Peptoids as Monodisperse, Multivalent Scaffolds for End-Labeled Free-Solution Electrophoresis (ELFSE) and Magnetic Resonance Imaging (MRI)

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The need for readily synthesized scaffold architectures to build monodisperse, high molar mass mobility modifiers or "drag-tags" in end-labeled free solution electrophoresis (ELFSE) led to the development of a novel class of multivalent molecular tools. Poly-N-substituted glycines (peptoids) were created with evenly spaced amino groups as branching points along the scaffold backbone. These molecules are comprised primarily of poly-N-(methoxyethyl)glycine (Nmeg) residues, as this side chain imparts many favorable properties such as water solubility, ease of synthesis in good yield and purity, and high chemical stability. The initial scaffold design allowed for the attachment of five carboxylate-terminated branches of varying lengths via peptide bond forming reactions. Optimization of conditions and reagents resulted in near quantitative yield and complete grafting at all five reaction sites. Most importantly, the product could be chromatographically purified to complete monodispersity, an essential criterion for an ELFSE drag-tag. Specifically, a 30mer poly(Nmeg) backbone with five amino (N-Lysine) groups was appended with tetramer- and octamer-Nmeg branches; these comb-like conjugates along with an unbranched 30mer (acetylated amino groups) were attached to short DNA primers and evaluated as drag-tags. The important result of this study was that electrophoretic "drag" or "" scaled somewhat linearly with molecular weight, demonstrating that increased mass is the key design parameter for this class of drag-tags. The octamer-branched drag-tag was further employed in a number of other studies, including multiplexed genotyping, DNA modified at both ends, and as the first example of DNA sequencing using a completely synthetic molecule. In the latter case, the seventy-monomer peptoid sequenced 80-100 bases of DNA in 16 minutes, close to the result achieved using a native protein (streptavidin), which is roughly eight times larger. A similar scaffold and synthetic strategy was further used to construct a multivalent contrast agent for magnetic resonance imaging (MRI). A molecule containing eight branching points for gadolinium ligands was successfully synthesized, metallated, and subsequent relaxivity values were calculated. The relaxivity value per gadolinium ion (Gd III) was 10.7 mM-1s-1 at 60 MHz as indicated by inductively coupled plasma (ICP), which corresponded to a relaxivity of 86 mM-1s-1 per fully derivatized molecule. This relatively high relaxivity value is impressive, especially given that the multivalency of the molecule will allow for the inclusion of additional functionalities that may make the contrast agent even more useful. Further study and syntheses of this class of multivalent molecules could potentially lead to drag-tags capable of sequencing hundreds of bases of DNA and contrast agents that possess therapeutic relevance. Such strategies are discussed in the final chapter.

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  • 09/12/2018
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