Triplex-Forming Peptide Nucleic Acid Controls Dynamic Conformations of RNA Bulges

Forced intercalation-induced light-up peptides as fluorogenic indicators for the HIV-1 TAR RNA-ligand assay

Fluorescence indicators capable of binding to human immunodeficiency virus-1 (HIV-1) trans-activation responsive (TAR) RNA are powerful tools for the exploratory studies of the identification of anti-HIV drug candidates. This work presents a new design strategy for fluorogenic indicators with a transactivator of transcription (Tat)-derived peptide based on the forced intercalation of thiazole orange (TO) dyes (FIT). The developed 9-mer FIT peptide (RKKRR-TO-RRR: named FiLuP) features the TO unit integrated onto a Dap (2,3-diaminopropionic acid) residue in the middle of the Tat peptide sequence; the Q (glutamic acid) residue in the Tat peptide (RKKRR-Q-RRR) is replaced with TO as if it were an amino acid surrogate. This facilitates a significant light-up response (450-fold at λem = 541 nm, Φfree = 0.0057, and Φbound = 0.61) upon binding to TAR RNA. The response of FiLuP is highly selective to TAR RNA over other non-cognate RNAs, and FiLuP maintains strong binding affinity (Kd = 1.0 ± 0.6 nM). Significantly, in contrast to previously developed Tat peptide-based FRET probes, FiLuP is able to discriminate between "competitive" and "noncompetitive" inhibitors when used in the fluorescence indicator displacement (FID) assay. The FID assay under stringent screening conditions is also possible, enabling super-strong competitive binders toward TAR RNA to be sieved out.

Triplex-forming peptide nucleic acids as emerging ligands to modulate structure and function of complex RNAs

Over the last three decades, our view of RNA has changed from a simple intermediate supporting protein synthesis to a major regulator of biological processes. In the expanding area of RNA research, peptide nucleic acid (PNA) is emerging as a promising ligand for triple-helical recognition of complex RNAs. As discussed in this feature article, the key advantages of PNAs are high sequence specificity and affinity for RNA (>10 fold higher than for DNA) that are difficult to achieve with small molecule ligands. Emerging studies demonstrate that triple-helical binding of PNAs can modulate biological function and control dynamic conformational equilibria of complex folded RNAs. These results suggest that PNA has a unique potential as a research tool and therapeutic compound targeting RNA. The remaining problems hampering advances in these directions are limitations of sequences that can be recognized by Hoogsteen triplexes (typically purine rich tracts), poor cellular uptake and bioavailability of PNA, and potential off-target effects in biological systems. Recent exciting studies are discussed that illustrate how synthetic nucleic acid chemistry provides innovative solutions for these problems.

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

Peptide nucleic acid (PNA) is emerging as a promising ligand for triple-helical recognition of folded biologically relevant RNA. Chemical modifications are actively being developed to achieve high affinity and sequence specificity under physiological conditions. In this study, we compared two modified PNA nucleobases, 2-aminopyridine (M) and 4-thiopseudisocytosine (L), as alternatives to protonated cytosine (unfavorable under physiological conditions), to form more stable triplets than C+·G-C. Both nucleobases formed M+·G-C and L·G-C triplets of similar stability; however, the L-modified PNAs showed somewhat reduced sequence specificity. In conclusion, M and L represent two alternative solutions to the problem of cytosine protonation in triple-helical recognition of RNA. In M, the pKa is increased to favor partial protonation, which improves solubility and cellular uptake of M-modified PNAs. In L, the sulfur substitution enhances favorable hydrophobic interactions, which may have advantages in avoiding off-target effects that may be caused by cationic modifications. However, our results showed that substituting Ms with Ls did not restore the sequence specificity of a PNA containing cationic groups.