Human immunodeficiency virus-1 (HIV-1) replication and gene expression entails specific interaction of the viral protein Tat with its transactivation responsive element (TAR), to form a highly stable stem-bulge-loop structure. Previously, we described triphenylphosphonium (TPP) cation-based vectors that efficiently deliver nucleotide analogs (PNAs) into the cytoplasm of cells. In particular, we showed that the TPP conjugate of a linear 16-mer PNA targeting the apical stem-loop region of TAR impedes Tat-mediated transactivation of the HIV-1 LTR in vitro and also in cell culture systems. In this communication, we conjugated TPP to cyclic and hairpin PNAs targeting the loop region of HIV-1 TAR and evaluated their antiviral efficacy in a cell culture system. We found that TPP-cyclic PNAs containing only 8 residues, showed higher antiviral potency compared to hairpin PNAs of 12 or 16 residues. We further noted that the TPP-conjugates of the 8-mer cyclic PNA as well as the 16-mer linear PNA displayed similar antiviral efficacy. However, cyclic PNAs were shown to be highly specific to their target sequences. This communication emphasizes on the importance of small constrained cyclic PNAs over both linear and hairpin structures for targeting biologically relevant RNA hairpins. 1. Introduction The transcriptional transactivation of the HIV-1 genome requires a specific interaction between the highly conserved TAR RNA hairpin fragment with the viral Tat protein and cellular factors (PTEFb-cyclin T1-CDK9 kinase complex). Both the six-nucleotide loop and the three-nucleotide bulge of TAR RNA (Figure 1(a)) are involved in the formation of this complex [1–3]. Therefore, molecules that can bind to the bulge or the loop of TAR are of great therapeutic interest, since disruption of the ternary complex formation leads to abortive mRNA synthesis and, consequently, to inhibition of viral replication. Figure 1: Sequence and secondary structure of (a) HIV-1 mini-TAR RNA, (b) R06 24 and R06 18 aptamers reported in this study. Bold bases indicate complementarity between aptamer and TAR loops. The crucial G and A residues flanking the R06 aptamers loop are in italics. During the last decade, a wide number of TAR ligands have been described [4, 5]. Among them, one can cite R06 aptamers (such as R0624 or R0618, Figure 1(b)), which were identified initially by in vitro selection [6]. These aptamers are folded RNA stem-loop structures which recognize the mini-TAR fragment (Figure 1(a)) not only on the basis of sequence complementarity, as classical antisense oligomers, but also on
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