DNA as molecular lego brickpart 2: introduction to self-assembly

hariadi@dna.caltech.edu

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for a long time, we have been mostly rely on

TOP-DOWN fabrication to build our daily objects

example 1: balinese wood carving

in TOP-DOWN assembly:

the final product is smaller than the starting material

and there must be a constructor, such as the balinese sculptor

in the example shown above

contrary to most NON-LIVING objects,

LIVING MATERIAL assembles by itself from

smaller components

example: cells -> human

this process is commonly called as

SELF-ASSEMBLY

or

BOTTOM-UP ASSEMBLY

the macro-scale analogy of molecular self-assembly

is LEGO bricks that bounce around and form

elaborate structures by itself !!!

“do it yourself” self-assembly

the movie (1.4 MB) can be freely downloaded at

http://www.pnas.org/content/suppl/2007/12/05/0709489104.DC1/09489Movie1.mov

shaking a bottle containing of

magnetized lego brick

(3)

(1) initial state:

unordered system(2)

(4) product:

ordered structure

the movie (1.4 MB) can be freely downloaded at

http://www.pnas.org/content/suppl/2007/12/05/0709489104.DC1/09489Movie1.mov

“do it yourself” self-assembly

yellow components represents smaller subunit

magnet represents physical interactions between subunits

shaking represents thermal vibrations

shaking a bottle containing of

magnetized components

thermal energy grows increasingly important as we look

at smaller scale

using equipartition theorem, at room temperature

we, human, shakes at the speed of ～0.00000000001 m/sec

hydrogen atom shakes at the speed of ～100 m/sec; so

thermal energy MATTERS at small scale

molecular self assembly uses thermal energy to shake

its components

v !!

kBT

mfrom the equipartition theorem

where KB is boltzmann’s constant, T is temperature in kelvin, and m is mass

PRINCIPLES of self-assembly

1. larger structure is built from smaller subunits

2. there are some physical interactions between

subunits- the shape and physical interactions determine the final

structure

3. energy source is required for shaking the subunits.

- life utilizes thermal energy for its self-assembly

4. the process is random (Stochastic). - Subunit can attach or detach to other subunit or a larger

structure.

- Larger structures form and disassemble by themselves all

the times

Achievements of DNA nanotechnology

CatalystALGORITHMIC

SELF ASSEMBLYMolecularmachinesCIRCUITDNA origami

Next: DNA ORIGAMI