Abstract
BackgroundDNA is a carrier of biological information. The hybridization process, the formation of the DNA double-helix from single-strands with complementary sequences, is important for all living cells. DNA microarrays, among other biotechnologies such as PCR, rely on DNA hybridization. However, to date the thermodynamics of hybridization is only partly understood. Here we address, experimentally and theoretically, the hybridization of oligonucleotide strands of unequal lengths, which form a bulged loop upon hybridization. For our study we use in-house synthesized DNA microarrays.ResultsWe synthesize a microarray with additional thymine bases in the probe sequence motifs so that bulged loops occur upon target hybridization. We observe a monotonic decrease of the fluorescence signal of the hybridized strands with increasing length of the bulged loop. This corresponds to a decrease in duplex binding affinity within the considered loop lengths of one to thirteen bases. By varying the position of the bulged loop along the DNA duplex, we observe a symmetric signal variation with respect to the center of the strand. We reproduce the experimental results well using a molecular zipper model at thermal equilibrium. However, binding states between both strands, which emerge through duplex opening at the position of the bulged loop, need to be taken into account.ConclusionsWe show that stable DNA duplexes with a bulged loop can form from short strands of unequal length and they contribute substantially to the fluorescence intensity from the hybridized strands on a microarray. In order to reproduce the result with the help of equilibrium thermodynamics, it is essential (and to a good approximation sufficient) to consider duplex opening not only at the ends but also at the position of the bulged loop. Although the thermodynamic parameters used in this study are taken from hybridization experiments in solution, these parameters fit our DNA microarray data well.
Highlights
DNA is a carrier of biological information
While molecular simulations give a very detailed view of the molecular dynamics, here we are interested in a simple scheme to assess the stability of bulged loops on a DNA microarray
In this paper we investigated the stability of DNA with a bulged loop
Summary
The hybridization process, the formation of the DNA double-helix from single-strands with complementary sequences, is important for all living cells. The hybridization process - the formation of the wellknown double-helix structure from two complementary nucleic acid strands (such that A · T and C · G base pairs are formed) - is pivotal to the living organism. Among other important biotechnological methods, PCR or DNA microarray technology rely on it. DNA microarrays are widely used in biological and biotechnological applications, the underlying physical mechanisms of the hybridization process are poorly understood. While molecular simulations give a very detailed view of the molecular dynamics, here we are interested in a simple scheme to assess the stability of bulged loops on a DNA microarray. Systematic experiments on short bulged loops have hardly been performed
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