Class 

Date 

Topics 

& Primary

Lecture

Notes

Required Reading

Secondary Lecture

Notes

 Student

Handouts 

Tues

Aug 28

Course Overview

Overview of DNA Nanostructures [PDF] [PPT]

Overview of DNA Robotics [PDF] [PPT]

Thurs

Aug 30

Overview of DNA structure

- DNA Overview

- dsDNA secondary and tertiary structure

- Base Stacking

- DNA Hybridization & Duplex DNA

-B, A, and Z form DNA

- DNA Structure Transitions: DNA B-Z transitions

Nonstandard DNA structures:

- DNA Triplex Conformations

- G Quadra-Complexes

Properties of dsDNA

- dsDNA Mechanical Properties

- Dependence on temperature, salinity, magnesium,

- crowding molecules

DNA Hybridization Reactions

- Hybridization reactions

- Toehold binding & Strand displacement

- Base stacking

Overview of DNA Structure :

Introduction to DNA Structure [PDF] [PPT.ZIP]

Video of DNA Structure

 Overview of DNA structure:

DNA Hridization and DNA Nanostructures

[DNA Structure: Lavery]

[DNAstucture: pharmacy.umn]

DNA Structure Transitions:

[DuplexTriplexTransition: Mao]

[B-Z.Transition: Mao]

DNA Mechanics:

[MechanicsofDNA:Bustamante]

Sudhansu 

Tues

Sept 4

Kinetics Modeling

- Introduction to Kinetics

- Stochastic Chemical Reaction Networks

- Kinetic Models of DNA Hybridization Reactions

- Kinetic Models of DNA Enzymic Reactions

- Kinetics simulation methods

- Probabilistic Model Checking & PRISM software

Primary Chemical Reaction Kinetics Lecture:

KineticsOverview: [PDF] [PPT]

Optional Chemical Reaction Kinetics Lectures:

Bookstaver: [PDF] [PPT]

Chieh: [PDF] [PPT]

Reid: [PDF] [PPT]

Optional Chemical Reaction Kinetics Lectures Applied to Biochemical Networks:

Schnell: [PDF] [PPT]

El-Samad: [PDF] [PPT]

Detailed Reading on Kinetics:

Vallance: [PDF]

Other Suggested Text Books

P. W. Atkins, Physical Chemistry

M. J. Pilling and P. W. Seakins, Reaction Kinetics,

K. J. Laidler, Chemical Kinetics

B. G. Cox, Modern Liquid Phase Kinetics,

Nikhil

Thurs

Sept 6

Thermodynamics and Kinetic Simulation of DNA Nanostuctures

Introduction to Kinetic Simulation of DNA Nanostructures (Nikhil) [PDF] [PPT]

Required Reading:

Kinetic Simulation o0f DNA Nanostructures:

Schaeffer Master Thesis: Stochastic Simulation of the Kinetics of Multiple Interacting DNA Strands

Reference Papers:

Reference Papers on DNA Thermodynamics & Kinetics

DNA Systems Modeling:

[DNAModeller: Sudheer]

Nikhil

Tues

Sept 11

DNA Nanostructures

DNA Tiles

- DNA crossovers junctions: Holliday junctions

- T-junctions

- DNA DX, TX tiles

- Crossover (4 x 4 and Mao's) and Double Decker Tiles

- Hexagonal Tiles

- other novel tile typesHao's Grid-tiles

- mult-arm tiles

DNA Lattices & Tubes

- 2D DNA lattices

- corregation methods to flatten assembly

- DNA Tubes

- Hao's work on Chirality of DNA Tubes

- 3D DNA lattices

Seeman's tensegrity tiles & lattices

DNA Nanostructures

[DNA Nanostructures: Reif]

Tiles via DNA Nanostructures

[DNA Nanostructures: Reif]

Sudhanshu

Makeup: Tues, Oct 9

DNA Origami

- 2D DNA Origami

- 3D DNA Origami

- Origami design software

DNA Origami

[PDF] [PPTX]

DNA Origami Primer [PDF]

