In this study , a number of different sequences were chosen to understand the effects of structure on hybridization reaction rates and to compare kinetics of these sequences in solution and on surfaces . Model sequences were chosen based on a series of stable single - stranded structures that form GNRA tetraloops where N can be A , G , C or T and R must be a purine ( 10)(11)(12)(13 ) . The hairpins that can form from the tetraloops are unique in that they do not consist of a series of repeating bases ( 14 ) or large multi - base loop regions ( 15 ) . The stability of the four - base loop arises from a number of factors including base stacking between the third and fourth A , hydrogen bonding between an amino proton on the G and an oxygen from the phosphate between the second and third A , and base pairing between the G and the third A in the loop ( 10 ) . In addition to the model tetraloop sequences , a series of random sequences , denoted as random coils , were used for comparison . These sequences have no known stable structure and have similar melting temperatures and identical lengths . To study the possible surface effects on the hybridization rates , kinetic data were obtained both in solution and when one strand was covalently bound to a silica microsphere .