AptaBlocks

AptaBlocks is a computational tool that facilitates the development of RNA-based therapeutics. It specifically addresses the challenge of designing suitable "sticky bridge" sequences that enable the assembly of aptamer-cargo complexes for targeted drug delivery.

Key points:

1. RNA aptamers can selectively deliver therapeutic RNA molecules into target cells by binding to surface receptors.

2. Aptamer-cargo complexes can be formed using a double-stranded "sticky bridge" approach, where complementary strands are conjugated to the aptamer and cargo.

3. Designing appropriate sticky bridge sequences is challenging due to various structural and functional constraints.

4. AptaBlocks is a computational method that designs RNA complexes that hybridize via sticky bridges, considering these constraints.

5. The effectiveness of AptaBlocks has been verified computationally and experimentally in the context of drug delivery to pancreatic cancer cells.

6. AptaBlocks is a general method that can be applied to other areas of RNA nanotechnology beyond drug delivery systems.

Topic

Biotherapeutics;Protein interactions

Detail

  • Operation: Sequence assembly

  • Software interface: Command-line interface

  • Language: C

  • License: Not stated

  • Cost: Free of charge

  • Version name: -

  • Credit: The Intramural Research Program of the National Institutes of Health, National Library of Medicine and the DNA/RNA Synthesis Core, the Chemical GMP Synthesis Facility of the City of Hope, funded in part by Cancer Center Support Grant (National Cancer Institute of the National Institutes of Health), to the City of Hope Comprehensive Cancer Center.

  • Input: -

  • Output: -

  • Contact: -

  • Collection: -

  • Maturity: -

Publications

  • AptaBlocks: Designing RNA complexes and accelerating RNA-based drug delivery systems.
  • Wang Y, et al. AptaBlocks: Designing RNA complexes and accelerating RNA-based drug delivery systems. AptaBlocks: Designing RNA complexes and accelerating RNA-based drug delivery systems. 2018; 46:8133-8142. doi: 10.1093/nar/gky577
  • https://doi.org/10.1093/NAR/GKY577
  • PMID: 29986050
  • PMC: PMC6144873

Download and documentation

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