Kinetics of DNA Duplexing in Various Ionic Strengths Using Stopped-Flow Spectroscopy

Ostrosky, Kara

Kinetics of DNA Duplexing in Various Ionic Strengths Using Stopped-Flow Spectroscopy

Persistent URL

http://hdl.handle.net/10456/7985

Author(s)

Ostrosky, Kara

Date Issued

April 21, 2009

Abstract

Stopped-flow spectroscopy was used to obtain rate constants for DNA duplexation in various NaCl buffer concentrations. DNA duplexation was observed for complementary DNA strands consisting of eight bases (DNA1: 5’-GTGCTGTG-‘3, DNA2: 5’-CACAGCAC-‘3) with equal concentrations of both strands in second-order reaction conditions. DNA concentrations ranged from 1 to 7 µM in NaCl buffer concentrations of 0.048 to 1.0 M. Data was fitted to a second-order integrated equation. It was found that the observed rate constants for DNA duplexation increase with increasing NaCl buffer concentrations and also with increasing DNA concentrations. Results showed a positive, linear relationship between NaCl concentrations and the rate constants for DNA duplexation, given by k = 11.89 [NaCl] + 0.9018. The results are ambiguous with respect to support for the Debye-Huckel theory. Another possible theory is the tight binding model, in which ions directly coordinate to the DNA strands. Furthermore, it is hypothesized that a decrease in the activation barrier due to ionic strength could explain the positive, linear relationship between salt concentrations and rate constants for DNA duplexation.

Honors

Chemistry, 2009

First Reader(s)

Deckert, Alice A.