Abstract:

This dissertation presents work on two different novel DNA sequencing methods. The first was based on using the atomic force microscope (AFM) to detect the changes in force as a nanopore is pulled over surface tethered single stranded DNA. This technique required the synthesis and verification of multiple chemical components. It was determined, both theoretically and experimentally, that the changes in force as purines or pyrimidines pass through the nanopore were too small to be measured using the AFM. However, the method was successfully applied to studying the opening of hairpins in single stranded DNA when a nanopore is forced over them. This geometry is similar to how polymerases approach hairpins while transcribing DNA. It differs from other techniques which pull the ends of the DNA apart in order to study secondary structures. The results show that the nanopore method requires higher forces and less strain when hairpins are opened, as compared to the other methods.

The work studying the translocation of DNA through a nanopore also informed the second sequencing method described. This technique is grounded in work using a scanning tunneling microscope (STM) to determine the conductance between Watson-Crick base pairs of DNA. The full sequencing method consists of a single strand of DNA, under an electrophoretic force, passing through a nanopore to a pair of electrodes functionalized such that the DNA bases form hydrogen bonds to one electrode through bases attached to the electrode, whereas its phosphate backbone forms hydrogen bonds to the other via guanidinium, completing the electrical circuit.

An important aspect of this method is the reversible hydrogen bonding between the phosphate backbone of DNA and guanidinium. Using the AFM, the adhesion of DNA was studied under various conditions. It was determined that the entropy change as DNA condenses out of solution dominates the DNA-guanidinium interaction. Results also confirmed that the hydrogen bonding is reversible and that the molecular friction of the DNA passing through the functionalized electrodes is strong enough that additional force may have to be applied in order for the DNA to translocate through the nanopore.