DNA as molecular lego brickpart 1: introduction to DNA

hariadi@dna.caltech.edu

me

the best way to reach me

lab website

my lab my university

do not print!

this modified presentation is designed to be viewed on screenprinting this document will waste a lot of ink

DNA = programmable engineering molecule

the MAIN message of my talk is ...

DNA = programmable engineering molecule

the best ?!V

the MAIN message of my talk is ...

People uses wood as engineering materialfor man-made constructions

utilization of BIOLOGICAL material for UNNATURAL purpose

is NOT a strange practice in our daily lives

example 1: wood

▲ tree furniture ▼

utilization of BIOLOGICAL material for UNNATURAL purpose

is NOT a strange practice in our daily lives

example 1: wood

similarly with silk

example 2: silk

▲ silkworm cocoon silk tie ▼

example 2: silk

James Watson Francis Crick

DNA has a 3D structure that you have to

know before you want to use it

distance between neighboring base pair

= 3.4 Å

1 full turn ~ 10.5 bp

diameter~ 20 Å

DNAdouble-helix

base pair

3’-AGTCTTCGAATGC-5’

5’-TCAGAAGCTTACG-3’

DNAbase pair

watson crick base pairs: A with T ; C with G

this is how dna stores information

3’-AGTCTTCGAATGC-5’

5’-TCAGAAGCTTACG-3’

DNA

base pair

most of the times, we use this restricted representation,

where horizontal line represents a base pair

DNA

in practice, we don’t even write the dna sequence

all we care is the strand complementarity

Chen and Seeman, Nature 350, 631 (1991)

note that DNA does not have to be

in a single long double helix form

single stranded DNA octahedron, William Shih, Harvard

another example of unnatural dna structures

shih, Quispe, joyce, nature 427, 618 (2004)

Why DNA?

• Historical perspective: RNA/DNA world is widely accepted as predecessor to our current protein world

• DNA is programmable

• Robust computational prediction for DNA structure, energetics, and kintetics is available.

• Easy to handle: spontaneous degradation for DNA is slow

• Cheap

• Superstructures can be made big enough for microscopy

the next few slides should make the idea of programming dna molecules clear

Designing DNA molecular complexesNadrian Seeman, 1980’s

let’s say

the OUTPUT of our molecular program

is this Y-shaped DNA structure

Designing DNA molecular complexesNadrian Seeman, 1980’s

GATTACA

CTAATGT

GATTACA

CTAATGTACTGGTG

TGACCAC

TGACCAC

ACTGGTG

TAGGCAG

ATCCGTC

ATCCGTC

TAGGCAG

one way to embed the program that

specify Y-shaped output is shown abovE

Yin et al, Nature 2008

Seeing is Believing! DNA superstructures can be made large enough for microscopy

i hope at this point you will have

sufficient background

to fully APPRECIATE the achievements

of dna nanotechnology

please take a look at the next part of my talk

Achievements of DNA nanotechnology

CatalystALGORITHMIC

SELF ASSEMBLYMolecularmachinesCIRCUITSTRUCTURES

Next ...