Fluorobenzene Nucleobase Analogues for Triplex‐Forming Peptide Nucleic Acids

Abstract

2,4‐Difluorotoluene is a nonpolar isostere of thymidine that has been used as a powerful mechanistic probe to study the role of hydrogen bonding in nucleic acid recognition and interactions with polymerases. In the present study, we evaluated five fluorinated benzenes as nucleobase analogues in peptide nucleic acids designed for triple helical recognition of double helical RNA. We found that analogues having para and ortho fluorine substitution patterns (as in 2,4‐difluorotoluene) selectively stabilized Hoogsteen triplets with U−A base pairs. The results were consistent with attractive electrostatic interactions akin to non‐canonical F to H−N and C−H to N hydrogen bonding. The fluorinated nucleobases were not able to stabilize Hoogsteen‐like triplets with pyrimidines in either G−C or A−U base pairs. Our results illustrate the ability of fluorine to engage in non‐canonical base pairing and provide insights into triple helical recognition of RNA.

Comparison of 2-Aminopyridine and 4-Thiopseudisocytosine PNA Nucleobases for Hoogsteen Recognition of Guanosine in RNA

“…21 Earlier, we have demonstrated that UV thermal melting experiments at 300 nm allowed measurement of triplex to duplex transitions only (due to unique absorbance of M heterocycles) without interference from melting of RNA hairpins than had a negligible absorbance at 300 nm. 31 Binding data showed that PNA3 having L at the variable position had similar affinity for the matched HRP1 than for the control PNA1 to HRP1 and PNA2 to HRP2 (Table 1). UV thermal melting suggested that the PNA3-HRP1 triplex was more stable by ΔT m = 5−8 °C compared to PNA1-HRP1 and PNA2-HRP2.…”

“…The binding affinity was measured using isothermal titration calorimetry (ITC) and UV thermal melting, as reported in our previous studies . Earlier, we have demonstrated that UV thermal melting experiments at 300 nm allowed measurement of triplex to duplex transitions only (due to unique absorbance of M heterocycles) without interference from melting of RNA hairpins than had a negligible absorbance at 300 nm …”

4′-Fluoro-nucleosides and nucleotides: from nucleocidin to an emerging class of therapeutics

“…For instance, the incorporation of fluorine motifs within nucleobases, and structural analogues thereof, has been investigated as a tool to mechanistically probe nucleic acids and proteins. [9][10][11][12][13] Incorporation of fluorine within a non-canonical sugar motif of a nucleoside and a nucleotide has been used to generate analogues with tailored conformation and properties when incorporated into oligonucleotides and thus optimise potential biological applications. [14][15][16] Additionally, modification of the nucleic acid backbone using fluorinated PNA monomers has been successfully explored, 17,18 as has the development of selectively fluorinated nucleoside amidate prodrugs as antivirals.…”

TFOFinder: Python program for identifying purine-only double-stranded stretches in the predicted secondary structure(s) of RNA targets

“…The peptide nucleic acid (PNA) backbone modification has been employed to eliminate this unfavorable interaction, which resulted in high TFO binding specificity and sensitivity, and with a greater mismatch discrimination as compared to using DNA or RNA TFOs [9][10][11]. Triplex formation can further be favored and stabilized by employing base modifications [11][12][13][14][15][16][17].…”