DNA Origami Rothemund Supplemental

3D DNA Origami - Shi

caDNAno Design Software for DNA Origami - Shi

3D DNA Origami Gridion - Han

Cadnano Tool Design DNA Origami [PDF]

Reeme

Makeup:

Software for DNA nanostructures

-CADnano

- other software

Coarse-Grain Modeling of DNA Nanostrctures: Graph & Cartoon Models

- Cartoon models of DNA

- Graph models for DNA and reactions

Graph Grammars for DNA reactions

Reeme

Thurs

Sept 13

Theory of CRNs

Introduction to Theory of CRNs (Nikhil) [PDF] [PPT]

Deterministic Function Computation with CRNs(Nikhil) [PDF]

Required Reading:

Papers on Theory of CRNs:

Deterministic Function Computation with Chemical Reaction Networks

Computation with finite stochastic chemical reaction networks

  Secondary Readings:

Shin Master Thesis: Compiling and Verifying DNA-Based Chemical Reaction Network Implementations

Programmability of Chemical Reaction Networks

DNA as a universal substrate for chemical kinetics

Computational Complexity Chemical Reaction Networks:

[Complexity Chemical Reaction Networks: Bruck]

[Complexity Stochastic Chemical Reaction Networks: Bruck]

Nikhil

Thurs

Sept 20

DNA Photonics

- Fluorescent labels

- Fluorescence resonance energy transfer (FRET)

- Quantum dots

- Optically-induced cutting of DNA

 DNA Photonics (Hieu) [PDF] [PPTX]

Hieu

Make up:

4:30 Mon

Oct 8

DNA Enzyme reactions:

- Ligation,

- Restriction enzymes

- Helicase enzymes

- Polymerization & Strand-displacing polymerases

DNA Enzyme Reactions (Hieu) [PDF] [PPTX]

Hieu & Sudhanshu

Tues

Oct 2

&

4:30

Tues

Oct 2

Overview of Theoretical Tile Assembly Models:

Wang tiling

Abstract tile assembly model (TAM)

Reversible tile assembly model

Kinetic tile assembly model (KTAM)

Staged tile assembly: Step-wise tile assembly model

Hierarchical tile assembly model Temperature Programmed Tiling: The multiple temperature tile assembly model

The q-tile tile assembly model

The flexible glue tile assembly model

Time-dependent glue tile assembly model

The unique shape tile assembly model

Invadable assembly model

Other models

Overview of Tile Assembly Models (Tianqi Song) [PDF] [PPTX]

 Survey of Tile Assembly Models (Patitz) [PDF]

  Wang tiling

-Tiling Computability

[Undecidability Tiling: Robinson]

[Complexity Assembly: Winfree]

 - Kinetic Model of Assembly:

[Simulations of Tiling Assembly: Winfree]

Tanqui 

Extra Short Lecture

4:30 pm

Tues

Oct 2

Tiling Computability of Tile Assembly Models

Required Reading:

[Complexity Assembly: Winfree]

Undecidability Tiling Assembly Models

Undecidability Wang tiling

[Undecidability Tiling: Robinson]

Undecidability aTAM

[Complexity Assembly: Winfree]

NP completeness of tiling on N x N square

[Garey, Johnson, Papadimitrou, 1977]

Tanqui 

Thurs

Oct 4

Tile Complexity of Deterministic Assembled Shapes

- Tile Complexity of Assembled Squares

- Exact Squares

- Approx Square

-Linear Structures

 Tile Complexity of Assembly of Squares and Linear Structures [PPT] [PDF]

Required Reading:

-Deterministic Tile Complexity Assembled Squares

[Tile Complexity Assembled Squares: Rothemund]

-

 -Deterministic Tile Complexity Assembled Squares

[Tile Complexity Assembled Squares: Rothemund]

Exact Det. Tile Complexity of Squares: [Tile Complexity Assembled Squares: Adleman]

 - Approximate Squares [Assembly of Approx Square Tilings Chandran]

 -Randomized 1D Assembly

[Tile Complexity of Linear Assemblies: Chandran] [PPT] [PDF]

