Towards autonomous DNA-based Nanodevices

Molecular recognition, programmability, self-assembling capabilites
and biocompatibility are unique features of DNA. The basic approach
of DNA nanotechnology is to exploit these properties in order to
fabricate novel materials and structures on the nanometer scale.
This cumulative dissertation deals with three aspects of this young
research area: fast analysis, autonomous control of functional
structures, and biocompatible autonomous delivery systems for
nanoscale objects. 1. At low temperatures and under favorable
buffer conditions, two complementary DNA strands will form a
double-helical structure in which the bases of the two strands are
paired according to the Watson-Crick rules: adenine bases bind with
thymine bases, guanine bases with cytosine bases. The melting
temperature TM of a DNA duplex is defined as the temperature at
which half of the double strands are separated into single strands.
The melting temperature can be calculated for DNA strands of known
sequences under standard conditions. However, it has to be
determined experimentally for strands of unknown sequences and for
applications under extreme buffer conditions. A method for fast and
reliable determination of DNA melting temperatures has been
developed. Stable gradients of the denaturing agent formamide were
generated by means of diffusion in a microfluidic setup. Formamide
lowers the melting temperature of DNA and a given formamide
concentration can be mapped to a corresponding virtual temperature
along the formamide gradient. Differences in the length of
complementary sequences of only one nucleotide as well as a single
nucleotide mismatch can be detected with this method, which is of
great interest for the detection of sequence mutations or
variations such as single nucleotide polymorphisms (SNPs). 2.
Knowledge of the stability of DNA duplexes is also of great
importance for the construction of DNA-based nanostructures and
devices. Conformational changes occuring in artificially generated
DNA structures can be used to produce motion on the nanometer
scale. Usually, DNA devices are driven by the manual addition of
fuel molecules or by the periodic variation of buffer conditions.
One prominent example of such a conformational change is the
formation of the so-called i-motif, which is a folded four-stranded
DNA structure characterized by noncanonical hemiprotonated
cytosine-cytosine base-pairs. In order to achieve controlled
autonomous motion, the oscillating pH-value of a chemical
oscillator has been employed to drive the i-motif periodically
through its conformational states. The experiments were conducted
with the DNA switch in solution and attached to a solid substrate
and constitute the first example of DNA-based devices driven
autonomously by a chemical non-equilibrium reaction. 3. Finally, a
DNA-crosslinked and switchable polyacrylamide hydrogel is
introduced, which is used to trap and release fluorescent colloidal
quantum dots in response to externally applied programmable DNA
signal strands. Trapping and release of the nanoparticles is
demonstrated by studying their diffusion properties using single
molecule fluorescence microscopy, single particle tracking and
fluorescence correlation spectroscopy. Due to the biocompatibility
of the polymerized acrylamide and the crosslinking DNA strands,
such gels could find application in the context of controlled drug
delivery, where the autonomous release of a drug-carrying
nanoparticle could be triggered by naturally occurring, potentially
disease-related DNA or RNA strands.