Chemical Details on Nucleolipid Supramolecular Architecture: Molecular Modeling and Physicochemical Studies Nada Taib, †,‡ Ahissan Aime ́ , †,‡ Said Houmadi, § Sabine Castano, § Philippe Barthe ́ le ́ my,* ,†,‡ Michel Laguerre, § and Isabelle Bestel* ,†,‡ † Universite ́ Bordeaux Segalen, Bordeaux, F-33076, France ‡ INSERM U869, Bordeaux, F-33076, France § Universite ́ de Bordeaux, IECB - CBMN UMR 5248 CNRS, 2 rue Robert Escarpit, F-33607 Pessac Cedex, France * S Supporting Information ABSTRACT: Nucleolipids are currently under investigation as vectors for oligonucleotides (ON) delivery thanks to their supramolecular organization properties and their ability to develop specific interactions (i.e., stacking and potential Watson and Crick hydrogen bonds) for lipoplexes formation. To investigate the factors that govern the interaction events at a molecular level and optimize nucleolipid chemical structures, physicochemical experiments (tensiometry, AFM, BAM, and ellipsometry) combined with molecular dynamics simulation were performed on a series of zwitterionic nucleolipids (PUPC, DPUPC, PAPC) featuring a phosphocholine chain (PC). After construction and initial equilibration, simulations of pure nucleolipid bilayers were run for 100 ns at constant temperature and pressure, and their properties were compared to experimental data and to natural dipalmitoylphosphatidylcholine (DPPC) bilayers. Nucleolipid-based membranes are significantly more ordered and compact than DPPC bilayers mainly due to the presence of many intermolecular interactions between nucleoside polar heads. The hydrophilic phosphocholine moieties connected to the 5′ hydroxyls are located above the bilayers, penalizing nucleic bases accessibility for further interactions with ON. Hence, a neutral nucleolipid (PUOH) without hydrophilic phosphocholine was inserted in the membranes. Simulations and experimental analysis of nucleolipid membranes in interaction with a single strand RNA structure indicate that PUOH interacts with ON in the subphase. This study demonstrates that molecular modeling can be used to determine the interactions between oligonucleotide and nucleolipids. ■ INTRODUCTION A body of evidence demonstrates that oligonucleotides (ON) including antisense and RNA interference (RNAi) hold great promise as drugs to complete the therapeutic arsenal against miscellaneous severe pathologies. 1-6 However, overcoming critical issues concerning, for instance, the poor stability and the limited cell-delivery of such ON-based therapeutics is a prerequisite to large-scale clinical applications. In the past decade, many efforts have been devoted to the implementation of ON effective delivery systems based on viral 7,8 or on more safe synthetic vectors. 9-13 However, despite important progress, several impediments still have to be circumvent, spurring the continuing interest in the development of delivery strategies. To date, most of the synthetic vectors overwhelmingly capitalize on either electrostatic interactions or electrostatic and hydrophobic interactions to assemble the negative ON to the cationic vectors and to form supramolecular assemblies required for ON delivery. One caveat with this approach is the binding of these positively charged vectors to serum proteins, mostly negatively charged at physiological pH. To date, many cationic molecule-based systems have failed or been unimpressive in clinical trials mainly due to toxicity. 14,15 In this context, new strategies of ON delivery based on reinforced interactions such as hydrogen bonds and π-π stacking to further modulate the interactions between ON and the synthetic vector are emerging. Among them, the development of hybrid molecules bearing both nucleic acid units (i.e., nucleoside) and amphiphilic moieties, also known as nucleolipids, is of major interest. 16-20 The peculiar behavior Received: February 21, 2012 Revised: April 3, 2012 Published: April 6, 2012 Article pubs.acs.org/Langmuir © 2012 American Chemical Society 7452 dx.doi.org/10.1021/la300744x | Langmuir 2012, 28, 7452-7460