Journal: Molecular Therapy. Nucleic Acids

Article Title: Aptamer Selection Technology and Recent Advances

doi: 10.1038/mtna.2014.74

Figure Lengend Snippet: The different steps (S1–S5) of the SELEX process. The in vitro selection starts with random ssDNA or ssRNA libraries flanked by fixed primer annealing sites necessary for enzymatic amplification. The library is incubated with the target molecule and aptamer-target complexes are traditionally separated from nonbinding sequences by methods like nitrocellulose filter binding, electrophoretic gel mobility shifts or bead-based capture systems. The remaining nucleic acids are amplified by PCR in DNA aptamer selections or RT-PCR and RNA transcription in RNA aptamer selections. This selection cycle has to be repeated for 8–16 times to enrich the high affinity binding nucleic acids which are identified by cloning and Sanger sequencing. Starting-points for optimization: S1: optimized libraries, S2: better separation techniques, S3: alternative protocols, S4: omitted amplifications, S5: high-throughput sequencing and bioinformatic analysis.

Article Snippet: Easy to use software tools like COMPAS provide a route to make the high-throughput sequencing technology accessible for SELEX labs without bioinformatic expertise.

Techniques: In Vitro, Selection, Amplification, Incubation, Binding Assay, Reverse Transcription Polymerase Chain Reaction, Cloning, Sequencing, Next-Generation Sequencing

Journal: Molecular Therapy. Nucleic Acids

Article Title: Aptamer Selection Technology and Recent Advances

doi: 10.1038/mtna.2014.74

Figure Lengend Snippet: Distributions of nucleotides and motifs of length six in a nonoptimized (left side) and a SELEX library which was optimized for equal nucleotide distribution (right side). ( a ) The nonoptimized SELEX library (left side) is dominated by “A” and “G” and has a very unbalanced distribution of bases over all positions. After adjustment of the synthesis protocol, an almost even distribution of all four nucleotide bases (25% each) over all random positions was obtained (right side). ( b ) The distribution of motifs (length of six) in the nonoptimized library (left side) is unbalanced: Some motifs (on the side of high copy numbers) are highly overrepresented. After library optimization (right side) motifs of length six are equally distributed (Gaussian profile). Data were obtained by bioinformatic analysis with the software COMPAS at AptaIT GmbH.

Article Snippet: Easy to use software tools like COMPAS provide a route to make the high-throughput sequencing technology accessible for SELEX labs without bioinformatic expertise.

Techniques: Software