A Caltech Library Service

Acridine−N Peptide Conjugates Display Enhanced Affinity and Specificity for boxB RNA Targets

Qi, Xin and Xia, Tianbing and Roberts, Richard W. (2010) Acridine−N Peptide Conjugates Display Enhanced Affinity and Specificity for boxB RNA Targets. Biochemistry, 49 (27). pp. 5782-5789. ISSN 0006-2960.

Full text is not posted in this repository. Consult Related URLs below.

Use this Persistent URL to link to this item:


Arginine-rich peptides and small-molecule intercalating agents utilize distinct molecular mechanisms for RNA recognition. Here, we combined these distinct binding modules in an effort to create conjugate ligands with enhanced affinity and specificity using the bacteriophage λ N peptide−boxB interaction as a model system. We first designed and synthesized a series of peptide−acridine conjugates using portions of the RNA-binding domain of N protein (11- and 22- residue peptide segments) and then compared the binding affinity, specificity, salt dependence, and structural properties of the RNA−peptide and RNA−peptide−acridine conjugate complexes using steady-state fluorescence, CD spectroscopy, NMR, and native gel mobility shift assays (GMSAs). These analyses revealed that the full-length peptide−acridine conjugate displayed substantially improved RNA binding affinity (~80-fold; K_d 15 pM) relative to that of the peptide alone (K_d ~ 1.2 nM). In accordance, we also observed specificity enhancement (~25-fold) as determined via comparison of the binding of the best conjugate to a cognate λ boxB RNA with that to a noncognate P22 RNA hairpin (80-fold vs 3.2-fold enhancement). Furthermore, the observed binding enhancement was unique to the full-length conjugate with a flexible linker, implying that the structural context of the acridine presentation was critical. Taken together, our observations support the idea that peptide- and intercalation-based binding can be combined to create a new class of high-affinity, high-specificity RNA-binding ligands.

Item Type:Article
Related URLs:
URLURL TypeDescription
Roberts, Richard W.0000-0002-8587-5097
Additional Information:© 2010 American Chemical Society. Received April 25, 2010; Revised Manuscript Received June 7, 2010. Publication Date (Web): June 8, 2010. This research is financially supported by National Institutes of Health Grant GM60416 (R.W.R.). We thank Drs. T. T. Takahashi and Ryan J. Austin for helpful discussions.
Funding AgencyGrant Number
Issue or Number:27
Record Number:CaltechAUTHORS:20100720-104100921
Persistent URL:
Official Citation:Acridine−N Peptide Conjugates Display Enhanced Affinity and Specificity for boxB RNA Targets Xin Qi, Tianbing Xia, Richard W. Roberts Biochemistry 2010 49 (27), 5782-5789
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:19123
Deposited By: Jason Perez
Deposited On:21 Jul 2010 18:29
Last Modified:09 Mar 2020 13:19

Repository Staff Only: item control page