nitrogen Mustard Formamidopyrimidine Monoadduct of Deoxyguanosine

“…O 6 -(2-Trimethylsilyethyl)-dGuo ( 1 ) was prepared in three steps according to a literature procedure 42 and was further protected at the 5′- O - and N 2 -positions to afford 3 in 43% overall yield from dGuo. Reaction of 3 with bis(2-chloroethyl)ethylamine in trifluoroethanol presumably gives the cationic N7-adduct ( 4 ), 18,26,28,45 which was not isolated.…”

“…A solution of 1 (42) (426 mg, 1.16 mmol) and N , N -dimethylformamide dimethyl acetal (1.22 mL, 9.3 mmol) in dry methanol (20 mL) was heated at 60 °C for 6 h. The methanol was then removed in vacuo on a rotary evaporator. Purification of the resulting solid by flash chromatography on silica afforded 2 (441 mg, 90%).…”

Aptamer-Based Proteomic Profiling Reveals Novel Candidate Biomarkers and Pathways in Cardiovascular Disease

“…They can be immobilized to streptavidin-coated beads and incubated with samples to assay analytes in a highly multiplexed manner. Emerging DNA aptamer-based proteomic technologies may address important limitations of existing proteomic techniques, 9–11 but data in humans are still limited, particularly studies integrating independent validation strategies. Applications to archived samples from population-based cohorts are also lacking.…”

Devices and approaches for generating specific high-affinity nucleic acid aptamers

“…A number of theoretical efforts have attempted to address this optimization problem using numerical methods and/or approximations. [22][23][24][25][26][27][28][29][30][31][32][33][34][35] These theories assume equilibrium solution binding, because time dependent models double the number of parameters (K d is the ratio of the kinetic binding off-rate and on-rate: k off /k on ) and generally require a significant amount of prior information about the initial library, such as the distribution of sequences ([S i ]) and affinities (K d,i ) to the target. In contrast, many selections are not performed in true equilibrium or with free molecules in solution, and little to no information is known about the initial library or its interaction with the target.…”