Prerequisite skills needed:

  • Nucleotide Structure
  • DNA/RNA Structure
  • DNA Replication
  • Relevant book sections: pages 1005-1012, 1016-1020

By completing this simulation, you will:

  • Be able to identify various types of DNA lesions that can lead to mutations
  • Understand the DNA repair mechanisms the cell employs to repair DNA lesions
  • Understand how the cell fixes collapsed replication forks and stalled replication forks
mutS, mutL mutH Pol III Exonuclease Ligase Helicase II
The genomic material inside a bacterial cell is constantly accumulating lesions, or sites of DNA damage. It is important to repair a lesion before it encounters a replication fork. Damaged DNA can cause a replication fork to stall or collapse. Replication across a region of DNA with mismatched bases will introduce permanent mutations into the genome. In this simulation, your task is to protect this bacterium from the deleterious effects of DNA lesions (indicated by yellow spots on the genome) by identifying various types of lesions and then repairing them. If the DNA with the lesion reaches a replication fork (green) before the damage can be repaired, the lesion will convert to a permanent mutation (red) in the genome. Accumulation of too many deleterious DNA mutations will kill the cell.
Click on a yellow lesion to begin.
 Step Name  Enzyme
 Protein 1  Protein 2
This area is used to simulate lesions and the repair mechanisms that fix them. Currently, no lesion is selected to fix. Find a lesion in the bacterium to the left, and click on it.
You have identified a lesion in the bacterium’s genome. The lesion is simulated below. Watch carefully. Do you recognize this type of lesion?
Congratulations, you have correctly identified the lesion type! Which repair mechanism is used to correct this type of lesion? Click the appropriate button.
Good job! U-G mismatches that result from cytosine deamination are corrected using base excision repair. Use BER to fix this lesion and prevent it from becoming a mutation. In the correct order, drag and drop onto the lesion the enzymes involved in regenerating a correct base pair.
Awesome! Photolyase is one of the repair mechanisms used to correct pyrimidine dimers. The cyclobutane thymine dimer shown below needs repair. The DNA photolyase is in place, but needs to be completed. Drag-and-drop the two chromophores where they bind photolyase. Once this is done, click on the required energy source.
Exactly! Base pair mismatches that result from errors in replication are corrected by Mismatch Repair. Use MMR to repair this mismatch and prevent it from becoming a permanent mutation. To begin, drag-and-drop the MutS, MutL to the correct location on the DNA below.
Good job! The MutS-MutL scans the DNA bidirectionally, forming a loop, and finds the nearest GATC site. Next, drag-and-drop the MutH protein to the correct location on the DNA. MutH cleaves the newly synthesized unmethlyated GATC sequence.
You're on a roll. Now drag-and-drop the two proteins that unwind and degrade the newly replicated DNA strand past the mismatch. You may drop them anywhere on the DNA structure.
Your bacterium is happy! Next, drag-and-drop the two proteins that fill the gap and seal the DNA. You may drop them anywhere on the DNA structure.
Outstanding! You have successfully navigated the mismatch repair mechanism and corrected the mismatch error. This mismatch will not become a permanent mutation. But DNA lesions continue to occur, so you must get back to work.
It's a great day for your bacterium! You successfully used BER to repair this cytosine deamination lesion. You cannot rest however, as there are more lesions occurring in the cell that you must fix.
Before you repair this lesion, you must identify it. What type of lesion is shown here? Click on the button for the correct lesion type.
Oh no—your cell is in trouble! The lesion you are repairing has passed into a replication fork just when there is a break or nick in the template DNA. The fork will collapse, and your bacterium will die unless a working replication fork is reconstructed. The pressure is on!
Murphy's law strikes! The replication fork has caught up to the DNA lesion you are trying to repair. You must rectify this situation to avoid permanently introducing a mutation into the genome. What’s worse, a non-working replication fork is lethal to the bacterium! In the correct order, drag and drop the steps involved in fixing the lesion and reestablishing a working replication fork. It’s crunch time!
The replication fork is collapsing below. You must reconstruct the fork using recombinational double strand break repair. In the correct order, drag and drop onto the fork each processing step (rectangles) and its required enzyme(s) (ovals) involved in recombinational DSBR. For your cell's sake, remember to drag and drop two icons for each step—one rectangle and one oval.
Stellar! You correctly defined all the steps of recombinational DSBR and reestablished the replication fork for your bacterium. However, your work is not done because lesions are continuing to occur in the cell.
Fabulous work! You correctly ordered all the steps required for fixing a DNA lesion in the template and restarting a stalled replication fork. However, your bacterium is continuing to experience lesions. So it's back to work to keep your bacteria cell alive.
Great! You successfully completed photorepair of the pyrimidine dimer lesion. Your cell thanks you, but reminds you that lesions continue to occur. So back to work!
Bingo! Nucleotide excision repair is one of the repair mechanisms used to correct a pyrimidine dimer lesion. Use NER to fix this lesion and prevent it from becoming a mutation. To begin, drag and drop onto the DNA lesion below the three enzymes that form a complex to scan the DNA for a damaged base pair. This complex will separate the strands to form a single-stranded DNA bubble containing the lesion.
You rock! Now click on the two enzymes that disassocaite from the DNA so the process for repairing the damaged DNA may continue.
Cool! UvrB is now tightly bound to the damaged site. In the next step of NER, UvrB recruits an enzyme to make precise incisions in the DNA backbone on the 5' (eighth phosphodiester bond) and 3' (fifth phosphodiester bond) sides of the damaged nucleotide(s). Drag and drop this enzyme onto UvrB below.
Impressive! You have created a 13 nucleotide fragment containing the lesion that must be released. Drag and drop onto the DNA lesion the enzyme that will release the oligonucleotide.
Over the moon! Drag and drop onto the DNA lesion the enzyme that will fill the gap that now exists in the DNA.
Nearing the finish line! Drag and drop onto the DNA lesion the enzyme that will fill the nick that still exists in the DNA.
You did it! You correctly defined all the steps of nucleotide excision repair to fix a pyrimidine dimer. This lesion will not turn into a mutation. However, your bacterium is continuing to experience new DNA lesions. So it's back to work to keep your bacterium alive.
Unfortunately, your choice of lesion type is incorrect. This lesion will not be repaired and it will become a permanent mutation in the bacterium’s DNA. Your cell is very worried about its future, so let's get it right the next time.
Not good! Your choice of repair mechanism is incorrect. This lesion will not be repaired and it will become a permanent mutation in the bacterium’s DNA. Your cell is very worried about its future, so let's get it right the next time.
Congratulations! You have successfully identified a variety of DNA lesions and repaired them before they could become harmful to the bacterium. Your score shows you have a solid understanding of DNA mutation and repair. Click the button below to begin the Tutorial Comprehension Quiz.
Congratulations! You have successfully identified a variety of DNA lesions and repaired them before they could become harmful to the bacterium. However, your score indicates you have some uncertainty with DNA mutation and repair. Consider reviewing your text, and then try the exercise again before taking the Tutorial Comprehension Quiz.
Unfortunately, you were unable to successfully identify the DNA lesions and repair them before they could become harmful to the bacterium. Consider reviewing your text, and then try the exercise again before taking the Tutorial Comprehension Quiz.