Palindromes and DNA Symmetry

Introduction

Introduce students to the difficult concept of restriction enzyme action in cleaving DNA using this fun-filled, engaging concept attainment activity. In concept attainment, students look at examples of items that contain attributes of the concept and compare them to examples that do not contain attributes of the concept. They separate them into two groups; “yes” examples, those that contain attributes of the concept, and “no” examples or non-examples, those that do not contain attributes of the concept. The students look for connections between the “yes” examples, in this case words on a set of cards, and then develop the concept themselves. Once they have discovered the concept, the proper terminology can be assigned. For example, the students may develop the concept that all the words are names of people; the terminology assigned to this would be proper nouns. In this case, the examples are all palindromes. 

Concepts

• Restriction enzymes

• DNA

Background

Restriction enzymes are bacterial proteins that catalyze the cleavage of DNA at specific sites. There are many different restriction enzymes, each capable of cutting DNA strands at different sites in the nucleotide sequence; thereby, producing discrete fragments of various lengths. The DNA is cut either through this specific site to produce blunt ends on the strand (see Figure 1); or off-center, producing short, single-strand segments on the ends, or sticky ends (see Figure 2). The site has the same nitrogen base sequence in the 5′–3′ direction on one strand as it does on the complementary strand in the 5′–3′ direction.

In Figure 1, HaeIII, a restriction enzyme isolated from the bacterium H. aegyptius, cuts the DNA between the G and C in the sequence GGCC. In Figure 2, EcoRI, a restriction enzyme isolated from the bacterium E. coli, cuts the DNA between the G and A in the sequence GAATTC. The same sequence in the top strand, read from left to right, is in the bottom strand, read from right to left. Since the same sequence is found on both strands and each strand runs in the opposite direction, the sequence is referred to as a palindrome. Palindromes are words, phrases or numbers that read the same forward and backward.

This activity will teach the concept of palindromes to students by having them recognize patterns of letters in simple words or phrases.

Materials

Safety Precautions

Although the materials in this activity are considered non-hazardous, please follow all normal laboratory safety guidelines.

Disposal

The items in this kit are meant to be reused and should be stored for future use.

Prelab Preparation

1. On the wall, whiteboard, or chalkboard, place the “yes” and “no” header cards so that the yes examples will be on the left and the no examples will be on the right.
2. Stack the cards in the following order: Mom, Sister, Cousin, Dad, Uncle, Pop, Ewe, Eye, Grandfather, Mother, Nun, Dog, Noon, Mark Ran, Level, Radar, Racecar, Madam I’m Adam, Was It Eliot’s Toilet I Saw, A Man A Plan A Canal Panama.

Procedure

1. Inform students that the cards with either examples or non-examples of a concept will be shown.
2. Point to the “yes” header and tell the students that examples of the concept will be placed on the left, under the “yes” header card.
3. Point to the “no” header and tell the students that non-examples will be placed on the right, under the “no” header card.
4. Tell the students that each time a card is held up they are to vote. If the students think it is a “yes” then they should point their right thumb up and if they think it is a “no” they should point it down, or some other appropriate form of voting. Everyone should vote for every card, to ensure total participation.
5. Show the students the first card that says Mom. Tell the students that the first example is always a “yes” example and place it under the “yes” header.
6. Show the students the second card that says Sister. Tell the students that the second example is always a “no.” At this point it should be clear whether they understand how to vote and where all the examples will be placed. This is a good time to remind them that all examples under the “yes” have some similar attributes, the concept, and that items under the “no” do not necessarily have similar attributes. The non-examples just do not contain the attributes that exemplify the concept and are not necessarily, as a group, another concept.
7. Continue placing the cards under the appropriate header in the order they are stacked. Remind students that they should not vocalize the attributes of the concept or the concept itself; they should just vote using the appropriate method. Students will form their own hypothesis regarding the concept and revise this hypothesis every time there is a change in the trends of the data. One trend in this activity that changes is that all the examples are printed on blue cards for the first three examples and then an example appears on a green card.
8. When students seem to know the concept as exemplified by their vote, ask them to give another example of the concept—not the concept itself. This works well just before a change in the data trends.
9. When most students seem to know the attributes of the concept, list them on the board. As more examples are shown they may want to refine the attributes.
10. Once the students have discovered that the words or phrases can be spelled the same forward and backward, the definition of the concept, introduce the term palindrome.
11. Now, introduce the concept of restriction enzymes cleaving DNA at palindrome sequences by allowing students to write double-stranded sequences, using any combination of the letters G, A, T and C that read the same, but in opposite directions.
12. Place student examples under the appropriate “yes” or “no” header card.
13. Use Figures 1 and 2, HaeIII and EcoRI, respectively, as examples of DNA sequences that are palindromes.

Teacher Tips

• As students think they have the concept, write their examples on the board or on note cards and place them under the “yes.”

• Attributes could be written on the board and reevaluated every few rounds to allow students to see how the trends in the data change. Allow students to present the attributes.
• When the students, in step 11, write their own palindromes, limit them to sequences of six to eight base pairs.
• Masking tape, magnetic tape, or hook and loop fasteners can be applied to each card so they may be temporarily attached to surfaces.
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References

Biggs, Alton, et al., Biology the Dynamics of Life, Glencoe, 1998.

The Howard Hughes Medical Institute, DNA in the Classroom, Department of Biological Sciences, Texas Tech University, 1997.