Helix 69 of Escherichia coli 23S ribosomal RNA as a peptide nucleic acid target

Kulik, Marta; Markowska-Zagrajek, Agnieszka; Wojciechowska, Monika; Grzela, Renata; Wituła, Tomasz; Trylska, Joanna

doi:10.1016/j.biochi.2017.04.001

Cited by 27 publications

(28 citation statements)

References 54 publications

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“…This means that although the band from the complex is visible, the attachment of vitamin B 12 to PNA somehow interferes with the formation of the complex. Thus similar as we previously observed for the (KFF) 3 K carrier 13 , vitamin B 12 may also decrease the ability of PNA to bind complementary RNA.…”

Section: Resultssupporting

confidence: 87%

“…The minimal inhibitory concentration for free (KFF) 3 K is >20 μM in both E. coli and S . Typhimurium 10 , 13 . Surprisingly, after treatment with PNA only, we observed a slightly higher level of OD 600 than for untreated cells but this observation corroborates with the observed RFU (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Typhimurium than E. coli ). Also, we have recently observed that conjugation of PNA with the (KFF) 3 K peptide hinders PNA hybridization efficiency with a complementary RNA strand 13 . To determine if the attachment of vitamin B 12 affects hybridization of a PNA oligomer with complementary RNA, we performed polyacrylamide gel electrophoresis (PAGE) experiments.…”

Section: Resultsmentioning

confidence: 99%

“…PNAs have been successfully tested as antimicrobials in a variety of bacterial species 2 , 6 , 7 . To inhibit bacterial growth, the mRNAs of several essential genes have been targeted, including acpP , the gene for the acyl carrier protein , gyrA encoding DNA gyrase subunit A, and murA and fabI , genes involved in cell wall and fatty acid biosynthesis, respectively 3 , 8 , 9 .In a separate approach, functional fragments of both 23S and 16S rRNA have been verified as targets for antisense PNAs 10 – 13 .…”

Section: Introductionmentioning

confidence: 99%

“…All of these peptides are cationic and amphipathic 23 , and their efficiency as PNA transporters is still far from perfect 24 . Moreover, we recently observed that conjugation with (KFF) 3 K decreased the ability of PNA to efficiently hybridize with an RNA hairpin even though the peptide is positively charged and thus attracted by the negatively charged RNA 13 . Also, conjugation of (KFF) 3 K with PNA (targeted at a functional site in 23S rRNA) decreased the level of inhibition of protein production in an E. coli cell-free transcription/translation system as compared to PNA alone.…”

Section: Introductionmentioning

confidence: 99%

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Vitamin B12 as a carrier of peptide nucleic acid (PNA) into bacterial cells

Równicki

Wojciechowska

Wierzba

et al. 2017

Sci Rep

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Short modified oligonucleotides targeted at bacterial DNA or RNA could serve as antibacterial agents provided that they are efficiently taken up by bacterial cells. However, the uptake of such oligonucleotides is hindered by the bacterial cell wall. To overcome this problem, oligomers have been attached to cell-penetrating peptides, but the efficiency of delivery remains poor. Thus, we have investigated the ability of vitamin B12 to transport peptide nucleic acid (PNA) oligomers into cells of Escherichia coli and Salmonella Typhimurium. Vitamin B12 was covalently linked to a PNA oligomer targeted at the mRNA of a reporter gene expressing Red Fluorescent Protein. Cu-catalyzed 1,3-dipolar cycloaddition was employed for the synthesis of PNA-vitamin B12 conjugates; namely the vitamin B12 azide was reacted with PNA possessing the terminal alkyne group. Different types of linkers and spacers between vitamin B12 and PNA were tested, including a disulfide bond. We found that vitamin B12 transports antisense PNA into E. coli cells more efficiently than the most widely used cell-penetrating peptide (KFF)3K. We also determined that the structure of the linker impacts the antisense effect. The results of this study provide the foundation for developing vitamin B12 as a carrier of PNA oligonucleotides into bacterial cells.

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Section: Resultssupporting

confidence: 87%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Vitamin B12 as a carrier of peptide nucleic acid (PNA) into bacterial cells

Równicki

Wojciechowska

Wierzba

et al. 2017

Sci Rep

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Effects of PNA Sequence and Target Site Selection on Function of a 4.5S Non‐Coding RNA

Saini,

Goel,

Ghosh

et al. 2024

ChemBioChem

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Peptide nucleic acid (PNA) based antisense strategy is a promising therapeutic approach to specifically inhibit target gene expression. However, unlike protein coding genes, identification of an ideal PNA binding site for non‐coding RNA is not straightforward. Here, we compare the inhibitory activities of PNA molecules that bind a non‐coding 4.5S RNA called SRP RNA, a key component of the bacterial signal recognition particle (SRP). A 9‐mer PNA (PNA9) complementary to the tetraloop region of the RNA was more potent in inhibiting its interaction with the SRP protein, compared to an 8‐mer PNA (PNA8) targeting a stem‐loop. PNA9, which contained a homo‐pyrimidine sequence could form a triplex with the complementary stretch of RNA in vitro as confirmed using a fluorescent derivative of PNA9 (F‐PNA13). The RNA‐PNA complex formation resulted in inhibition of SRP function with PNA9 and F‐PNA13, but not PNA8 highlighting the importance of target site selection. Surprisingly, F‐PNA13 which was more potent in inhibiting SRP function in vitro, showed weaker antibacterial activity compared to PNA9 likely due to poor cell penetration of the longer PNA. Our results underscore the importance of suitable target site selection and optimum PNA length to develop better antisense molecules against non‐coding RNA.

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Peptide nucleic acid conjugates and their antimicrobial applications—a mini-review

Tsylents,

Siekierska,

Trylska

2023

Eur Biophys J

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Peptide nucleic acid (PNA) is a nucleic acid mimic with high specificity and binding affinity to natural DNA or RNA, as well as resistance to enzymatic degradation. PNA sequences can be designed to selectively silence gene expression, which makes PNA a promising tool for antimicrobial applications. However, the poor membrane permeability of PNA remains the main limiting factor for its applications in cells. To overcome this obstacle, PNA conjugates with different molecules have been developed. This mini-review focuses on covalently linked conjugates of PNA with cell-penetrating peptides, aminosugars, aminoglycoside antibiotics, and non-peptidic molecules that were tested, primarily as PNA carriers, in antibacterial and antiviral applications. The chemistries of the conjugation and the applied linkers are also discussed.

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Helix 69 of Escherichia coli 23S ribosomal RNA as a peptide nucleic acid target

Cited by 27 publications

References 54 publications

Vitamin B12 as a carrier of peptide nucleic acid (PNA) into bacterial cells

Vitamin B12 as a carrier of peptide nucleic acid (PNA) into bacterial cells

Effects of PNA Sequence and Target Site Selection on Function of a 4.5S Non‐Coding RNA

Peptide nucleic acid conjugates and their antimicrobial applications—a mini-review

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