Towards autonomous DNA-based nanodevices [Elektronische Ressource] / vorgelegt von Tim Liedl

Tim Liedl

Sujets

• Biologie

Informations

• Publié par: ludwig-maximilians-universitat_munchen
• Publié le: 01 janvier 2007
• Nombre de lectures: 11
• Langue: English
• Poids de l'ouvrage: 18 Mo

Extrait

Towards autonomous DNA-based
Nanodevices
Tim Liedl
Mun¨ chen 2007Towards autonomous DNA-based
Nanodevices
Tim Liedl
Dissertation an der Fakult¨at fur¨ Physik
der Ludwig–Maximilians–Universit¨at
Munchen¨
vorgelegt von
Tim Liedl
aus Munch¨ en
Munchen,¨ den 4.4.2007Erstgutachter: PD Dr. F. C. Simmel
Zweitgutachter: Prof. Dr. J. O. R¨adler
Tag der mund¨ lichen Prufung:¨ 23.5.2007Contents
1 Introduction - DNA-based Nanodevices 1
1.1 DNA-based structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.2 devices (Ref. [1]) . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.3 Enzymatically driven DNA-based devices (Ref. [1]) . . . . . . . . . . . . . 4
2 Theoretical and Experimental Basics 7
2.1 Physical properties of DNA . . . . . . . . . . . . . . . . . . . . . . . . . . 7
2.2 Thermodynamics of DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
2.3 Characterization of DNA-based nanodevices . . . . . . . . . . . . . . . . . 11
2.3.1 Energy transfer between fluorophores . . . . . . . . . . . . . . . . . 11
2.3.2 Energy transfer near metal surfaces . . . . . . . . . . . . . . . . . . 13
3 Determination of DNA Melting Temperatures 15
3.1 DNA melting temperature determination by thermal denaturation . . . . . 15
3.2 DNA Melting temperature determination in chemical gradients (Ref. [2]) . 17
4 A DNA switch driven by a Chemical Oscillator 21
4.1 Non-equilibrium systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
4.2 Reaction di!usion processes . . . . . . . . . . . . . . . . . . . . . . . . . . 23
4.3 Oscillatory systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
4.4 pH-sensitive DNA devices . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
4.5 Switching the conformation of a DNA molecule with a chemical oscillator
(Ref.[3]) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
4.6 A surface-bound DNA switch driven by a chemical oscillator (Ref.[4]) . . . 32
4.7 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
5 Controlled Trapping and Release of Quantum Dots 35
5.1 Reversible hydrogels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
5.2 Fluorescent nanocrystals as colloidal probes in complex fluids (Ref. [5]) . . 38
5.3 DNA-crosslinked gels as programmable drug delivery system (Ref. [6]) . . 41
5.4 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
6 Glossary 47vi Inhaltsverzeichnis
Appendix 49
Determination of 1D di!usion constants . . . . . . . . . . . . . . . . . . . . . . 49
Reference [1] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53 [2] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Reference [3] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71 [4] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Reference [5] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93 [6] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Bibliography 106List of Figures
1.1 DNA cube . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.2 DNA tweezers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.3 Enzymatically driven DNA device . . . . . . . . . . . . . . . . . . . . . . . 5
2.1 DNA double helix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2.2 F¨ orster resonance energy transfer . . . . . . . . . . . . . . . . . . . . . . . 12
3.1 Melting behavior of DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
3.2 Formamide lowers T . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17M
3.3 Multilayer microfluidics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
3.4 DNA dissociation along a formamide gradient . . . . . . . . . . . . . . . . 19
3.5 Microfluidic for 2D gradients . . . . . . . . . . . . . . . . . . . . . . . . . . 20
4.1 Cell in non-equillibrium . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
4.2 Pattern formation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
4.3 Activator-substrate reaction . . . . . . . . . . . . . . . . . . . . . . . . . . 26
4.4 Predator-prey model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
4.5 Activatior-substrate reaction without di!usion . . . . . . . . . . . . . . . . 28
4.6 Belousov-Zhabotinsky reaction . . . . . . . . . . . . . . . . . . . . . . . . . 29
4.7 pH-dependent DNA devices . . . . . . . . . . . . . . . . . . . . . . . . . . 30
4.8 pH-Oscillator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
4.9 DNA tethered to gold islands . . . . . . . . . . . . . . . . . . . . . . . . . 33
5.1 Polyacrylamide network . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
5.2 Antigen responsive hydrogel . . . . . . . . . . . . . . . . . . . . . . . . . . 38
5.3 Fluorescent nanocrystals . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
5.4 Fluorescent correlation spectroscopy . . . . . . . . . . . . . . . . . . . . . . 40
5.5 Saturation of fluorophores . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
5.6 Acrydite . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
5.7 Gel crosslinking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
5.8 Trapped quantum dots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
5.9 Dissolution of a DNA crosslinked hydrogel . . . . . . . . . . . . . . . . . . 44
6.1 Particle displacement statistics . . . . . . . . . . . . . . . . . . . . . . . . . 50viii Abstract
Abstract
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 sys-
tems for nanoscale objects.
1. At low temperatures and under favorable bu!er 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 T of a DNA duplex isM
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 bu!er 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 di!usion
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. Di!erences 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 bu!er 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 exter-
nally applied programmable DNA signal strands. Trapping and release of the nanoparticles
is demonstrated by studying their di!usion 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, suchAbstract ix
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, poten-
tially disease-related DNA or RNA strands.x Zusammenfassung
Zusammenfassung
DNA, der Tr¨ager der Erbinformation, ist n