Date

2016

Document Type

Dissertation

Degree

Doctor of Philosophy

Department

Chemical Engineering

First Adviser

Jagota, Anand

Other advisers/committee members

Mittal, Jeetain; Vezenov, Dmitri; Rotkin, Vyacheslav; Snyder, Mark

Abstract

Since DNA-SWCNT hybrids have a number of potential biomedical applications such as molecular sensing, drug delivery and cell imaging, it is essential to characterize them and to understand their structure and properties. Certain single stranded DNA (ssDNA) sequences are known to recognize their partner single wall carbon nanotube (SWCNT). We report here the activation energies for removal of several ssDNA sequences from a few SWCNT species by a surfactant molecule. We found that DNA sequences systematically have higher activation energy of dissociation from their carbon-nanotube recognition partner than on non-partner species. Since the difference in binding affinity and difference in partitioning can depend on DNA structure on the single walled carbon nanotube (SWCNT), we studied the partitioning of the various DNA sequences in an aqueous two phase system. We found that for two sequences of same length, (CCA)10 on (6,5) SWCNT requires much higher amount of modulant to be moved from the relatively hydrophilic phase to the more hydrophilic phase as compared to (GT)15 on (6,5), suggesting that the solvation energy depends greatly on the DNA sequence. We also found that various sequences with the same length but different repeating units of two bases exhibit different hydration energies on the same SWCNT (6,5). Unlike the majority of DNA structures in bulk that are stabilized by canonical Watson-Crick pairing between Ade-Thy and Gua-Cyt, those adsorbed on surfaces are often stabilized by non-canonical base pairing, quartet formation, and base-surface stacking. All-atom molecular simulations of DNA bases in two cases - in bulk water and strongly adsorbed on a graphite surface – are conducted to study the relative strengths of stacking and hydrogen bond interactions for each of the ten possible combinations of base pairs. We find that stacking interactions exert the dominant influence on the stability of DNA base pairs in bulk water in the order, Gua-Gua > Ade-Gua > Ade-Ade > Gua-Thy > Gua-Cyt > Ade-Thy > Ade-Cyt > Thy-Thy > Cyt-Thy > Cyt-Cyt. On the other hand, mutual interactions of surface adsorbed base pairs are stabilized mostly by hydrogen bonding interactions in the order, Gua-Cyt > Ade-Gua > Ade-Thy > Ade-Ade > Cyt-Thy > Gua-Gua > Cyt-Cyt > Ade-Cyt > Thy-Thy > Gua-Thy. Interestingly, several non-Watson-Crick base pairings, that are commonly ignored, have similar stabilization free energies due to inter-base hydrogen bonding as Watson-Crick pairs. This clearly highlights the importance of non-Watson-Crick base pairing in the development of secondary structures of oligonucleotides near surfaces. Hybrids of single stranded DNA and single walled carbon nanotubes have proven very successful in separating various chiralities and, very recently, enantiomers of carbon nanotubes using aqueous two-phase separation. This technique sorts objects based on small differences in hydration energy, which is related to corresponding (small) differences in structure. Separation by handedness requires that a given ssDNA sequence adopt different structures on the two SWCNT enantiomers. Here we study the physical basis of such selectivity using a coarse grained model to compute the energetics of ssDNA wrapped around an SWCNT. Our model suggests that difference by handedness of the SWCNT requires spontaneous twist of the ssDNA backbone. We also show that differences depend sensitively on the choice of DNA sequence.

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