Do It Your-Self-Assembly ................................................................ 1
Overview ................................................................................... 1
Brief Background Information .................................................. 3
Activity 1: Molecular Do-Si-Do ....................................................... 4
Overview ................................................................................... 4
Game 1 ...................................................................................... 4
Game 2 ...................................................................................... 5
Activity 2: Shake and Make; Charge Recognition .......................... 8
Overview ................................................................................... 8
Setup ......................................................................................... 8
Procedure .................................................................................. 8
Links and References .............................................................. 10
Activity 3: 3D-tection; Molecular Shape Recognition ................... 11
Overview ................................................................................. 11
Setup ....................................................................................... 11
Procedure ................................................................................ 11
Extended Background Information for Teachers.................... 14
Vocabulary .............................................................................. 15
Links and References .............................................................. 16
6th - 8th Grade
The following is a series of three activities that illustrate the
requirements of molecular recognition. Altogether, the activities
require three 50-minute class periods to complete. All of the
activities involve group work.
Self-assembly is a process by which molecules recognize each
other and stick together.
Molecules that stick together during self-assembly may form
themselves into specific, ordered structures under the right
conditions.
Nano is very, very small.
Self-assembly can be used by scientists to create objects on the
nano-scale.
Researchers in the field of nanotechnology are studying selfassembly and molecular recognition in order to create new
materials and technologies.
Confusion about bonding, chemical reactions, molecular behavior
Confusion about particles at all levels: atoms, molecules, cells, and
types of molecules involved in body functions.
Students act as molecules and simulate self-assembly of different
structures.
Students identify rules and conditions that apply to the selfassembly of molecules. (Self-assembly happens when molecules
recognize each other and stick together.)
Through a lock and key activity, students understand the concept
of molecular recognition. (i.e. When two molecules stick together,
it means that they have recognized each other’s unique shapes
and electrical charges.)
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Students identify the challenges scientists face in simulating selfassembly at the molecular (nano) level.
Students understand that the natural process of self-assembly can
be used to manufacture large quantities of very, very small things.
It can also be used to build small- or large-scale nanostructures.
Particle Model of Matter
Grades 6 – 8 (one 8-10 week unit at Middle School Level)
 Structure and behavior of Atoms and Molecules (includes
particle concept, movement, and conservation principles).
Modeling across topics such as matter and energy (Modeling is
fore grounded)
Across Grades 4 – 8
 Important aspects of understanding and engaging in using
models, (constructing, critiquing, and revising models) as well
as important aspects of the nature of models (understanding
that models are tools for making predictions and
explanations).
Atomic molecular theory
Across grades K – 8
 Concepts central to this theory such as particles, motion of
particle, conservation, etc.
Nature of matter (Nanoscience literacy)
Across grades 7 – 14
 Structure of matter, periodic table, and ionic forces (i.e.
interatomic forces)
Laboratory experiences in life sciences
Grades 1 – 13
Atomic theory
Grades 7 – 14
 Atomic composition and structure subatomic, inter-atomic
interactions
Material kinds have characteristic properties that can be
measured and explained
Grades K – 8
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
Matter can be transformed, but not created or destroyed,
through physical and chemical processes.
Good measurements provide more reliable and useful
information about object properties than common sense
impressions
Grades K – 8
 We can learn about the world through measurement
Modeling is concerned with capturing key relations among ideas
rather than surface appearance
Grades K – 8
 We can learn about the world through modeling
Arguments use reasoning to connect ideas and data
Grades K – 8
 We can learn about the world through argument
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All biological processes are made possible through chemical
attractions between molecules. Molecules identify and bind to
each other based on several properties including their threedimensional shapes as well as their electronic charges.
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Activity 1 involves two games that help students to establish the
rules of molecular recognition. Students act as molecules and
follow specific rules that determine how they will bond with each
other to form structures. They will learn that scientists may
discover and exploit the properties of molecules to build
structures not found in nature but useful in the design and
construction of new nanoscale devices.
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(Adapted from http://pbskids.org/dragonflytv/pdf/DragonflyTV_SelfAssemblyGames.pdf.)
20 minutes
None
None
NOTE: An even number of participants is needed. An extra
student may assist players and check that the group is following
the rules.
