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Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids
Published on: September 21, 2017
Facilitating mismatch discrimination by surface-affixed PNA probes via ionic regulation
Srabani Ghosh1, Sourav Mishra, Trambaki Banerjee
1Department of Biological Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, India.
Langmuir : the ACS Journal of Surfaces and Colloids
|February 19, 2013
Summary
Peptide nucleic acid (PNA) probes show enhanced DNA detection and single base mismatch discrimination on surfaces. Ionic conditions significantly impact PNA probe performance, differing from solution-based behavior.
Area of Science:
- Biotechnology
- Nucleic Acid Chemistry
- Surface Science
Background:
- DNA probes face limitations in nucleic acid detection technologies.
- Peptide nucleic acid (PNA) offers an alternative with a non-ionic peptidic backbone, providing nuclease resistance and high affinity DNA binding.
- PNA can self-assemble on substrates like gold(111) with controlled orientation.
Purpose of the Study:
- To investigate the ionic modulation of single base mismatch discrimination by surface-tethered PNA probes.
- To determine the "on-surface" melting temperatures of PNA-DNA duplexes.
- To compare the performance of surface-tethered PNA probes with DNA probes.
Main Methods:
- Formation and analysis of PNA-DNA duplexes on a gold(111) surface.
- Utilizing fluorescence measurements to determine "on-surface" melting temperatures.
- Systematically varying ionic conditions (cation concentration, anion type, cation type) in hybridization buffers.
Main Results:
- Surface-tethered PNA forms stabler duplexes than DNA and exhibits superior single base mismatch discrimination.
- Ionic composition of the hybridization buffer significantly affects PNA probe mismatch discrimination.
- Decreasing cation concentration generally enhances PNA-DNA duplex stability and mismatch discrimination.
- Anion effects on stability follow the Hofmeister series, indicating the role of hydrophobic interactions.
- Ionic dependence of "on-surface" PNA mismatch detection differs from solution behavior.
Conclusions:
- Surface-tethered PNA probes are effective for high-affinity DNA detection and mismatch discrimination.
- Ionic strength and composition are critical factors modulating PNA probe performance on surfaces.
- Understanding these ionic effects is crucial for optimizing PNA-based biosensor design and application.
