Development of a Molecular Aptamer Beacon Applied to Magnetic-Assisted RNA Extraction for Detection of Dengue and Zika Viruses Using Clinical Samples

Int J Mol Sci. 2022 Nov 10;23(22):13866. doi: 10.3390/ijms232213866.


Limitations in the detection of cocirculating flaviviruses such as Dengue and Zika lead us to propose the use of aptameric capture of the viral RNA in combination with RT-PCR (APTA-RT-PCR). Aptamers were obtained via SELEX and next-generation sequencing, followed by colorimetric and fluorescent characterizations. An APTA-RT-PCR assay was developed, optimized, and tested against the viral RNAs in 108 serum samples. After selection, sequence APTAZC10 was designed as a bifunctional molecular beacon (APTAZC10-MB), exhibiting affinity for the viral targets. APTA-RT-PCR was able to detect Dengue and Zika RNA in 43% and 8% of samples, respectively. Our results indicate that APTAZC10-MB and APTA-RT-PCR will be useful to improve the detection of Dengue and Zika viruses in a fast molecular assay for the improvement of infectious disease surveillance.

Keywords: RT-PCR; diagnosis; flavivirus; hybridization; oligonucleotides.

MeSH terms

  • Dengue* / diagnosis
  • Humans
  • Magnetic Phenomena
  • Oligonucleotides
  • RNA, Viral / genetics
  • Zika Virus Infection* / diagnosis
  • Zika Virus* / genetics


  • Oligonucleotides
  • RNA, Viral