Anticipatory set:
Inform students that they will shrink a billion times to the nanosize of molecules floating in human body fluid. When they come
in contact with another molecule (student) they will stick (bond)
to them if certain rules are maintained.
1. Tell students the following rules:
a) They must hold hands. No hand can be left untouched.
b) The RIGHT hand must touch someone else’s right hand
and the LEFT hand must touch someone else’s left hand.
c) They may NOT cross arms.
The result of the game:
Participants will be standing in a complete circle with each child
alternating in the direction they are facing.
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1. When assembling your circle, what were some key rules
required to make it?
[Possible Responses]
 They must hold hands. No hand can be left untouched.
 The RIGHT hand must touch someone else’s right hand
and the LEFT hand must touch someone else’s left hand.
 They may NOT cross arms.
2. What do you think would happen if you were allowed to cross
arms?
 A different shape would form.
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(Adapted from http://pbskids.org/dragonflytv/pdf/DragonflyTV_SelfAssemblyGames.pdf.)
NOTE: You need a total of 15 kids for this activity. If you have 30
students, you can repeat the following instructions for both groups
of 15. Extra students may assist the players as they assemble
according to the rules of the game.
35 minutes
Each set of 15 students will need:
 Red gloves or paper wrist bands (6 pairs per 15 students)
 Blue gloves or paper wrist bands (6 pairs per 15 students)
Gather gloves
Anticipatory set:
Ask students to explain what they think of when they hear the
phrase “Laws of Attraction.”
1. Remind them that they are molecules floating in cellular fluid,
which is mostly water, and that they are a billion times smaller
than their normal size. When they come in contact with
another molecule (student) they will stick (bond) to them if
certain rules are maintained.
2. Divide each set of 15 participants into three groups as
described below:
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Group 1 = 3 participants
Group 2 = 6 participants
Group 3 = 6 participants
3. Distribute gloves (or wrist bands)
Group 1: Give each participant a pair of RED gloves to put on
each hand.
Group 2: Give each participant one red glove and one blue
glove. Place one glove on each hand (it doesn’t matter which
color goes on which hand).
Group 3: Give each participant only one blue glove (they can
put it on either hand).
4. Read the rules for each group
Group 1:
 They must hold hands. No hand can be left untouched.
 They may only hold hands with someone who has the
SAME color glove that they do.
 They may NOT hold hands with any other members of
Group 1.
Group 2:
 They must hold hands. No hand can be left untouched.
 They may only hold hands with someone who has the
same colored glove as they do.
 They may NOT hold hands with any other members of
Group 2.
Group 3:
 They may only hold hands with someone who has the
same color glove as they do.
 They may NOT hold hands with any other members of
Group 3.
The result of the game:
The students create a star pattern.
When assembling your star shape, what were some key rules
required to make it?
Possible Responses or Points for a Mini-Lecture:
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Laws of attraction: A blue colored glove could only touch a
blue colored glove and red colored glove could only touch a
red colored glove.
The same rules apply to atoms and molecules, but the rules
are a little different. If the blue colored glove (atom) is a
positive charge and the red colored glove (atom) is a negative
charge, they would bond. In this case, two red gloves would
never touch each other just like two negative charges repel
each other. (This is similar to how the opposite poles of
magnets attract and the same poles repel one another).
Shape (lock and key): Along with polarity, a molecule’s shape
is also an important factor in assembly. For the snowflake
activity, the shapes where bonding occurred were hands (as
opposed to feet or elbow or ears, etc.). Molecules often fit
together like a lock and key or pieces of a puzzle. Only one
shape will fit into another shape to bond, and only if the
charges of the two molecules allow it. Shape AND charge are
important for molecular recognition.
What can you conclude from the way you all followed the same
set of rules about the pattern you got? What can you conclude
about how molecules would behave if the conditions for them are
exactly the same?
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Activity 2 demonstrates how molecules bind to each other
according to forces of attraction or repulsion. The placement of
charge determines the possible structures that molecules can
make when they come together. This activity can be performed
as a demonstration if purchasing the magnetic pieces is cost
prohibitive. Or, you can purchase one set and incorporate it as
one activity in a rotation that includes several of the pre/post
activities.
