Abstract Title

Utilizing Extremophile DNA within Selex to Select for Aptamers That Bind Metal Ions

Additional Funding Sources

This project is funded through the Idaho National Laboratory (LDRD 20A44-203FP) and the Career Path Internship program from Idaho State University. The Department of Chemistry provided equipment and other resources for this project.

Abstract

Aptamers are short sequences of amino acids or nucleotides that display affinity towards molecules or ions. These oligopeptides or oligonucleotides are obtained through a process known as Systemic Evolution of Ligands by EXponential enrichment (SELEX). SELEX can be seen as evolution in a test tube.

Small molecules and ions have been notoriously difficult to capture using aptamer-based systems. The lack of functional groups on small molecules and ions often prevents bonds from forming between the aptamer and the molecules. Alternative methods have to be devised to counter this problem.

We hypothesized that modified and fragmented DNA from Halobacterium salinarum NRC-1, an extreme halophile, will display affinity towards nickel and other metals. H. salinarum DNA contains high-percentages of guanine, which has been shown to demonstrate affinity towards a wide variety of metals (1). We proposed using SELEX as the vehicle to explore the feasibility of the hypothesis. Our results suggest that the H. salinarum DNA-based aptamers do display affinity for nickel and cobalt. Our results also suggest that sequences with high guanine and cytosine concentrations display a high affinity for both metals. Future work involves the further characterization of the aptamers through de novo sequence motif analysis and computer molecular modeling as well as testing that they are more stable and durable than aptamers obtained from random generated libraries.

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Utilizing Extremophile DNA within Selex to Select for Aptamers That Bind Metal Ions

Aptamers are short sequences of amino acids or nucleotides that display affinity towards molecules or ions. These oligopeptides or oligonucleotides are obtained through a process known as Systemic Evolution of Ligands by EXponential enrichment (SELEX). SELEX can be seen as evolution in a test tube.

Small molecules and ions have been notoriously difficult to capture using aptamer-based systems. The lack of functional groups on small molecules and ions often prevents bonds from forming between the aptamer and the molecules. Alternative methods have to be devised to counter this problem.

We hypothesized that modified and fragmented DNA from Halobacterium salinarum NRC-1, an extreme halophile, will display affinity towards nickel and other metals. H. salinarum DNA contains high-percentages of guanine, which has been shown to demonstrate affinity towards a wide variety of metals (1). We proposed using SELEX as the vehicle to explore the feasibility of the hypothesis. Our results suggest that the H. salinarum DNA-based aptamers do display affinity for nickel and cobalt. Our results also suggest that sequences with high guanine and cytosine concentrations display a high affinity for both metals. Future work involves the further characterization of the aptamers through de novo sequence motif analysis and computer molecular modeling as well as testing that they are more stable and durable than aptamers obtained from random generated libraries.