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09:04
Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids
Published on: September 21, 2017
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Synthesis and RNA-Binding Properties of Extended Nucleobases for Triplex-Forming Peptide Nucleic Acids
Ilze Kumpina1, Nikita Brodyagin2, James A MacKay3
1Latvian Institute of Organic Synthesis , Aizkraukles 21 , Riga LV-1006 , Latvia.
The Journal of Organic Chemistry
|September 21, 2019
Summary
Researchers developed modified peptide nucleic acids (PNAs) to recognize specific DNA and RNA sequences, overcoming limitations of existing triple-helix formation methods for pyrimidine recognition.
Area of Science:
- Molecular Biology
- Biochemistry
- Synthetic Chemistry
Background:
- Triple-helix formation is a method for sequence-specific recognition of double-stranded nucleic acids via Hoogsteen hydrogen bonding.
- Current applications are limited to homopurine sequences due to challenges in recognizing pyrimidines.
Purpose of the Study:
- To overcome limitations in pyrimidine recognition for triple-helix formation.
- To design and synthesize novel peptide nucleic acid (PNA) monomers with extended nucleobases capable of forming three hydrogen bonds.
Main Methods:
- Design of five new nucleobase triples with extended scaffolds.
- Confirmation of hydrogen bonding feasibility using ab initio calculations.
- Synthesis of PNA monomers and incorporation into short PNA sequences.
- Isothermal titration calorimetry to assess binding affinity to double-stranded RNA (dsRNA).
- Molecular modeling to analyze PNA-dsRNA helix structures.
Main Results:
- Designed and synthesized PNA monomers with modified nucleobases.
- Confirmed hydrogen bonding feasibility of new nucleobase triples computationally.
- Observed modest binding affinity of modified nucleobases to dsRNA targets.
- Molecular modeling indicated structural deviations and disrupted π-stacking as reasons for modest affinity.
Conclusions:
- Modified PNAs with extended nucleobases show potential for improved sequence-specific nucleic acid recognition.
- Further structural optimization is needed to enhance binding affinity for practical applications.
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