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One 50-minute class period
Each group will need:
 Skrooz or Roger’s Connection pieces are magnetic
construction toys consisting of plastic building pieces
containing embedded neodymium magnets and steel bearing
balls which can be connected together to form various
geometric shapes and structures. 50 rods, 26 balls
http://www.magz.com/, 84-piece set, $28.95
https://www.rogersconnection.com, 88-piece set = $38.95
 Shoe boxes (one per group)
(5 minutes)
Create some 2-D and 3-D
shapes with the Skrooz
Set out Skrooz and shoeboxes
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Anticipatory Set:
Discussion: Ask students to explain the term “self-assembly.” Ask
them if they can think of anything that can self-assemble. Answers
may be written on a note pad or white board.
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Explain to students that scientists are researching ways to
replicate how molecules can naturally self-assemble, but they face
many challenges. This activity will provide a some insight to those
challenges.
1. Separate students into groups of 3 or 4.
2. Provide each group is with a handful of magnetic pieces.
3. On a piece of paper or an overhead, show students examples
of different premade 2-D and 3-D shapes (show examples).
4. Ask students to build the same magnetic shapes found in the
example (transferred to PowerPoint or overhead).
5. Once the shapes are created by hand, ask the students to pull
apart the pieces and place those required to make those
shapes in a shoe box.
6. Ask students to shake the shoe box, with the magnetic pieces
inside, to see if self-assembly of the shapes they just created
occurs. Observe how frequently those patterns occur.
How often did the patterns you created with your hands occur in
the box?
What was different about the assembly process of creating the
desired shapes?
How efficient was the process in terms of time and yield?
Molecules will always follow the same assembly patterns if the
conditions are exactly the same. The trick for scientists is to figure
out the specific conditions that cause certain molecules to bond in
certain ways (temperature, shapes, etc.). Scientists can grow
really tiny molecular structures in a lab as long as they can figure
out what conditions to set. If they set the right conditions, the
atoms and molecules do the work and form the specific structures
they want. To facilitate this, recognition elements must be built in
so that assembly is specific and spontaneous.
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Share the following examples of self-assembled biological
structures and show the associated video clip which demonstrates
each process:
a) formation of lipid bilayers which surround and contain the
contents of cells,
Bilayer Formation Through Molecular Self-Assembly:
http://www.youtube.com/watch?v=lm-dAvbl330
b) Unraveling of DNA helices to access the genetic code which
gets copied into proteins and subsequent folding of
polypeptide chains into 3D proteins which creates all of the
structures of our bodies,
DNA Transcription and Protein Assembly:
http://www.allthingsscience.com/video/535/DNA-Transcription-and-Protein-Assembly
c) The assembly of enzymes and their substrates to make
reactions happen than they naturally would,
Industrial Enzymes Animation Clip:
http://www.youtube.com/watch?v=lrKgjbqZTwU&feature=related.
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Activity 3 demonstrates how molecules must fit together, like a
lock and key, in order to identify each other and initiate a new
function as a combined unit.
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One 50-minute class period
Each group will need:
 Play-dough (or Sculpey)
Play-dough Recipe: http://www.instructables.com/id/How-toMake-Playdough-Play-doh/?ALLSTEPS – OR –
Sculpey clay: http://www.sculpey.com/
 Rolling Pins (one per group if available)
 Assortment of different types of keys (several per group, may
be obtained for free from hardware store as they generally
keep extras or mistakes)
 One small, opaque bag containing a small item with unique
and distinctive shape (per group)
Set out play dough, rolling pins, keys, and objects for each group
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Anticipatory Set:
Hold up a key. Ask students what it is used for (students will likely
say that it is to lock/unlock something). Ask them if it could unlock
the door to their house or a car (students will likely say no). Ask
them why this key could not unlock the door to their house or a
car (students should likely say that only a certain key can open the
door to their house or a car).
Explain to students that the self-assembly of molecules work very
much like a lock and key. This helps molecules identify each other
and initiate a new function as a combined unit.
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1. Divide students into groups of three or four students.
2. Give some Play-dough (or Sculpy), a rolling pin, and keys to
each group.
3. Inform students that, based on their new knowledge of selfassembly, they will use Play-dough (or Sculpy) to design their
own molecular models that will address how shapes of
molecules are important to self-assembly.
4. Inform students that their goal will be to create two
“molecules that will fit together in only one unique pattern,
like a lock and key.”
