Synthesis and structure–activity relationship of peptide nucleic acid probes with improved interstrand-crosslinking abilities: application to biotin-mediated RNA-pulldown

Cadoni, Enrico; Pennati, Francesca; Muangkaew, Penthip; Elskens, Joke; Madder, Annemieke; Manicardi, Alex

doi:10.1039/d2cb00095d

Cited by 5 publications

(2 citation statements)

References 50 publications

(79 reference statements)

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“…In view of the capacity of PNA to bind both DNA and RNA strands, this methodology can be conveniently adapted to target RNA G4 structures. In addition, the methodology can be further exploited for ‘on-bench’ applications, such as for the pull-down of specific G4 and iM-forming sequences, exploiting the reversibility of this type of alkylation at high temperatures ( 59 ).…”

Section: Discussionmentioning

confidence: 99%

A red light-triggered chemical tool for sequence-specific alkylation of G-quadruplex and I-motif DNA

Cadoni

Paepe

Colpaert

et al. 2023

Nucleic Acids Research

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The importance of non-canonical DNA structures such as G-quadruplexes (G4) and intercalating-motifs (iMs) in the fine regulation of a variety of cellular processes has been recently demonstrated. As the crucial roles of these structures are being unravelled, it is becoming more and more important to develop tools that allow targeting these structures with the highest possible specificity. While targeting methodologies have been reported for G4s, this is not the case for iMs, as evidenced by the limited number of specific ligands able to bind the latter and the total absence of selective alkylating agents for their covalent targeting. Furthermore, strategies for the sequence-specific covalent targeting of G4s and iMs have not been reported thus far. Herein, we describe a simple methodology to achieve sequence-specific covalent targeting of G4 and iM DNA structures based on the combination of (i) a peptide nucleic acid (PNA) recognizing a specific sequence of interest, (ii) a pro-reactive moiety enabling a controlled alkylation reaction, and (iii) a G4 or iM ligand orienting the alkylating warhead to the reactive residues. This multi-component system allows for the targeting of specific G4 or iM sequences of interest in the presence of competing DNA sequences and under biologically relevant conditions.

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Section: Discussionmentioning

confidence: 99%

A red light-triggered chemical tool for sequence-specific alkylation of G-quadruplex and I-motif DNA

Cadoni

Paepe

Colpaert

et al. 2023

Nucleic Acids Research

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“…Peptide nucleic acid (PNA) was first reported three decades ago 1,2 and the field continues to draw attention from the community by virtue of its exceptional properties (for recent examples, see ref. [3][4][5][6][7][8][9][10][11][12][13][14][15][16]. It is an artificial mimetic of DNA or RNA wherein the phosphoribosyl backbone has been replaced by a peptidic backbone.…”

Section: Introductionmentioning

confidence: 99%

Impact of charges on the hybridization kinetics and thermal stability of PNA duplexes

López-Tena,

Winssinger

2024

Org. Biomol. Chem.

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Peptide Nucleic Acids: From Origami to Editing

Carson,

Watson

2024

ChemPlusChem

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Peptide nucleic acids (PNAs) combine the programmability of native nucleic acids with the robustness and ease of synthesis of a peptide backbone. These designer biomolecules have demonstrated tremendous utility across a broad range of applications, from the formation of bespoke biosupramolecular architectures to biosensing and gene regulation. Herein, we explore some of the key developments in the application of PNA in chemical biology and biotechnology in the last 5 years and present anticipated key areas of future development.

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Synthesis and structure–activity relationship of peptide nucleic acid probes with improved interstrand-crosslinking abilities: application to biotin-mediated RNA-pulldown

Abstract: The development of interstrand-crosslinking (ICL) probes for the covalent targeting of DNA and RNA sequences of interest has been extensively reported in the past decade. However, most of the reactions...

Cited by 5 publications

References 50 publications

A red light-triggered chemical tool for sequence-specific alkylation of G-quadruplex and I-motif DNA

A red light-triggered chemical tool for sequence-specific alkylation of G-quadruplex and I-motif DNA

Impact of charges on the hybridization kinetics and thermal stability of PNA duplexes

Peptide Nucleic Acids: From Origami to Editing

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