Selection of DNA aptamer against prostate specific antigen using a genetic algorithm and application to sensing

• Published in: Biosensors & bioelectronics Vol. 26; no. 4; pp. 1386 - 1391
• Main Authors: Savory, Nasa, Abe, Koichi, Sode, Koji, Ikebukuro, Kazunori
• Format: Journal Article Conference Proceeding
• Language: English
• Published: Kidlington Elsevier B.V 15-12-2010; Elsevier
• Subjects: Affinity; Algorithms; Antigens; Aptamers, Nucleotide - chemistry; Aptamers, Nucleotide - genetics; Aptamers, Nucleotide - isolation & purification; Base Sequence; Biological and medical sciences; Biosensing Techniques - methods; Biosensing Techniques - statistics & numerical data; Biotechnology; Deoxyribonucleic acid; Detection; DNA aptamer; Enrichment; Fundamental and applied biological sciences. Psychology; Gene Library; Genetic algorithm; Genetic algorithms; Humans; In silico maturation; Male; Nucleic Acid Conformation; Oligonucleotides; Prostate; Prostate specific antigen; Prostate-Specific Antigen - analysis; Prostate-Specific Antigen - blood; Prostatic Neoplasms - blood; Prostatic Neoplasms - diagnosis; Screening; SELEX Aptamer Technique; Prostate specific antigen; In silico maturation; DNA aptamer; Genetic algorithm; Ripening; DNA; Selection; Aptamer; Application; Bioinformatics; Computer aided analysis
• ISSN: 0956-5663; 1873-4235
• DOI: 10.1016/j.bios.2010.07.057

In order to construct an aptasensor, aptamers that show high affinity for target molecules are required. While the systematic evolution of ligands by exponential enrichment (SELEX) is an efficient method for selecting aptamers, it sometimes fails to obtain aptamers with high affinity and so additional improvements are required. We applied a genetic algorithm (GA) to post-SELEX screening as an
in silico maturation of aptamers. First, we pre-selected DNA aptamers against prostate specific antigen (PSA) through three rounds of SELEX. To improve the PSA-binding ability of the aptamers, we carried out post-SELEX screening using GA with the pre-selected oligonucleotide sequences. For screening using GA, we replicated the oligonucleotide sequences obtained through SELEX, crossed over and mutated
in silico resulting in 20 sequences. Those oligonucleotide sequences were synthesized and assayed
in vitro. Then, the oligonucleotides were ranked according to PSA-binding ability and the top sequences were selected for the next cycle of GA operation. After GA operations, we identified the aptamer showing a 48-fold higher PSA-binding ability than candidates obtained by SELEX. The dissociation constant (
K
D) of the obtained aptamer was estimated to be several tens of nM. We demonstrated sensing of PSA using the obtained aptamer and succeeded in sensing PSA concentrations between 40 and 100
nM. This is the first report of a DNA aptamer against PSA and its application to PSA sensing.