Makeup: Tues

Oct 9

Advanced DNA Origami

Advanced DNA Origami [PDF] [PPTX]

Thurs

Oct 11

Alternative Tiling Assembly Models:

Modified Glue Models for Tiling Assembly

Tile Complexity of Temperature Programmed Assembly

Staged Assembly & Hierarchical Assembly

Alternative Tile Assembly Models (Tianqi Song) [PDF] [PPTX]

Required Reading:

   Survey of Tile Assembly Models (Patitz) [PDF]

  -Modified Glue Models for Tiling Assembly:

[Models Self Assembly: Aggarwal]

Self-Assembly Model of Time-Dependent Glue Strength Sahi [PPT]

-Staged Assembly

[Reif]

[Staged Assembly O(1) glues: Demaine]

- Temp Programmed Assembly

[Temp Programmed Assembly: Kao]

  Tanqui 

Tues

Oct 16

No Class - Fall BREAK

 Tues

Oct 23

Assembly Error-Correction     

- Assembly Error-Correction via Proofreading

- Compact Assembly Error-Correction:

- Error-Correction Lower Bounds

- Self-Healing

- Invadable Self-Assembly

- Reversible Selfrepair

Overveiw of Assembly Error-Correction via Proofreading & Snaking [PDF] [PPT]

Required Reading:

  Assembly Error-Correction via Proofreading:

[Proofreading Tile Sets: Winfree]

- Compact Assembly Error-Correction:

[Compact Error Resilient Assembliy: Reif]

Reducing Facet Nucleation

Via Snaked Proofreading:

[Error Correction Assembly: Goel]

- Assembly Error-Correction via Proofreading:

[Proofreading Tile Sets: Winfree]

[Compact Proofreading: Zhang Winfree]

- Compact Assembly Error-Correction:

[Compact Error Resilient Assembliy: Reif] Talk: [PDF] [PPT]

[Limits to Errorcorrection: Sahu] Talk: [PPT]

 Assembly Error-Correction:

Reducing Facet Nucleation

Via Snaked Proofreading:

[Error Correction Assembly: Goel]

PPT: [Error Correction Assembly: Goel PPT]

[Reducing Facet Nucleation Assembly Errors: Winfree]

Self-Healing:

[Self-HealingTilings: Winfree]

[Invadable Self-Assembly: Chen]

[Reversible Selfrepair: Majumder]

Possible extra lecture

Tile Complexity of General Shapes

Tile Complexity of Randomized Assembly

- Exact Shapes

- Approx Shape

-Linear Structure

 Assembling Shapes

Deterministic Tile Complexity of Assembling Shapes:

[Complexity Assembled Shapes: Winfree]

[Assembling Shapes: Becker]

 -Randomized Tile Complexity of Assembling Shapes:

[Randomized Assembly Exact Shapes: Doty]

[Randomized Assembly Approx Shapes: Schellerr]

Possible extra lecture

Tiles with State Changes:

[Error Suppression Self-assembly: Fujibayashi]

Activatable Tiles for Compact Error-Resilient Directional Assembly [Harish et al]

[PDF]. Talk: [PPT]

Thurs

Oct 25

DNA Computation using Polymerase

- Autonomous DNA Computation via Polymerase Reactions: Whiplash PCR

- Isothermal Whiplash

Whiplash PCR Overview [PPT] [PDF]

 Required Reading:

[Whiplash PCR: Winfree]

[Isothermal Whiplash PCR: Reif] [PPT] [PDF]

DNA Computation s using Polymerase:

- Autonomous DNA  Computation via Polymerase Reactions: Whiplash PCR

[Whiplash PCR: Winfree]

[Simulating Whiplash PCR: Hagiya]

[Isothermal Whiplash PCR: Reif] [PPT] [PDF]

Tues

Oct 30

DNA Computation

Autonomous DNA Computation using Restriction Enzymes

- Shapiro's FSA Computations

DNA Computation using DNAzyme

- Yin's Devices

DNA Autonomous Computation using Restriction Enzymes:

