Characterization and modelling of polymer/olygonucleotide complexes

In this study, the interactions between triblock copolymers that are synthesized previously by our group as antisense oligonucleotide carriers, methoxy poly(ethylene glycol)-b-poly(?-caprolactone)-b-poly(ethylene imine) (mPEG-b-PCL-b-PEI) and methoxy poly(ethylene glycol)-b-poly(L-lactate)-b-poly(ethylene imine) (mPEG-b-PLL-b-PEI), with c-myc AS ODN were characterized by experimentally and modelling. C-myc is an important gene type which plays important role in controlling cell growth and it is often targeted in cancer treatment studies because abnormal c-myc activities have been observed in especially breast cancer tumors. Corresponding AS ODNs of c-myc mRNAs can be used to inhibit expression of damaged c-myc genes. The use of polycationic vectors for effective and safe transfer of these AS ODNs into tumor cells is quite a common approach. In the first part of the study, structural characterizations of the polymeric carriers and polycation/ODN complexes were carried out because the achievement of DNA transfer studies is related with physicochemical parameters such as complex?s size, molecular weight and charge. For this purpose, polycation/ODN complexes that were prepared in different nitrogen (N)/phosphor (P) ratios were characterized by using dynamic light scattering and sedimentation equilibrium techniques. In the second part of the study, the interactions between polycations with ODN and formed structures investigated by using Amber molecular dynamics software. According to the experimental results, highly monodisperse and stable complex structures are formed in the solution. Also, it is found out that the size and molecular weight of the complexes can be adjusted by N/P ratio and synthesized polycations have high delivery capacity. According to the modelling results, complexes are formed by PEI and ODN molecules come closer in a short time, ODN is compacted a little by complexation, complexations occurred by Na+ ions releasing from vicinity of phosphor atoms of ODN and by approaching of protonated amine nitrogen atoms of PEI to vicinity of phosphor atoms of ODN and H-bondings are formed between oxygen atoms of phosphate groups of ODN and protonated amine nitrogen atoms of PEI. Also, according to the calculated binding energies, triblock copolymers can be used as potential polymeric vectors in gene therapy. Furthermore, according to both modelling and experimental results, the length of hydrophobic chains in backbone of polymers affects complexation and it is found out that the sizes, molecular weights, number of binding units and binding energies of complexes between ODN and triblock copolymers containing PCL are less than complexes between ODN and triblock copolymers containing PLL due to the fact that PCL has more hydrophobic alkyl chains than PLL.