Selection by phage display of peptides targeting the HIV-1 TAR element

As transcription regulatory element, the HIV-1 TAR RNA element is a promising target to inhibit viral replication; indeed, ligands of TAR RNA could prevent the transcription trans-activation process. Phage display in vitro selection was undertaken to select peptidic ligands of TAR RNA. In preliminary experiments, the selection was performed in a magnesium rich buffer (3 mM), but only phages targeted to plastic wells or streptavidin emerged; in addition, a "super-infectious" phage present in the New England Biolabs library (SVSVGMKPSPRP) selected by others with different targets was cloned, due to a high amplification potential. In contrast, the absence of magnesium or an increasing magnesium concentration (0 to 0.5 mM) led to phage selection with 57 amino acid peptides. K(D)s of 420-550 nM were measured by filter binding assays; a significant specificity was obtained when TAR target was compared with unrelated RNA targets. Surprisingly, the binding of selected peptides does not depend on the magnesium concentration.