- Autonomous DNA  Computation via Restriction Enzyme Reactions

Overview of Enzymic Molecular FSA Shapiro [PPT] [PDF]

Computation using DNAzyme

[DNAzyme Computation: Reif PPT]

 Required Reading:

DNA Autonomous Computation using Restriction Enzymes:

- Autonomous DNA  Computation via Restriction Enzyme Reactions

[FSA Computation: Shapiro Nature 2001 PPT]

[More FSA Computation: Shapiro PNAS 2003 PPT]

[Stochastic FSA Computation: Shapiro PNAS 2004]

[DNA Doctor: Shapiro Nature 2004 FIGS]

[DNA Doctor: Shapiro Nature 2004]

Computation using DNAzyme

[DNAzyme Computation: Reif]

Thurs

Nov 1

Molecular Computation via DNA hybridization:

Adleman’s Experiment

Autonomous DNA Computation using DNA Hairpins

- Seelig's Catalyzed Metastable DNA Fuel

- Turberfield's DNA Hairpin Fueling Devices

- Winfree's DNA Hairpin Hybridization

Molecular Computation via DNA hybridization(Sudhanshu): [PPTX][PDF]

Required Reading

Molecular Computation via DNA Hybridization:

DNA Hairpins Fueling Autocatalytic Reactions:

[Catalyzed Metastable DNA Fuel: Seelig]

[DNA Hairpin Fueling Devices: Turberfield]

[DNA Hairpin Hybridization Circuits: Winfree]

Sudhanshu

Tues

Nov 6

DNA Reaction Networks Fueled by Strand Displacement

- Winfree's Seesaw Gates

- Yurke's DNA Catalytic Cascades

- Zhang's DNA Reaction Networks and Allosteric DNA Catalytic Reactions

- Soloveichi's DNA Chemical Kinetics

- Cardelli's DNA Strand Algebracuits

DNA Reaction Networks Fueled by Strand Displacement(HieuBui): [PPTX][PDF]

DNA Reaction Networks Fueled by Strand Displacement:

[Seesaw Gates: Winfree]

[DNA Catalytic Cascades: Yurke Slides]

 [DNA Reaction Networks: Zhang]

Hieu (aided Sudhanshu)

Thurs

Nov 8

DNA Reaction Networks Fueled by Strand Displacement. cont

DNA Reaction Networks Fueled by Strand Displacement(HieuBui): [PPTX][PDF]

[Allosteric DNA Catalytic Reactions: Zhang]

[DNA Chemical Kinetics: Soloveichik]

[DNA Catalytic Reactions: Zhang]

Tues

Nov 13

DNA Strand Algebra

DNA Strand Algebra(Cardelli) Talk:

[PDF]

DNA Strand Algebra(Cardelli) Paper:

[PDF]

Extra Material to presented in Makeup

Autocatalytic Hybridization Reactions for Detection:

- Pierce's Hybridization Chain Reaction

- Other Autocatalytic Hybridization Chain Reactions

  Required Reading:

Autocatalytic Hybridization Reactions for Detection:

[Hybridization Chain Reaction: Pierce]

 Tanqui (aided by Hieu & Sudhanshu)

Thurs

Nov 15

Intro to DNA Robotics: Natural & Re-Engineered Protein Molecular Motors

- Molecular Robotics Principals

- Brownian Ratchets & Quantum Ratchets

- Natural Protein Molecular Motors: Polymerase, Myosin, Kinesin, Polymerase

- Re-Engineered Protein Molecular

 Molecular Ratchets for Protein Molecular Motors (Mokhtar) [PDF] [PPTX]

  Required Reading:

Intro to DNA Robotics: Natural Protein Molecular Motors

-Molecular Ratchets:

[Brownian Ratchet Motors: Elmer]

[Feynman Notes V1 Ch46: Ratchet & Pawl]

[Overviews of Brownian Ratchets]

[Biophysics of Brownian Ratchets: PPT]

[More Slides on Brownian Ratchets]

Examples: Myosin & Kinesin

[Examples of Molecular Ratchets]

[Mechanics Kinesin: Cross]

