FIT-PNAs as RNA-Sensing Probes for Drug-Resistant Plasmodium falciparum

Odelia Tepper, Itamar Peled, Yair Fastman, Adina Heinberg, Vera Mitesser, Ron Dzikowski*, Eylon Yavin

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


Detecting RNA at single-nucleotide resolution is a formidable task. Plasmodium falciparum is the deadliest form of malaria in humans and has shown to gain resistance to essentially all antimalarial drugs including artemisinin and chloroquine. Some of these drug resistances are associated with single-nucleotide polymorphisms (SNPs). Forced-intercalation peptide nucleic acids (FIT-PNAs) are DNA mimics that are designed as RNA-sensing molecules that fluoresce upon hybridization to their complementary (RNA) targets. We have previously designed and synthesized FIT-PNAs that target the C580Y SNP in the K13 gene of P. falciparum. In addition, we have now prepared FIT-PNAs that target the K76T SNP in the CRT gene of P. falciparum. Both SNPs are common ones associated with artemisinin and chloroquine drug resistance, respectively. Our FIT-PNAs are conjugated to a simple cell-penetrating peptide (CPP) that consists of eight d-lysines (dK8), which renders these FIT-PNAs cell-permeable to infected red blood cells (iRBCs). Herein, we demonstrate that FIT-PNAs clearly discriminate between wild-type (WT) strains (NF54-WT: artemisinin-sensitive or chloroquine-sensitive) and mutant strains (NF54-C580Y: artemisinin-resistant or Dd2: chloroquine-resistant) of P. falciparum parasites. Simple incubation of FIT-PNAs with live blood-stage parasites results in a substantial difference in fluorescence as corroborated by FACS analysis and confocal microscopy. We foresee FIT-PNAs as molecular probes that will provide a fast, simple, and cheap means for the assessment of drug resistance in malaria─a tool that would be highly desirable for the optimal choice of antimalarial treatment in endemic countries.

Original languageAmerican English
Pages (from-to)50-59
Number of pages10
JournalACS Sensors
Issue number1
StatePublished - 28 Jan 2022

Bibliographical note

Funding Information:
This research was supported by the Israel Innovation Authority (Nofar Program, Grant No. 62597). E.Y. acknowledges the David R. Bloom Center for Pharmacy and the Alex Grass Center for Drug Design and Novel Therapeutics for financial support. R.D. is supported by the Israeli Academy for Science, Israel Science Foundation (ISF) Grant 1523/18 and in part by the European Research Council ( Consolidator Grant 615412 and the Ministry of Science and Technology Grant 3-16285 (to R.D.). R.D. is also supported by the Dr. Louis M. Leland and Ruth M. Leland Chair in Infectious Diseases. Y.F. and V.M. were supported by Dr. Emanuel and Mrs. Olga Lourie PhD Scholarships in Tropical Medicine and V.M. by a Minerva fellowship. The NF54-C580Y strain was kindly provided by Dr. Lopez-Rubio (University of Montpellier, France).

Publisher Copyright:
© 2022 American Chemical Society


  • SNP
  • artemisinin
  • chloroquine
  • drug resistance
  • malaria
  • Malaria, Falciparum
  • Plasmodium falciparum/genetics
  • Peptide Nucleic Acids/pharmacology
  • RNA
  • Humans
  • Antimalarials/pharmacology
  • Protozoan Proteins/genetics
  • RNA Probes
  • Chloroquine/therapeutic use


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