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Proceedings of the 31 st European Peptide SymposiumMichal Lebl, Morten Meldal, Knud J. Jensen, Thomas Hoeg-Jensen (Editors)European Peptide Society, 2010Tubomicelle of Gene Transfection Agent 1,4-DihydropyridineLipid and Its Binding with DNAInta Liepina 1 , Ainars Zemitis 1 , Gunars Duburs 1 , Cezary Czaplewski 3 ,and Adam Liwo 31 Latvian Institute of Organic Synthesis, Aizkraukles str. 21, Riga LV1006, Latvia,2 Department of Chemistry, and University of Gdansk, ul. Sobieskiego 18, 80-952Gdansk, PolandIntroductionArtificial lipids are in wide use for gene and drug delivery [1-3]. In our prior work [4] weshowed with molecular dynamics (MD) simulation, that the gene transfection agent,1,1’-{[3,5-bis(dodecyloxycarbonyl)-4-phenyl-1,4-dihydropyridin-2,6-diyl]dimethylene}bispyridinium dibromide (1,4-DHP lipid) (Figure 1) [5,6] formed a tubular micelle, ifstarted from a lipid bilayer, and the existence of worm-like structures was confirmed byelectron microscopy.The present work investigates the stability of the tubular micelleand its binding with the 15-mer DNA: TGG-CGT-CTT-CCA-TTT.1,4-DHP lipid tubomicelle was taken from [4] and:1) immersed in a bigger amount of water (system 1) andsubjected for 22 ns of MD run,2) four tubomicellaes were put together (system 2) andsimulated by MD for 63 ns,3) four tubomicellaes were surrounded by additional water(system 3) and subjected to MD for 42 ns,4) System of five tubomicellaes was complexed with the 15-mer DNA double helix (system 4) and simulated by MD for 32 ns.All the systems were subjected to MD with AMBER 9.0program package, f99 force field, NTP protocol (constant numberof particles, temperature, pressure), using a periodic water box ofvexplicit water molecules, MD simulation were started at T=10KFig. 1. 1,4-DHP lipid. and heated up till T=309K, and then the calculations werecontinued at constant temperature of T=309K.Results and DiscussionSystem 1, 1,4-DHP lipid tubomicelle in the bigger amount of water. During the course ofsimulation a gap appeared in the tubomicelle, - after about 6 ns of MD, then after about 12ns the classical micellae split away from the tubular structure. After about 17 ns the rest ofthe tubula split into two round micellaes.System 2, four tubomicellaes together, showed the stability of tubular structure during thewhole simulation time of 63 ns.System 3, four tubomicellaes surrounded by water, kept their tubular structure during thewhole course of MD simulation of 42 ns, however there few cuts are formed in the tubulassuggesting that with the time some round micellae form could emerge.System 4, five tubomicellaes complexed with the DNA, showed that the DNA double helixis stable during the whole course of simulation. The DNA rod was put aside from the fivetubomicallaes, during the 1 ns of MD simulation it edged between two tubular micellaes,become squeezed there, and then, after about 12 ns the part of the third tubular micellestarted to move towards the DNA rod.ConclusionsA 1,4-DHP lipid tubomicelle is stable in water, but in smaller 1,4-DHP lipid concentrationsclassic micelle can split from the tubomicelle, and tubomicelle can transform to roundmicellaes. This is in agreement with electron microscopy showing both tubular and roundstructures.The DNA could be bound between two tubular micellaes maintaining its doublehelical structure and showing stability during the course of simulation. The 1,4-DHP ringstend to take tangential position towards the tubular micellaes' surface.630