In silico approaches to RNA aptamer design

    Research output: Contribution to journalArticle

    5 Citations (Scopus)

    Abstract

    RNA aptamers are ribonucleic acids that bind to specific target molecules. An RNA aptamer for a disease-related protein has great potential for development into a new drug. However, huge time and cost investments are required to develop an RNA aptamer into a pharmaceutical. Recently, SELEX combined with high-throughput sequencers (i.e., HT-SELEX) has been widely used to select candidate RNA aptamers that bind to a target protein with high affinity and specificity. After candidate selection, further optimizations such as shortening and modifying candidate sequences are performed. In these steps, in silico approaches are expected to reduce the time and cost associated with aptamer drug development. In this article, we review existing in silico approaches to RNA aptamer development, including a method for ranking the candidates of RNA aptamers from HT-SELEX data, clustering a huge number of aptamer sequences, and finding motifs amidst a set of significant RNA aptamers. It is expected that further studies in addition to these methods will be utilized for in silico RNA aptamer design, permitting a minimal number of experiments to be performed through the utilization of sophisticated computational methods.

    Original languageEnglish
    JournalBiochimie
    DOIs
    Publication statusAccepted/In press - 2017

    Fingerprint

    Nucleotide Aptamers
    Computer Simulation
    Pharmaceutical Preparations
    Costs and Cost Analysis
    Computational methods
    Cluster Analysis
    Costs
    Proteins
    Throughput
    RNA
    Molecules

    Keywords

    • Clustering
    • HT-SELEX
    • Motif finding
    • RNA secondary structures
    • SELEX
    • Tertiary structure predictions

    ASJC Scopus subject areas

    • Biochemistry

    Cite this

    In silico approaches to RNA aptamer design. / Hamada, Michiaki.

    In: Biochimie, 2017.

    Research output: Contribution to journalArticle

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