Computational simulation of adapter length-dependent lasso probe capture efficiency

Jingqian Liu, Syukri Shukor, Shuxiang Li, Alfred Tamayo, Lorenzo Tosi, Benjamin Larman, Vikas Nanda, Wilma K. Olson, Biju Parekkadan

Research output: Contribution to journalArticlepeer-review

Abstract

Multiplexed cloning of long DNA sequences is a valuable technique in many biotechnology applications, such as long-read genome sequencing and the creation of open reading frame (ORF) libraries. Long-adapter single-stranded oligonucleotide (LASSO) probes have shown promise as a tool to clone long DNA fragments. LASSO probes are molecular inversion probes (MIP) engineered with an adapter region of user-defined length, flanked between template-specific probe sequences. Herein, we demonstrate that the adapter length is a key feature of LASSO that influences the efficiency of gene capture and cloning. Furthermore, we applied a model based on Monte Carlo molecular simulation in order to study the relationship between the long-adapter length of LASSO and capture enrichment. Our results suggest that the adapter length is a factor that contributes to the free energy of targetprobe interaction, thereby determining the efficiency of capture. The results indicate that LASSOs with extremely long adapters cannot capture the targets well. They also suggest that targets of different lengths may prefer adapters of different lengths.

Original languageEnglish (US)
Article number199
JournalBiomolecules
Volume9
Issue number5
DOIs
StatePublished - May 2019

Keywords

  • DNADNA interaction
  • Gene-capture probe
  • LASSO probe
  • OxDNA
  • VMMC simulation

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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