5. Ask students to use their rolling pin to smooth out a piece of
Play-dough. Ensure that each Play-dough chunk is big and
thick enough to retain the shape of a key pressed into it.
6. Once they have rolled out their Play-dough, have students
press some keys into the Play-dough to create a print (mold)
of a key.
7. Mix the keys and see if members of the group can match each
key to each mold without distorting the molds.
8. Ask: How long did it take? Was it easy or difficult? Were
there any keys for which it was difficult to discriminate which
mold they matched?
9. Inform the students that this process usually takes place in a
suspension of liquid which fills your body cells.
10. Next, distribute bags with small items, one per group. Tell
students not to look at the items within. They may use their
hands to feel the shapes of the items. Ask each student to
create a Play-dough mold (molecule) that will recognize the
shape within the bag. After students have created their
molecules, ask them to remove the item from the bag and see
if it can bond with the molecule that they made out of Playdough without distorting the molds.
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Imagine all of the reasons why your body cells would need to be
able to identify and link to other cells or molecules in the way we
simulated using Play-dough. (Teacher: make a list of student
responses and keep it posted in the classroom.)
What did you discover when you tried out different key molds?
Possible Response: It took a bit of movement and jostling to
get the keys to fit into the molds without changing the shape
of the molds.
What did you discover when you tried to match the Play-dough
molds to the items in the bags?
Possible Response: Students will have to move the molds over
the surface of the items, testing various orientations, in order
to find the right fit. This takes time and energy. The molds
really have to be exact to get them to fit together.
What if you had to use couldn’t use your eyes to judge whether
the mold and the item fit together?
Possible Response: The shapes of the molds must be
extremely precise and unique for each specific object in order
to discriminate between them. The movements one would
make to test the fit need to be tiny and incremental so that no
possible matching points are overlooked.
What do you think might happen if there is a problem with the
key not fitting properly into the lock? In other words, what might
happen to the body if the molecules do not self-assemble
properly? For example, what would happen if the antibody could
not bind to the antigen? What do you think might cause this to
happen?
Possible Response: Disease causing organisms could go
undetected, within the body, reproduce and cause symptoms.
Our body would not be able to find them and destroy them.
Or, molecules in charge of causing reactions to happen might
not be able to find and attach to the ingredients they
need…therefore reactions won’t happen and this might cause
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symptoms because important work might not get done inside
the body.
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Understanding self-assembly is key to understanding how
scientists research, design and create things at the nano level.
Nature has been self-assembling things for billions of years by
exploiting the “rules” of the nanoscale. Now scientists are using
this information to create new materials and devices, such as:

medical treatments for different diseases

miniature diagnostics called “labs on chips”

diagnostic methods that can determine whether someone has
a disease before they even have symptoms.
The “rules” of the nanoscale define way that matter sticks
together and behaves. Atoms are attracted to each other based
on electric charge and bind to form molecules. Molecules then
stick together based on electrical charge and three-dimensional
shape. When they match, molecules snap together like magnetic
locks and keys. This is known as molecular recognition. When
this process requires very little to no energy, the scientific
community calls it self-assembly, since the formation of
molecules happens by itself. Biological molecules rely on selfassembly to form and maintain the structures of life.
Cells rely on molecular recognition to sense their environment, to
communicate, and to identify their “friends” and “foes.” Just as
you recognize and respond to your surroundings using your
senses of sight, sound, touch and smell, cells use surface
molecules to collect information about their surroundings and
react accordingly.
For example, bacterial cells have sugar sensors on their surfaces.
When a sensor nears a sugar molecule, it binds to it and causes
the cell to creep in the direction of increasing sugar
concentration. Why does it creep in that direction? Because it
has sensed one sugar molecule and wants more. It’s sort of like
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when you smell chocolate chip cookies baking in the oven and
move toward the delicious smell so that you can eat some!
Scientists have discovered thousands of these sensor molecules
(also called antigens) that cells use to probe their surroundings
and now use them to connect cells together into shapes that are
useful to them.
Sensor molecules must have very exact and picky shapes that can
only “dock” with certain molecules from their environment. This
pickiness is called specificity, because each molecule only
recognizes a specific mate. Each sensor must dock with only one
very special type of molecule so that cells can tell the difference
between different conditions and react in the best way.
