Surface plasmon resonance study of PNA interactions with double-stranded DNA

Ananthanawat, Cheeraporn; Hoven, Voravee P.; Vilaivan, Tirayut

doi:10.1016/j.bios.2010.05.027

Cited by 23 publications

(17 citation statements)

References 46 publications

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“…Other groups further improved SPR measurements by introducing chemical modifications to PNA probes [73,74] and achieved better stability and reusability of the sensors. Likewise, dsDNA has been detected by use of a duplex invasion method [75], and localized SPR has been used by Endo et al [76] to detect 6.7×10 −13 mol L −1 ssDNA with base mismatch specificity. Additional reports have described the detection of E. coli ribosomal RNA [77], and the development of a signal-amplification strategy that uses DNA-templated polyaniline deposition [78].…”

Section: Optoelectronicmentioning

confidence: 99%

Applications of peptide nucleic acids (PNAs) and locked nucleic acids (LNAs) in biosensor development

2012

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Nucleic acid biosensors have a growing number of applications in genetics and biomedicine. This contribution is a critical review of the current state of the art concerning the use of nucleic acid analogues, in particular peptide nucleic acids (PNA) and locked nucleic acids (LNA), for the development of high-performance affinity biosensors. Both PNA and LNA have outstanding affinity for natural nucleic acids, and the destabilizing effect of base mismatches in PNA- or LNA-containing heterodimers is much higher than in double-stranded DNA or RNA. Therefore, PNA- and LNA-based biosensors have unprecedented sensitivity and specificity, with special applicability in DNA genotyping. Herein, the most relevant PNA- and LNA-based biosensors are presented, and their advantages and their current limitations are discussed. Some of the reviewed technology, while promising, still needs to bridge the gap between experimental status and the harder reality of biotechnological or biomedical applications.

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Section: Optoelectronicmentioning

confidence: 99%

Applications of peptide nucleic acids (PNAs) and locked nucleic acids (LNAs) in biosensor development

2012

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“…Evidently, the PNA ligand was sufficiently homomorphous to DNA and possessed the binding affinity to invade an otherwise stable duplex structure harboring a complementary sequence, resulting in a complex where two PNA molecules engaged the Watson-Crick (WC) and Hoogsteen (HN) faces, respectively, of the same target strand (Figure 2A [8]). Confirmatory evidence [31] for this binding mode has since incentivized synthetic strategies to optimize the binding efficacy of PNA oligomers for duplex DNA targets, since invasion of B-form DNA at near-physiologic osmolality and acidity has been recognized, then [32] and now [33], as a major challenge for PNA binding. Indeed, it is the evolution of the PNA compound in pursuit of more favorable binding that has largely enabled strategies for PNA-induced gene editing [34].…”

Section: Pna Chemistrymentioning

confidence: 99%

Peptide Nucleic Acids and Gene Editing: Perspectives on Structure and Repair

et al. 2020

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Unusual nucleic acid structures are salient triggers of endogenous repair and can occur in sequence-specific contexts. Peptide nucleic acids (PNAs) rely on these principles to achieve non-enzymatic gene editing. By forming high-affinity heterotriplex structures within the genome, PNAs have been used to correct multiple human disease-relevant mutations with low off-target effects. Advances in molecular design, chemical modification, and delivery have enabled systemic in vivo application of PNAs resulting in detectable editing in preclinical mouse models. In a model of β-thalassemia, treated animals demonstrated clinically relevant protein restoration and disease phenotype amelioration, suggesting a potential for curative therapeutic application of PNAs to monogenic disorders. This review discusses the rationale and advances of PNA technologies and their application to gene editing with an emphasis on structural biochemistry and repair.

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“…The corresponding list ranges from the investigation of single nucleotide mismatches using hybridization experiments [79] and the research of triplexes consisting of dsDNA and peptide nucleic acid (PNA) [80] to the kinetic analysis of small molecule-nucleic acid interactions involving binding of heterocyclic diamidines to AT sequences [81]. …”

Section: Applicationsmentioning

confidence: 99%

Real-Time Analysis of Specific Protein-DNA Interactions with Surface Plasmon Resonance

Ritzefeld

Sewald

2012

Journal of Amino Acids

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Several proteins, like transcription factors, bind to certain DNA sequences, thereby regulating biochemical pathways that determine the fate of the corresponding cell. Due to these key positions, it is indispensable to analyze protein-DNA interactions and to identify their mode of action. Surface plasmon resonance is a label-free method that facilitates the elucidation of real-time kinetics of biomolecular interactions. In this article, we focus on this biosensor-based method and provide a detailed guide how SPR can be utilized to study binding of proteins to oligonucleotides. After a description of the physical phenomenon and the instrumental realization including fiber-optic-based SPR and SPR imaging, we will continue with a survey of immobilization methods. Subsequently, we will focus on the optimization of the experiment, expose pitfalls, and introduce how data should be analyzed and published. Finally, we summarize several interesting publications of the last decades dealing with protein-DNA and RNA interaction analysis by SPR.

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Surface plasmon resonance study of PNA interactions with double-stranded DNA

Cited by 23 publications

References 46 publications

Applications of peptide nucleic acids (PNAs) and locked nucleic acids (LNAs) in biosensor development

Applications of peptide nucleic acids (PNAs) and locked nucleic acids (LNAs) in biosensor development

Peptide Nucleic Acids and Gene Editing: Perspectives on Structure and Repair

Real-Time Analysis of Specific Protein-DNA Interactions with Surface Plasmon Resonance

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