Nucleic acid synthetic, water-soluble

Gel electrophoresis is widely used in the routine analysis and separation of many well-known biopolymers such as proteins or nucleic acids. Little has been reported concerning the use of this methodology for the analysis of synthetic polymers, undoubtedly since in many cases these polymers are not soluble in aqueous solution - a medium normally used for electrophoresis. Even for those water-soluble synthetic polymers, the broad molecular weight dispersities usually associated with traditional polymers generally preclude the use of electrophoretic methods. Dendrimers, however, especially those constructed using semi-controlled or controlled structure synthesis (Chapters 8 and 9), possess narrow molecular weight distribution and those that are sufficiently water solubile, usually are ideal analytes for electrophoretic methods. More specifically, poly(amidoamine) (PAMAM) and related dendrimers have been proven amendable to gel electrophoresis, as will be discussed in this chapter. 

In summary, dendrimers are a unique class of monodispersed synthetic molecules reminiscent of proteins or nucleic acids. If they can be functionalized to be soluble in water with appropriately charged terminal groups, they are generally ideal candidates for gel electrophoretic analyses. 

Chitosan is one of the most commonly studied polymers in nonviral gene delivery [106]. Indeed, its positive charges under slightly acidic conditions allow its interaction with nucleic acids such as DNA or siRNA and the condensation of the nucleic acids into nanoparticles. In addition, the biocompatibility and low toxicity of chitosan enable its in vivo use [107]. However, the poor buffering capacity and poor solubility in water [46] make chitosan less efficient than other catioiuc synthetic polymers, such as PEI or PEL. 

Aqueous SEC was first reported in 1959 by Porath and Flodin [1]. They separated proteins and salts according to molecular size by using cross-linked dextran gels. Since then it has been widely employed, especially in the field of biochemistry, for various purposes such as purification of proteins and nucleic acids, estimation of molecular masses of proteins and determination of molecular mass distributions of polysaccharides. In addition, it has been a powerful tool for the determination of molecular mass distributions of water-soluble synthetic polymers since high-performance aqueous SEC was realized in 1978 by the development of semirigid microparticulate macroporous supports based on hydrophilic synthetic polymers [2-4]. 

TSKgel PW series columns have been used in the separation of water-soluble synthetic polymers, poly- and oligo-saccharides, and proteins [ref. 34-41]. Recently it has been shown that the columns can be used for lipoproteins and nucleic acids. TSKgel PW columns are available from Toyo Soda, and in other countries, from the dealers listed in Table 3. Showa Denko developed an analogous type of columns, namely OHpak B-800 [ref. 42, 43]. Properties of these columns are represented in Table 4. 

Interaction of the synthetic polymers and polynucleotides were estimated from the hypochromicity values in UV spectra. The UV spectra were measured with a JASCO UV-660 spectrometer equipped with a temperature controller at 20 C. Polynucleotides were obtained from Yamasa Shoyu Co. Ltd. Water soluble poly(ethyleneimine) derivatives containing nucleic acid bases and polynucleotides were dissolved in Kolthoff buffer (pH 7.0, O.IM KH2PO4 -0.05M Na2B40 -10H20). These solutions were stocked for 2 days at 20 C, and then mixed to give a polymer mixture of 10 total concentration of nucleic acid base units in aqueous solution. 

Natural and synthetic polynucleotides are known to form polymer complexes by specific base-base interactions between nucleic acid bases. The synthetic nucleic acid analogs such as poly (methacryamide), poly-(ethyleneimine) and poly(L-lysine) derivatives containing nucleic acid bases were also found to form polymer complexes with polynucleotides by specific base-base interactions. Since the solubilities of these nucleic acid analogs in water were low, the specific interactions should be studied in organic solvents or water-organic mixed solvents, such as dimethyl sulfoxide, ethylene glucol, and water-propylene glycol. 

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