Peptide Nucleic Acids (<scp>PNAs</scp>)

Achim, Catalina; Armitage, Bruce A.; Ly, Danith H.; Schneider, James W.

doi:10.1002/9780470048672.wecb435

Cited by 11 publications

(9 citation statements)

References 52 publications

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“…1–3 The neutral backbone eliminates electrostatic repulsion between PNA and DNA or RNA targets, which leads to fast binding kinetics, high affinity and mismatch discrimination superior to that of DNA probes. Taken together with high chemical stability, resistance to enzymatic degradation by proteases and nucleases and straightforward synthesis, the unique physicochemical properties have made PNA an ideal candidate for the detection of DNA or RNA sequences in life sciences.…”

Section: Introductionmentioning

confidence: 99%

Synthesis and properties of peptide nucleic acid labeled at the N-terminus with HiLyte Fluor 488 fluorescent dye

Hnedzko

McGee

Rozners

2016

Bioorganic & Medicinal Chemistry

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Fluorescently labeled peptide nucleic acids (PNAs) are important tools in fundamental research and biomedical applications. However, synthesis of labeled PNAs, especially using modern and expensive dyes, is less explored than similar preparations of oligonucleotide dye conjugates. Herein, we present a simple procedure for labeling of the PNA N-terminus with HiLyte Fluor 488 as the last step of solid phase PNA synthesis. A minimum excess of 1.25 equiv of activated carboxylic acid achieved labeling yields close to 90% providing a good compromise between the price of dye and the yield of product and significant improvement over previous literature procedures. The HiLyte Fluor 488-labeled PNAs retained the RNA binding ability and in live cell fluorescence microscopy experiments were brighter and significantly more photostable than PNA labeled with carboxyfluorescein. In contrast to fluorescein-labeled PNA, the fluorescence of PNAs labeled with HiLyte Fluor 488 was independent of pH in the biologically relevant range of 5-8. The potential of HiLyte Fluor 488-labeling for studies of PNA cellular uptake and distribution was demonstrated in several cell lines.

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Section: Introductionmentioning

confidence: 99%

Synthesis and properties of peptide nucleic acid labeled at the N-terminus with HiLyte Fluor 488 fluorescent dye

Hnedzko

McGee

Rozners

2016

Bioorganic & Medicinal Chemistry

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“…Peptide nucleic acid (PNA) is a synthetic analogue of DNA that has a pseudo-peptide backbone instead of the sugar diphosphate backbone of the DNA (Scheme 1). [1][2][3] PNA forms homoduplexes by Watson-Crick hybridization. To date, crystal structures have been reported for a palindromic 6-base pair (bp) PNA duplex, [4] for another 6-bp PNA duplex with the same sequence but with a lysine at the C terminus, [5] as well as for a partly self-complementary singlestranded (ss) PNA that formed both short duplex and triplex motifs within the crystal.…”

Section: Introductionmentioning

confidence: 99%

The Crystal Structure of Non‐Modified and Bipyridine‐Modified PNA Duplexes

Yeh

Pohl

Truan

et al. 2010

Chemistry A European J

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Peptide nucleic acid (PNA) is a synthetic analogue of DNA that commonly has an N-aminoethlyl-glycine backbone. The crystal structure of two PNA duplexes, one containing eight standard nucleobase pairs (GGCATCGG)2 (pdb: 3MBS), and the other containing the same nucleobase pairs and a central pair of bipyridine ligands (pdb: 3MBU), has been solved with a resolution of 1.2 Å and 1.05 Å, respectively. The non-modified PNA duplex adopts a P-type helical structure s i m i l a r t o that of previously characterized PNAs. The atomic-level resolution of the structures allowed us to observe for the first time specific modes of interaction between the terminal lysines of the PNA and the backbone and nucleobases situated in the vicinity of the lysines, which are considered an important factor in the induction of a preferred handedness in PNA duplexes. These results support the notion that while PNA typically adopts a P-type helical structure, its flexibility is relatively high. For example, the base pair rise in the bipyridine-containing PNA is the largest measured to date in a PNA homoduplex. The two bipyridines are bulged out of the duplex and are aligned parallel to the minor groove of the PNA. In the case of the bipyridine-containing PNA, two bipyridines from adjacent PNA duplexes form a π-stacked pair that relates the duplexes within the crystal. The bulging out of the bipyridines causes bending of the PNA duplex, which is in contrast to the structure previously reported for biphenyl-modified DNA duplexes in solution, where the biphenyls are π-stacking with adjacent nucleobase pairs and adopt an intrahelical geometry [Johar et al., Chem. Eur. J., 2008, 14, 2080]. This difference shows that relatively small perturbations can significantly impact the relative position of nucleobase analogues in nucleic acid duplexes.

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“…Cell-penetrating peptides, 36−38 cationic side chain modifications 25,29,39,40 or small molecule conjugates 41 have all been used to deliver PNAs into cells. In addition, a recent paper reported site-specific genome editing in vivo by γPNA delivered via a polymeric nanoparticle vehicle.…”

Section: ■ Discussionmentioning

confidence: 99%

In Vitro Reversible Translation Control Using γPNA Probes

et al. 2015

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On-demand regulation of gene expression in living cells is a central goal of chemical biology and antisense therapeutic development. While significant advances have allowed regulatory modulation through inserted genetic elements, on-demand control of the expression/translation state of a given native gene by complementary sequence interactions remains a technical challenge. Toward this objective, we demonstrate the reversible suppression of a luciferase gene in cell-free translation using Watson-Crick base pairing between the mRNA and a complementary γ-modified peptide nucleic acid (γPNA) sequence with a noncomplementary toehold. Exploiting the favorable thermodynamics of γPNA-γPNA interactions, the antisense sequence can be removed by hybridization of a second, fully complementary γPNA, through a strand displacement reaction, allowing translation to proceed. Complementary RNA is also shown to displace the bound antisense γPNA, opening up possibilities of in vivo regulation by native gene expression.

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Peptide Nucleic Acids (PNAs)

Cited by 11 publications

References 52 publications

Synthesis and properties of peptide nucleic acid labeled at the N-terminus with HiLyte Fluor 488 fluorescent dye

Synthesis and properties of peptide nucleic acid labeled at the N-terminus with HiLyte Fluor 488 fluorescent dye

The Crystal Structure of Non‐Modified and Bipyridine‐Modified PNA Duplexes

In Vitro Reversible Translation Control Using γPNA Probes

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