Exploring DNA Binding with the Molecule World DNA

Exploring DNA Binding with the Molecule World DNA Binding Lab www. Digital-World-Biology. com 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? www. Digital-World-Biology. com

Move & resize the DNA to find the major and minor grooves Drag to rotate Pinch & spread fingers apart to zoom in and out www. Digital-World-Biology. com

Identify the elements in DNA Tap the palette to view the color key www. Digital-World-Biology. com

Identify the elements in DNA www. Digital-World-Biology. com

Does DNA have a positive or negative charge? Tap the atom icon to see drawing & coloring options www. Digital-World-Biology. com

Does DNA have a positive or negative charge? 1. Tap charge 2. Touch the window to apply the change www. Digital-World-Biology. com

Does DNA have a positive or negative charge? Tap the palette to view the color key www. Digital-World-Biology. com

Is DNA hydrophilic or hydrophobic? 1. Tap Hydrophobicity 2. Touch the window to apply the change www. Digital-World-Biology. com

Is DNA hydrophilic or hydrophobic? Tap the palette to view the color key www. Digital-World-Biology. com

How many distinct molecules are in DNA? 1. Tap Molecule 2. Touch the window to apply the change www. Digital-World-Biology. com

How many distinct molecules are in DNA? www. Digital-World-Biology. com

How many different bases are in this DNA fragment? 1. Tap Tubes 2. Tap Residue 3. Touch the window www. Digital-World-Biology. com

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. www. Digital-World-Biology. com

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. Restriction enzymes cut DNA B. DNA polymerases copy DNA (PCR) 3. Some drugs bind to DNA & block replication A. Anti-cancer drugs – tamoxifen for breast cancer B. Anti-viral drugs – valacyclovir www. Digital-World-Biology. com

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 www. Digital-World-Biology. com

1. How can we determine if a substance is binding to the major groove, or minor groove, or both? www. Digital-World-Biology. com

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 www. Digital-World-Biology. com

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 www. Digital-World-Biology. com

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. www. Digital-World-Biology. com