PNA Clamping in Nucleic Acid Amplification Protocols to Detect Single Nucleotide Mutations Related to Cancer

Fouz, Munira F.; Appella, Daniel H.

doi:10.3390/molecules25040786

Cited by 23 publications

(19 citation statements)

References 80 publications

(67 reference statements)

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“…Employing PNA in cells or tissues is more challenging, as the matrix becomes increasingly complex, more extensively modified PNAs are required to facilitate solubility and cellular uptake while maintaining selectivity. As a result, PNA has been found to have many applications as a research and diagnostic tool both in the lab and in the clinic [7][8][9], while advancement of PNA therapeutics, especially when compared to other nucleic acid derivatives [10,11], has notably lagged behind. To better understand the potential of PNA-based technologies, we will examine selected research and diagnostic applications highlighting the versatility of PNA as well as key limitations that hinder the extension of these technologies to therapeutic applications.…”

Section: Pna Probes For Research and Diagnostic Applicationsmentioning

confidence: 99%

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Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

Brodyagin

Katkevičs

Kotikam

et al. 2021

Beilstein J. Org. Chem.

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Peptide nucleic acid (PNA) is arguably one of the most successful DNA mimics, despite a most dramatic departure from the native structure of DNA. The present review summarizes 30 years of research on PNA’s chemistry, optimization of structure and function, applications as probes and diagnostics, and attempts to develop new PNA therapeutics. The discussion starts with a brief review of PNA’s binding modes and structural features, followed by the most impactful chemical modifications, PNA enabled assays and diagnostics, and discussion of the current state of development of PNA therapeutics. While many modifications have improved on PNA’s binding affinity and specificity, solubility and other biophysical properties, the original PNA is still most frequently used in diagnostic and other in vitro applications. Development of therapeutics and other in vivo applications of PNA has notably lagged behind and is still limited by insufficient bioavailability and difficulties with tissue specific delivery. Relatively high doses are required to overcome poor cellular uptake and endosomal entrapment, which increases the risk of toxicity. These limitations remain unsolved problems waiting for innovative chemistry and biology to unlock the full potential of PNA in biomedical applications.

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Section: Pna Probes For Research and Diagnostic Applicationsmentioning

confidence: 99%

“…Since its inception, PNA has become an extremely useful research tool and enabling component of many assays and diagnostics [4,[7][8][9]. On the other hand, development of PNA based therapeutics has notably lagged behind other nucleic acid technologies [10,11].…”

Section: Introductionmentioning

confidence: 99%

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

Brodyagin

Katkevičs

Kotikam

et al. 2021

Beilstein J. Org. Chem.

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“…The modified nucleic acid can stop the DNA amplification reaction by blocking modification on the terminal, in addition to the start of amplification and targeting. In SNP detection studies, the detection of SNPs by stopping the SNP amplification region with a modified nucleic acid has been studied [87].…”

Section: Bna (Lna) and Pnamentioning

confidence: 99%

Challenges for Accurate Quantification of RNA

Hasegawa

Hapsari

Iwahashi

2021

RAS

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Ribonucleic acid (RNA) quantification is an essential technique in biology. There has been remarkable progress in RNA quantification techniques over the recent years; however, the specificity of these techniques to quantify a very small amount of RNA is doubtful because of factors which can inhibit precise quantification. To develop a technique that leads to the most sensitive RNA quantification, these problems must be overcome. In this article, we first review the factors that inhibit precise quantification of RNA: the quality of RNA, secondary structure of RNA, efficiency of the enzyme reaction, annealing conditions, limitations of the experimental protocol and equipment, and detection sensitivity of the equipment. Next, we discuss the possible methods which contribute to these factors: RNA quality control focused on target RNA degradation, isothermal amplification, techniques for avoiding amplification errors, RNase H-dependent PCR, targeting using a fluorescent-labeled probe, targeting using a padlock probe, bridged/locked nucleic acid (BNA/LNA) and peptide nucleic acid (PNA), and the clustered regularly interspaced short palindromic repeat (CRISPR) system. One of the goals for the development of an ultrasensitive RNA quantification technique is the absolute quantification of RNA. Here, we discuss the techniques used for this type of RNA quantification.

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“…The DNA mimic peptide nucleic acid (PNA) was discovered three decades ago, and has since inspired researchers from as diverse fields as molecular and cell biology, drug discovery, medicinal chemistry, genetic diagnostics, combinatorial chemistry and nanoscience to utilize PNA oligomers as molecular tools and reagents. [1][2][3][4][5][6][7] Thus, PNA oligomers have been studied extensively for their therapeutic potential as gene therapeutic drugs as well as diagnostic and nanotechnology tools. Importantly, PNA is a biopolymer possessing enhanced sequence-specific binding to both RNA and DNA.…”

Section: Introductionmentioning

confidence: 99%

Optimized Synthesis of Fmoc/Boc‐Protected PNA Monomers and their Assembly into PNA Oligomers.

et al. 2021

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Continuous advancement of application of peptide nucleic acid (PNA) oligomers encouraged exploration of rapid and efficient synthesis of PNA monomers and oligomers. Among the PNA monomers developed, only a few are commonly used in automated PNA synthesis. Herein, we report short and efficient protocols suitable for large-scale synthesis of Fmoc/Bocprotected PNA monomers with advantageous solubility properties; these also facilitate purification due to the traceless nature of the Boc protecting group. Initially, several coupling reagents were screened for assembly of a pentamer containing all four nucleobases, and then the most promising reagents were tested in the synthesis of a decamer. The Fmoc/Boc-protected monomers proved compatible with both manual synthesis and assembly on an automated peptide synthesizer at room temperature or at 40°C. As compared to the commonly used coupling agent, 1-[bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium 3-oxide hexafluorophosphate (HATU), both 2-(1H-benzotriazol-1-yl)-1,1,3,3-tetramethyluronium hexafluorophosphate (HBTU) and [ethyl cyano(hydroxyimino) acetatoÀ O 2 ]tri-1-pyrrolidinylphosphonium hexafluorophosphate (PyOxim) proved more favorable, with the latter being superior. A previously reported side reaction of guanine bases in the presence of benzotriazol-1-yl-oxytripyrrolidinophosphonium hexafluorophosphate (PyBOP) was not observed with the phosphonium salts.

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PNA Clamping in Nucleic Acid Amplification Protocols to Detect Single Nucleotide Mutations Related to Cancer

Cited by 23 publications

References 80 publications

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

Challenges for Accurate Quantification of RNA

Optimized Synthesis of Fmoc/Boc‐Protected PNA Monomers and their Assembly into PNA Oligomers.

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