-Quantum Ratchets

[Quantum Ratchets]

Surveys:

[Synthetic Molecular Motors Survey: Zerbetto]

  Reeme

Extra material

DNA Robotics via External State Changes:

- Yurke-Tuberfield DNA Tweezers

- DNA Nanostructure Actuation using DNA B-Z transitions

- PX Nanomechanical Devices

- DNA Robotics using Duplex to Triplex Transitions

- DNA Walkers using external state changes          

  Overview of Molecular Motors (Mokhtar) [PDF] [PPTX]

Required Reading:

DNA Robotics via External State Changes:

-DNA Nanostructure Actuation using DNA B-Z transitions

[PX Nanomechanical Devi: Seeman & Yan]

Duplex to Triplex Transitions

[DuplexTriplexTransition: Mao]

Yurke-Turberfield DNA Tweezers

[DNA Tweezer: Yurke & Tuberfield]

[DNA Tweezer: Step 1]

[DNA Tweezer: Step 2]

[DNA Tweezer: Step 3]

 Further Reading:

DNA Walkers using external state changes:

[DNA Biped Walking Device: Sherman&Seeman]

[DNA Walker: Pierce]

[DNA Walkers Survey: Kelly]

  Reeme (aided by Sudhanshu)

Tues

Nov 20

DNA Computation & Robotics using Enzymes:

DNA Computation & Robotics using Polymerase:

- Autonomous DNA  Computation via Polymerase Reactions: Whiplash PCR

-- DNA  Robotics via Polymerase

  -- DNA  Robotics via Polymerase

[Polymerase DNA Transport: Sahu]

Required Reading:

DNA Computation & Robotics using Enzymes:

-- DNA  Robotics via Polymerase

[Polymerase DNA Transport: Sahu]

   Reeme (aided by Hieu)

  Tues

Nov 27

DNA Autonomous Computation & Robotics using Restriction Enzymes:

- Autonomous DNA  Computation via Restriction Enzyme Reactions

- Autonomous Molecular Robotics using Restriction Enzyme Reactions  

   Required Reading:

  - Autonomous Molecular Robotics using Restriction Enzyme Reactions 

Yin  Reif Restriction Enzyme DNA Walker:

[Restriction Enzyme DNA Walker Design: Yin]

[Restriction Enzyme DNA Walker Experiments: Yin]

[Restriction Enzyme DNA Walker Paper: Yin]

[Restriction Enzyme DNA Walker Turing Computation: Yin]

Further Restriction Enzyme DNA Walkers

[Restriction Enzyme DNA Walker: Turberfield]

[Restriction Enzyme DNA Walker: Yamamura]

Sudhanshu

  Extra material

DNA Robotics using DNAzymes:

- Spiders: Autonomous Molecular Robotics using DNAzyme 

   Required Reading: 

DNARobotics using DNAzymes:

[DNAzyme Nanomotor: Mao]

[Improved DNAzyme Motor: Klavins]

[DNAzyme Walker: Mao]

- Spiders: Autonomous Molecular Robotics using DNAzymes: 

[DNAzyme Spiders: Stojanovic]

[DNAzyme Spiders: Stojanovic PPT]

Further Reading:

 - Autonomous Molecular Computation via DNAzyme  Reactions

[DNAzyme Computation: Stojanovic]

  Reeme (aided by Hieu)

Thurs

Nov 29

DNA Robotics via DNA Hybridization:

- Autonomous

Molecular Walkers using DNA hybridization

- Turberfield's Autonomous DNA Walker:

- Seeman's Piped Walker

- Molecular Assembly Lines and Reaction Factories

 Required Reading: 

  DNA Robotics via DNA Hybridization:

- Autonomous

Molecular Motors & Walkers using Hybridization Reactions

[DNA motor: Pierce]

[Autonomous DNA Walker: Turberfield]

[Piped Walker: Seeman Slides]

[Piped Walker: Seeman]

Molecular Gears

[Molecular Gears: Mao]

  Reeme (aided by Sudhanshu)

Dec 16

FINAL PROJECTS DUE