Nucleic acid partitioning

ATP extraction has been used for the separation and large-scale purification of enzymes.45 47 Proteins and nucleic acids partition between the two phases differently due to differences in their surface charges and hydrophobic-hydrophilic domains. Proteins generally prefer the aqueous phase rich in... 

Mueller [103-104] has adopted the polyethylene glycol)-dextran partition system pioneered by Albertson [105] to develop an efficient chromatographic method for the resolution of proteins and nucleic acids. He used supports such... 

Cieplak, P., Caldwell, J. W., Kollman, P. A., Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation aqueous solution free energies of methanol and IV-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases, J. Comput. Chem. 2001, 22, 1048-1057... 

Table 11.3 Absolute free energies of solvation (kcal mol ) and chloroform/water partition coefficients (logio units) for nucleic acid bases at the SM5.4/AM1 Icvcf ...

The similar accuracies of different well-parameterized continuum models implies that they will also perform similarly for the computation of partition coefficients, and that has proven to be the case in most studies to date (see, for example, Bordner, Cavasotto, and Abagyan 2002 and Curutchet et al. 2003b). In Table 11.4 the previously presented SMx results for the chloroform/water partitioning of die methylated canonical nucleic acid bases are compared to results from die MST-ST/HF/6-31G method, and also to purely electrostatic results obtained using a multipole expansion SCRF method. As the latter does not include any accounting for non-electrostatic effects, its performance is significantly degraded compared to the other two. 

Because of the different interactions involved in partition and adsorption processes, they may be applied to different separation problems. Partition processes are the most effective for the separation of small molecules, especially those in homologous series. Partition chromatography has been widely used for the separation and identification of amino acids, carbohydrates, and fatty acids. Adsorption techniques, represented by ion-exchange chromatography, are most effective when applied to the separation of macromolecules including proteins and nucleic acids. 

At this point, the RNA constructs have been purified away from any protein and small reactant molecules. To further dialyze the sample, it can be diluted and concentrated once again on a 30 kDa MWCO filter and recovered in the desired buffer. This should leave pure modified nucleic acids ready to enter the affinity-capture stage of the in vitro selection - partitioning. 

Selective capturing of the active nucleic acid sequences is a crucial factor in determining the success of an RNA catalyst in vitro selection. A convenient technique for partitioning active from inactive RNA sequences involves capture of biotin by streptaviclin. Biotin is a widely used affinity tag because of its strong binding (K 10-15) to streptavidin. Potential substrates are typically synthesized with... 

Although the oldest type of columns, these are presently the most popular nonpartition columns because they can separate large biological molecules such as proteins and nucleic acids. By means of controlled pore sizes, they separate compounds by their molecular size and shape. The resolution achieved by a size resolution column is not nearly as great as that shown by ion exchange or by partition. You will need a 100% difference in molecular weights to achieve a clean separation. Partition can separate on the basis of a proton up or down out of 13 protons on a compound. 

TABLE 3 Effect of Nucleic Acids on Partition Coefficients... 

TABLE 4 Partition Coefficients of Total Proteins, TDH, and Nucleic Acids from Crude Cell Homogenate in the Two Phases of ATP System... 

Jaeske, A., Fuertste, J. P., Erdmann, V. A., and Cech, D. (1994). Hybridization-based affinity partitioning of nucleic acids using PEG-coupled oligonucleotides. Nucleic Acids Res. 22, 1880 1884. 

Amidon GL, Anik S, Rubin J (1975) An energy partitioning analysis of base-sugar intramolecular C-H—O hydrogen bonding in nucleosides and nucleotides. In Sundaralingam M, Rao ST (eds) Structure and conformation of nucleic acids and protein-nucleic acid interactions. University Park Press, Baltimore, pp 729- 744... 

Mechanical Models for Organic and Biological Systems Going Beyond the Atom Centered Two Body Additive Approximation Aqueous Solution Free Energies of Methanol and N-Methyl Acetamide, Nucleic Acid Base, and Amide Hydrogen Hydrogen Bonding and Chloroform/Water Partition Coefficients of the Nucleic Acid Bases. 

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