Exploring DNA Binding with
the Molecule World DNA
Binding Lab
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1
Explore the properties of the example DNA
1.
Identify major & minor
grooves
2.
Identify elements
3.
Does DNA have a positive or
negative charge?
4.
Is DNA hydrophobic or
hydrophilic?
5.
How many distinct molecules
are in DNA?
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Move & resize the DNA to find the major and
minor grooves
Drag to
rotate
Pinch & spread
fingers apart to
zoom in and out
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Identify the elements in DNA
Tap the
palette to
view the
color key
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Identify the elements in DNA
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Does DNA have a positive or
negative charge?
Tap the
atom icon
to see
drawing &
coloring
options
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Does DNA have a positive or
negative charge?
1. Tap charge
2. Touch the window to
apply the change
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Does DNA have a positive or
negative charge?
Tap the
palette to
view the
color key
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Is DNA hydrophilic or
hydrophobic?
1. Tap
Hydrophobicity
2. Touch the window to
apply the change
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Is DNA hydrophilic or
hydrophobic?
Tap the
palette to
view the
color key
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How many distinct molecules
are in DNA?
1. Tap Molecule
2. Touch the window to
apply the change
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How many distinct molecules
are in DNA?
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How many different bases
are in this DNA fragment?
1. Tap
Tubes
2. Tap
Residue
3. Touch the window
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How many different bases
are in this DNA fragment?
Each base has a different
color. Count the bases to
find the number of
residues in each chain.
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Why study how molecules interact with DNA?
1. All genetic information is stored in DNA
A. Proteins bind to DNA to use information
B. Proteins bind DNA to copy it
C. Proteins bind DNA to repair it
2. Proteins that bind DNA are used in biotechnology
A.
B.
Restriction enzymes cut DNA
DNA polymerases copy DNA (PCR)
3. Some drugs bind to DNA & block replication
A.
B.
Anti-cancer drugs – tamoxifen for breast cancer
Anti-viral drugs – valacyclovir
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What do we know about molecules that bind DNA?
1. Proteins or drugs often bind to specific regions in
DNA
A.
Some bind to the major groove
B.
Some bind in the minor groove
C. Some contact both the major and minor groove
2. Some proteins and / or drugs bind to specific
DNA sequences
A.
Restriction enzymes
B.
Transcription factors
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1. How can we
determine if a
substance is binding
to the major groove,
or minor groove, or
both?
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Answer: use different coloring and drawing styles to
look at the two examples and see which visualization
options show binding most clearly.
Example major groove binding
Example minor groove binding
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2. How can we tell if the substance bound to DNA is
a protein or another kind of chemical, like a drug
or something else?
Answer: use residue coloring and the color key to see which
objects don’t contain amino acid residues.
Example major groove binding
Example minor groove binding
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Assessment
Tap the
camera
icon
Students can send an image
in an email or save an image
to the photo library, paste it
into a document and write
about it.
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