Date of Award


Document Type

Open Access

Degree Name

Bachelor of Science






This work examines the conformations of various ollgonucleotides as a function of two environmental conditions, neighboring base combinations and surrounding media. The conformations were determined by molecular mechanical energy refinement using the internal minimization function of a program written by Ken Miller. The first condition examined was the effect of various neighboring base combinations on the conformation of the interior base. Our results indicate that the NH2 a,,lino groups are the primary factors in determining differences in conformations of various base pairs sequences. One way in which the NH2 amino groups are able to affect the conformation of the molecule is by repulsi"G forces which separate the two groups when C and A groups are stacked upon each other. The second way is that the distance between the amino group of a nucleotide base and the C1' carbon directly influences the value of the dihedral angle Xi, which is between the C4 and CS carbon atoms. The second condition examined was the effect of including rough approximations of solvent and cations conditions that exist in the cellular environment into the energy refinement calculations. Our results Indicate that the mere inclusion of hydrated sodium cations, in the proximity of the phosphate groups along the oligonucleotide backbone, insulates the phosphate groups from the substantial repulsive forces they were observed to exert upon each other in the gaseous medium calculations.

Included in

Chemistry Commons



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In Copyright - Educational Use Permitted.