Researchers can mimic the specificity of molecular recognition to
design and build sensors that identify and respond to chemicals in
the body or in the environment.
For example, miniature glucose sensors, made up of small pieces
of specially-shaped proteins mounted on a surface, can detect the
exact concentration of sugar in a diabetic patient’s blood,
communicate that amount to the patient and even deliver an
appropriate concentration of insulin in response. (The insulin
allows diabetic cells to absorb and store the glucose, which they
normally cannot do by themselves.)
While there are still many challenges in simulating molecular
recognition and self-assembly, scientists and engineers get better
at it every day.
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Antibody (ˈantiˌbädē/): proteins generally found in the blood that
detect and destroy invaders.
Antigen: (ˈantijən/): a harmful substance which enters the body
which causes the body to make antibodies as a response to fight
off disease.
Atom (/ˈatəm/): the basic unit of matter, sometimes described as
building blocks.
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Cell (sel/): the smallest structural and functional unit of an
organism.
Cell surface receptors: proteins on the surface of cells that allow
other proteins to bind to the cells.
Law of Attraction: the name given to the belief that “like attracts
like.”
Molecule (/ˈmäləˌkyool/): a group of two or more atoms that stick
together.
Molecular Recognition (mə¦lek·yə·lər ′rek·ig′nish·ən)):the specific
interaction/recognition between two or more molecules .
Nanoscale (ˈnanəˌskāl,): Very very small. Having dimensions
measured in nanometers.
Nanotechnology (ˌnanəˌtekˈnäləjē): the science of working with
atoms and molecules to build devices that are extremely small.
Receptor (/riˈseptər/): specialized proteins in the cell membrane
that take part in communication between the cell and the outside
world.
Self-assembly (self/ \-ə-ˈsem-blē\ ): the process by which a
complex macromolecule (as collagen) or a supramolecular system
(as a virus) spontaneously assembles itself from its components.
Specificity (\ˌspe-sə-ˈfi-sə-tē\): the quality of being specific.
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Image of antibody/antigen lock and key binding
Each antibody binds to a specific antigen; similar to a lock and key.
Image courtesy of Fvasconcellos,
http://en.wikipedia.org/wiki/Antibody
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Antibodies and antigens: Like Play-dough molds and hands,
antibodies and antigens fit together, like a lock and key. Antigens
are foreign particles not recognized by the body that can cause
illness and/or disease. An antibody is part of the body’s immune
system and attaches to the antigen to help fight off (neutralize)
the disease (antigen). Antibodies are important in keeping our
bodies in balance. All lock-and-key-type reactions take place in
the fluids of the body, which is about 65% water.
Antibody Immune Response:
http://www.youtube.com/watch?v=lrYlZJiuf18
The molecules of the body are constantly in motion. Their shapes
flip and flop between all of the positions that they can possibly
take and that require the least amount of energy. If molecular
shapes and charges match, this constant motion allows molecules
to wiggle around until they are able snap together. This is how
Nature accomplishes the millions of reactions that take place to
keep us alive. If a reaction requires more energy than simple
wiggling provides, then Nature uses special molecules, called
enzymes, to provide more energy, bring molecules close together
and that cause specific shape changes to happen.
Computer simulations can help us predict how molecules might
interact and design molecules to interact in ways that are
beneficial to us.
The Molecular Recognition Waltz:
http://www.youtube.com/watch?v=ozUmnZY6PC8
Disco Docking – Computational Drug Design:
http://www.youtube.com/watch?v=TTtrk0Ue-Cg&NR=1&feature=endscreen
Bilayer Formation Through Molecular Self-Assembly:
http://www.youtube.com/watch?v=lm-dAvbl330
DNA Transcription and Protein Assembly:
http://www.allthingsscience.com/video/535/DNA-Transcription-and-Protein-Assembly
Industrial Enzymes assembly Animation Clip:
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\http://www.youtube.com/watch?v=lrKgjbqZTwU&feature=related.
Antibody Immune Response:
http://www.youtube.com/watch?v=lrYlZJiuf18
Play-dough Recipe:
http://www.instructables.com/id/How-to-Make-Playdough-Play-doh/?ALLSTEPS
– OR –
Sculpey clay:
http://www.sculpey.com/
http://askabiologist.asu.edu/body-depot
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