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1 Synthesis and Characterization of Self-Assembled DNA Nanostructures&Chenxiang Lin,Yonggang Ke,Rahul Chhabra,Jaswinder Sharma,Yan Liu,and Hao Yan 1

2 Protocols for Self-Assembly and Imaging of DNA Nanostructures&Thomas L.Sobey and Friedrich C.Simmel 13

3 Self-Assembly of Metal-DNA Triangles and DNA Nanotubes with Synthetic Junctions&Hua Yang,Pik Kwan Lo,Christopher K.McLaughlin,Graham D.Hamblin,Faisal A.Aldaye,and Hanadi F.Sleiman 33

4 DNA-Templated Pd Conductive Metallic Nanowires&Khoa Nguyen,Stephane Campidelli,and Arianna Filoramo 49

5 A Method to Map Spatiotemporal pH Changes Inside Living Cells Using a pH-Triggered DNA Nanoswitch&Souvik Modi and Yamuna Krishnan 61

6 Control of Helical Handedness in DNA and PNA Nanostructures&Roberto Corradini,Tullia Tedeschi,Stefano Sforza,Mark M.Green,and Rosangela Marchelli 79

7 G-Quartet,G-Quadruplex,and G-Wire Regulated by Chemical Stimuli&Daisuke Miyoshi and Naoki Sugimoto 93

8 Preparation and Atomic Force Microscopy of Quadruplex DNA&James Vesenka 105

9 Synthesis of Long DNA-Based Nanowires&Alexander Kotlyar 115

10 G-Wire Synthesis and Modification with Gold Nanoparticle&Christian Leiterer,Andrea Csaki,and Wolfgang Fritzsche 141

11 Preparation of DNA Nanostructures with Repetitive Binding Motifs by Rolling Circle Amplification&Edda Reiβ,Ralph H？lzel,and Frank F.Bier 151

12 Controlled Confinement of DNA at the Nanoscale:Nanofabrication and Surface Bio-Functionalization&Matteo Palma,Justin J.Abramson,Alon A.Gorodetsky,Colin Nuckolls,Michael P.Sheetz,Shalom J.Wind,and James Hone 169

13 Templated Assembly of DNA Origami Gold Nanoparticle Arrays on Lithographically Patterned Surfaces&Albert M.Hung and Jennifer N.Cha 187

14 DNA-Modified Single Crystal and Nanoporous Silicon&Andrew Houlton,Bernard A.Connolly,Andrew R.Pike,and Benjamin R.Horrocks 199

15 The Atomic Force Microscopy as a Lithographic Tool:Nanografting of DNA Nanostructures for Biosensing Applications&Matteo Castronovo and Denis Scaini 209

16 Trapping and Immobilization of DNA Molecules Between Nanoelectrodes&Anton Kuzyk,J.Jussi Toppari,and P？ivi T？rm？ 223

17 DNA Contour Length Measurements as a Tool for the Structural Analysis of DNA and Nucleoprotein Complexes&Claudio Rivetti 235

18 DNA Molecular Handles for Single-Molecule Protein-Folding Studies by Optical Tweezers&Ciro Cecconi,Elizabeth A.Shank,Susan Marqusee,and Carlos Bustamante 255

19 Optimal Practices for Surface-Tethered Single Molecule Total Internal Reflection Fluorescence Resonance Energy Transfer Analysis&Matt V.Fagerburg and Sanford H.Leuba 273

20 Engineering Mononucleosomes for Single-Pair FRET Experiments&Wiepke J.A.Koopmans,Ruth Buning,and John van Noort 291

21 Measuring DNA-Protein Binding Affinity on a Single Molecule Using Optical Tweezers&Micah J.McCauley and Mark C.Williams 305

22 Modeling Nanopores for Sequencing DNA&Jeffrey R.Comer,David B.Wells,and Aleksei Aksimentiev 317

Index 359