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NAME: Destiny Carte

Effect of Linker Length and Structure on DNA Binding Performance

Self-assembling single-stranded DNA (ssDNA) monolayers on gold surfaces have numerous applications in biosensor technology. One application of particular interest involves the utilization of DNA aptamers for probe strands.  Because the affinity of DNA aptamers to target analytes depends on their folded three dimensional structures, they simultaneously demonstrate the specificity of a protein and the stability of a nucleic acid. Self-assembling monolayers (SAMs) composed of thiol-modified dendrons bound to DNA probes via NHS-maleimide linkers, can be used to capture a variety of target analytes, from nucleic acids to proteins. The analyte binding efficiencies of each monolayer will be analyzed under various conditions using the Langmuir Adsorption Model, in which a low dissociation constant, KD, is indicative of a high binding frequency between analyte and DNA probe strand.  The KD values for each linker length and structure will be observed in order to determine whether linker length has an effect on binding frequency.   Preliminary research has demonstrated that among linkers with similar rigidity, length and binding capacity are positively correlated.  Preliminary research has also indicated that greater linker rigidity promotes increased analyte binding. This may be explained by the increased likelihood tendency of probe entanglement with SAMs made with less rigid linkers. For a given length, linkers with internal cyclohexane functional groups have better binding capacities than linkers with internal aliphatic chains. Although linkers containing internal cyclohexane groups are more rigid than linkers with internal aliphatic groups, linkers with aromatic groups should be even more rigid due to the fact that cyclohexane can adopt different conformations.  Because increased rigidity appears to increase binding capacity, linkers with planar aromatic groups should demonstrate the greatest binding capacity.