ArticleBiochemistry2016
Probing of miniPEGγ-PNA-DNA Hybrid Duplex Stability with AFM Force Spectroscopy.
Article in Biochemistry, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 18 citations in OpenAlex.
- Parameterization of the miniPEG-Modified γPNA Backbone: Toward Induced γPNA Duplex Dissociation.Journal of chemical theory and computation · 2023Article
- Molecular Recognition in Confined Space Elucidated with DNA Nanopores and Single-Molecule Force Microscopy.Nano letters · 2023Article
- Recent developments in DNA-based mechanical nanodevices.Chemical communications (Cambridge, England) · 2022Review
- Molecularly resolved, label-free nucleic acid sensing at solid-liquid interface using non-ionic DNA analogues.RSC advances · 2022Article
- DNA Nanotechnology as an Emerging Tool to Study Mechanotransduction in Living Systems.Small (Weinheim an der Bergstrasse, Germany) · 2019Review
- Calcium increases titin N2A binding to F-actin and regulated thin filaments.Scientific reports · 2018Article
- Focus on PNA Flexibility and RNA Binding using Molecular Dynamics and Metadynamics.Scientific reports · 2017Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Peptide nucleic acids (PNA) are synthetic polymers, the neutral peptide backbone of which provides elevated stability to PNA-PNA and PNA-DNA hybrid duplexes. It was demonstrated that incorporation of diethylene glycol (miniPEG) at the γ position of the peptide backbone increased the thermal stability of the hybrid duplexes (Sahu, B. et al. J. Org. Chem. 2011, 76, 5614-5627). Here, we applied atomic force microscopy (AFM) based single molecule force spectroscopy and dynamic force spectroscopy (DFS) to test the strength and stability of the hybrid 10 bp duplex. This hybrid duplex consisted of miniPEGγ-PNA and DNA of the same length (γ(MP)PNA-DNA), which we compared to a DNA duplex with a homologous sequence. AFM force spectroscopy data obtained at the same conditions showed that the γ(MP)PNA-DNA hybrid is more stable than the DNA counterpart, 65 ± 15 pN vs 47 ± 15 pN, respectively. The DFS measurements performed in a range of pulling speeds analyzed in the framework of the Bell-Evans approach yielded a dissociation constant, koff ≈ 0.030 ± 0.01 s⁻¹ for γ(MP)PNA-DNA hybrid duplex vs 0.375 ± 0.18 s⁻¹ for the DNA-DNA duplex suggesting that the hybrid duplex is much more stable. Correlating the high affinity of γ(MP)PNA-DNA to slow dissociation kinetics is consistent with prior bulk characterization by surface plasmon resonance. Given the growing interest in γ(MP)PNA as well as other synthetic DNA analogues, the use of single molecule experiments along with computational analysis of force spectroscopy data will provide direct characterization of various modifications as well as higher order structures such as triplexes and quadruplexes.
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