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Gamma-FIT-PNAs as sensitive RNA probes
Manoj Kumar Gupta1, Salam Maree1, Eylon Yavin1
1Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Hadassah Ein-Kerem Jerusalem 91120 Israel manojkumar.gupta@mail.huji.ac.il eylony@ekmd.huji.ac.il.
RSC Chemical Biology
|January 22, 2026
Summary
New gamma-l-serine PNA (γPNA) modifications significantly enhance FIT-PNA probes. These modified probes show increased fluorescence and improved binding affinity for detecting RNA biomarkers.
Area of Science:
- Biochemistry
- Molecular Biology
- Nucleic Acid Chemistry
Background:
- Oligonucleotide-based probes, including FIT-PNAs (forced intercalation-peptide nucleic acids), are crucial for specific RNA and DNA sensing.
- Existing modifications like cpPNA and LNA have improved sensor performance, but further enhancements are sought for RNA biomarker detection.
Purpose of the Study:
- To investigate the biophysical properties of FIT-PNAs modified with gamma-l-serine PNA (γPNA) monomers.
- To evaluate the impact of γPNA incorporation on fluorescence and binding affinity of FIT-PNA probes for RNA targets.
Main Methods:
- Synthesis of FIT-PNAs incorporating γPNA monomers at specific positions relative to the fluorophore (BisQ).
- Characterization of fluorescence properties of the modified FIT-PNA:RNA duplexes.
- Determination of RNA binding affinity using melting temperature (Tm) analysis.
Main Results:
- A single γPNA flanking the BisQ fluorophore increased fluorescence 46-fold, comparable to cpPNA.
- Two flanking γPNAs significantly enhanced RNA binding affinity, evidenced by an 8 °C increase in melting temperature (Tm).
- γPNA modification leads to brighter FIT-PNAs with superior binding to target RNA.
Conclusions:
- Gamma-l-serine PNA (γPNA) represents a beneficial chemical modification for FIT-PNA probes.
- γPNA incorporation enhances both the fluorescence intensity and the binding affinity of FIT-PNAs for RNA.
- These improved FIT-PNAs hold promise for sensitive and selective detection of RNA biomarkers.
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