Functional synthetic DNA nanostructures:
Gespeichert in:
| 1. Verfasser: | |
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| Format: | Abschlussarbeit Buch |
| Sprache: | English |
| Veröffentlicht: |
2014
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| Schlagworte: | |
| Online-Zugang: | kostenfrei https://nbn-resolving.org/urn:nbn:de:bvb:91-diss-20140207-1184338-0-0 Inhaltsverzeichnis |
| Beschreibung: | XV, 198 S. Ill., graph. Darst. |
Internformat
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| 245 | 1 | 0 | |a Functional synthetic DNA nanostructures |c Thomas Gerhard Martin |
| 264 | 1 | |c 2014 | |
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Datensatz im Suchindex
| _version_ | 1804151882530160640 |
|---|---|
| adam_text | CONTENTS
ABSTRACT XI
INTRODUCTION XIII
1. THEORETICAL BACKGROUND 1
1.1. DEOXYRIBONUCLEIC ACID (DNA) 1
1.1.1. DNA STRUCTURE 1
1.1.2. THERMODYNAMICS OF DOUBLE-STRANDED DNA 5
1.1.3. DOUBLE-STRANDED DNA AS A SECONDARY STRUCTURE UNIT 6
1.2. SELF-ASSEMBLED DNA NANOSTRUCTURES 7
1.2.1. DESIGN OF SCAFFOLDED DNA NANOSTRUCTURES 9
1.2.2. OPTIMIZATIONS CONCERNING SCAFFOLDED DNA NANOSTRUCTURES 14
1.3. ANALYTICAL METHODS FOR DNA NANOSTRUCTURES 14
1.3.1. GEL ELECTROPHORESIS 15
1.3.2. TRANSMISSION ELECTRON MICROSCOPY (TEM) 16
1.3.3. CLASS AVERAGING 18
1.4. NANOPORE SENSING 19
2. CRYO-EM STRUCTURE OF A 3D DNA-ORIGAMI OBJECT 21
2.1. MOLECULAR SELF-ASSEMBLY WITH DNA 21
2.2. DNA-TEMPLATED DESIGN AND SYNTHESIS 22
2.3. CRYO-EM SINGLE-PARTICLE ANALYSIS AND MODEL GENERATION 23
2.4. ANALYSIS OF STRUCTURAL FEATURES 23
2.5. PREVIOUSLY UNOBSERVED DNA TOPOLOGIES 26
2.6. USING CRYO-EM FEEDBACK TO OPTIMIZE DNA OBJECT DESIGN 27
2.7. CONCLUSIONS 29
3. DNA ORIGAMI GATEKEEPERS FOR SOLID STATE NANO PORES 31
3.1. DNA NANOTECHNOLOGY AND SOLID-STATE NANOPORES 31
3.2. DNA-BASED NANOPLATES FOR SOLID-STATE NANOPORES 31
3.3. DNA NANOPLATES AS GATEKEEPERS 35
3.4. CONCLUSION 37
4. DNA ORIGAMI CHANNELS FOR LIPID BILAYERS 39
4.1. RELEVANCE OF TRANSMEMBRANE CHANNELS 39
4.2. GEOMETRY OF DNA CHANNELS 39
4.3. CHOLESTEROL DEPENDENT VESICLE INTERACTIONS 41
4.4. TEM BASED EVIDENCE FOR MEMBRANE INCORPORATION 43
4.5. ELECTROPHYSIOLOGY 45
4.6. DESIGN IMPROVEMENTS BASED ON EXPERIMENTAL RESULTS 49
I
HTTP://D-NB.INFO/104926312X
CONTENTS
4.6.1. ADJUSTABLE STEM AND VESTIBULAR AREA 50
4.6.2. INCREASED NUMBER OF CHOLESTEROL ANCHORS 52
4.7. CONCLUSION 53
5. MOLECULAR TOMOGRAPHY FOR ELECTRON MICROSCOPY 55
5.1. SCIENTIFIC RELEVANCE OF POSITIONAL CONSTRAINS 55
5.2. FUNCTIONAL PRINCIPLE AND DESIGN REALIZATION 56
5.3. TAL EFFECTOR PROTEIN AS TARGET STRUCTURE 59
5.4. DESIGN FEATURES OF THE DNA SUPPORT 60
5.5. EXPECTED ANGULAR FLUCTUATIONS 60
5.6. SCAFFOLD PERMUTATION DETERMINATION 62
5.7. DESIGN OF A CLOSED STRUCTURE WITH 90 CORNERS 62
5.8. ANNEALING REACTION AND PURIFICATION 65
5.9. ATTACHMENT OF THE TILT AXIS 66
5.10. PROOF OF CONCEPT: MOLECULAR TOMOGRAPHY 67
5.11. CONCLUSION 68
6. OUTLOOK AND CONCLUSIONS 71
APPENDICES 75
A. SELF-ASSEMBLY OF DNA NANOSTRUCTURES 77
A.L. PARAMETERS INFLUENCING THE ASSEMBLY PROCESS 77
A.2. OPTIMIZED THERMAL ANNEALING REACTIONS 77
A.3. SCAFFOLD AND STAPLE CONCENTRATIONS 81
A.4. CONCLUSION 82
A.5. TEMPERATURE DEPENDENT SECONDARY STRUCTURE OF THE SCAFFOLD 83
B. PURIFICATION METHODS 85
B.L. THE NEED FOR PURIFICATION 85
B.2. GEL ELECTROPHORESIS 85
B.3. SPIN COLUMN FILTRATION 88
B.4. POLYETHYLENE GLYCOL (PEG) PRECIPITATION 89
B.4.1. OPTIMAL PRECIPITATION CONDITIONS 90
B.4.2. AGGREGATION AND YIELD 92
B.4.3. PEG PRECIPITATION CONCLUSION 93
B.5. PURIFICATION METHOD COMPARISON 93
B.6. CONCLUSION 93
B.7. MATERIALS & METHODS 95
B.7.1. ABSORBANCE MEASUREMENTS TO DETERMINE DNA CONCENTRATIONS ... 95
B.7.2. DETERMINATION OF AN ABSORBANCE REFERENCE 97
B.7.3. GEL ELECTROPHORESIS 99
B.7.4. PEG PRECIPITATION 99
B.7.5. ABSORBANCE MEASUREMENTS 100
B.7.6. GEL ELECTROPHORESIS 100
B.7.7. ADDITIONAL PURIFICATION PROTOCOLS 103
B.7.8. GEL PURIFICATION 103
II
CONTENTS
C. MAGNESIUM FREE FOLDING 105
C.L. MAGNESIUM IN DNA NANOTECHNOLOGY 105
C.2. SELF ASSEMBLY IN THE PRESENCE OF EITHER MAGNESIUM OR SODIUM 106
C.3. SHAPE- AND DESIGN-SPECIFIC SODIUM REQUIREMENTS 108
C.4. A MEASURE FOR DESIGN QUALITY ILL
C.5. CONCLUSION 112
C.6. UNPUBLISHED SUPPORTING MATERIAL 113
D. POST FOLDING SALT INFLUENCE ON THE LONG TERM STABILITY OF DNA NANOS-
TRUCTURES 117
D.L. IMPORTANCE OF POST FOLDING STABILITY 117
D.2. LONG TERM STABILITY 117
D.3. CONCLUSION 120
D.4. TEM LIBRARIES 120
E. SUPPORTING MATERIAL: CRYO-EM STRUCTURE OF A 3D DNA-ORIGAMI OBJECT 133
E.L. MATERIALS AND METHODS 133
E.L.L. DNA-TEMPLATED DESIGN AND SYNTHESIS 133
E.1.2. ELECTRON CRYO-MICROSCOPY 133
E.1.3. IMAGE PROCESSING 133
E.L.4. MODEL BUILDING 134
E.2. SUPPLEMENT 135
E.2.1. ESTIMATION OF THE INTRINSIC VARIABILITY OF THE STRUCTURE 135
E.2.2. SUPPORTING FIGURES 135
F. SUPPORTING MATERIAL: DNA ORIGAMI CHANNELS FOR LIPID BILAYERS 151
F.L. CLASS AVERAGE LIBRARIES 151
F.2. CADNANO DESIGN DIAGRAMS AND STAPLE SEQUENCES 157
G. SUPPORTING MATERIAL: MOLECULAR TOMOGRAPHY FOR ELECTRON MICROSCOPY 163
G.L. ANGLED TILT AXIS ATTACHMENT 163
G.2. MATERIALS AND METHODS 164
G.2.1. NEGATIVE STAINING PROTOCOL 164
G.2.2. URANYL FORMATE STAIN 164
G.2.3. THERMAL ANNEALING PROTOCOLS 165
G.3. PARTICLE LIBRARIES 165
G.4. CADNANO DESIGN DIAGRAMS AND STAPLE SEQUENCES 177
G.5. TAL EFFECTOR PROTEIN AMINO ACID SEQUENCE 183
BIBLIOGRAPHY 184
III
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| spelling | Martin, Thomas Gerhard Verfasser aut Functional synthetic DNA nanostructures Thomas Gerhard Martin 2014 XV, 198 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier München, Techn. Univ., Diss., 2014 (DE-588)4113937-9 Hochschulschrift gnd-content Erscheint auch als Online-Ausgabe urn:nbn:de:bvb:91-diss-20140207-1184338-0-0 http://mediatum.ub.tum.de/node?id=1184338 Verlag kostenfrei Volltext https://nbn-resolving.org/urn:nbn:de:bvb:91-diss-20140207-1184338-0-0 Resolving-System DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=027093734&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Martin, Thomas Gerhard Functional synthetic DNA nanostructures |
| subject_GND | (DE-588)4113937-9 |
| title | Functional synthetic DNA nanostructures |
| title_auth | Functional synthetic DNA nanostructures |
| title_exact_search | Functional synthetic DNA nanostructures |
| title_full | Functional synthetic DNA nanostructures Thomas Gerhard Martin |
| title_fullStr | Functional synthetic DNA nanostructures Thomas Gerhard Martin |
| title_full_unstemmed | Functional synthetic DNA nanostructures Thomas Gerhard Martin |
| title_short | Functional synthetic DNA nanostructures |
| title_sort | functional synthetic dna nanostructures |
| topic_facet | Hochschulschrift |
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