The DNA Discovery Kit© Discovering the Structure of DNA

...where molecules become realTM

TheThe DNADNA DiscoveryDiscovery KitKit© The Guided Discovery Approach & Teacher Notes

Photos by Sean Ryan

Contents of The Guided Discovery Approach

Contents of the DNA Discovery Kit© Discovering the Structure of DNA ...... 10 12 Base Pair Kit ...... 2 Mini-Toober DNA ...... 14 © Contents of the DNA Discovery Kit Three Frequently Asked Questions . . . . .16 2 Base Pair Kit ...... 2 Student Handout ...... 19 Assembly Instructions ...... 3 Transparency Templates The DNA Backbone ...... 6 Chemical Structures ...... 22 The Four Deoxyribonucleotides ...... 8 Information Available to Purines and Pyrimidines ...... 9 Watson & Crick in 1953 ...... 24 Important Features of DNA ...... 9

Contents of The DNA Discovery Kit© 12 Base Pair Kit

6 each of Adenosine, Thymine, Guanine Black Rod and Cytosine Nucleotides Black Base 48 Nucleotide Labels Assembly Instructions 2 Mini-Toobers Black Helix Guide

Contents of The DNA Discovery Kit© 2 Base Pair Kit

1 Each: Adenosine, Guanine, Thymine and Assembly Instructions Cytosine Nucleotides 8 Nucleotide Labels

Contents of Online Resources found at 3dmoleculardesigns.com/resources.php

Contents & Introduction PDFs DNA Resource Information DNA Discovery Kit© Introduction Read Me First DNA Contents & Assembly Directions Teacher Notes Student Worksheet DNA Activities & Teacher Notes PDFs Student Answer Sheet The Discovery Approach The Guided Discovery Approach DNA Websites Student Handout Additional DNA Resources Three Frequently Asked Questions

Watson & Crick Papers PDFs Watson & Crick April 1953 Watson & Crick May 1953 Annotated Version of Watson & Crick Paper 2 The Guided Discovery Approach 3D Molecular Designs Copyright 2013 The Guided Discovery Approach Teacher Notes

DNA Discovery Kit© Assembly Instructions

Nucleotides Assembled The nucleotides are preassembled. You have the option of using labeled or unlabeled nucleotides. To label a nucleotide, peel a letter from its protective backing and press it into the depression on a corresponding base. After placing the label on one side, flip the base over and repeat with another label. Use the photo to correctly place the labels on the nucleotides. (Labels only fit inside the larger depression on the Adenosine and Guanine nucleotides.)

Phosphodiester Bond Magnets Simulate Bonding

Magnets

The nucleotide models have Hydrogen Bonds magnets embedded in them to simulate the spontaneous bonding that occurs between complementary base pairs (hydrogen bonds) and between the phosphate group of one nucleotide to the deoxyribose of another nucleotide (phosphodiester bonds). Arrows in the photo above point to the magnet(s) in each piece. You can break the hydrogen bonds by pulling apart the G-C and A-T base pairs. When examining the deoxyribose and phosphate groups, you will see the single magnet embedded in the deoxyribose group and one embedded in the phosphate group.

Nucleotides Separate Into Component Parts Each nucleotide separates into its three component parts the nitrogenous base, deoxyribose group and phosphate group. To separate the pieces, pull the three pieces apart as shown in the photos. Be sure to pull the pieces apart with a straight motion. The attachment posts can break if a twisting or bending motion is used.

Three Ways to Display DNA Discovery Kit© We encourage you to leave the DNA Discovery Kit© pieces out on a table for your students to explore in their free time. You can also easily display or store the fully assembled double helix - by setting up the black base and black rod that are included in the 12 Base Pair DNA Discovery Kit©. Or you can hang the double helix from a ceiling by threading a strong cord through the eyelet at the top of the rod. Do not use the black base when hanging the DNA.

Setting Up Base & Rod to Display DNA

Eyelet for Hanging DNA on Rod

Push the bottom of the rod (end without the eyelet) into the black base. Press down firmly so it rests securely in the base. The lowest disk will rest about 3/4 inch above the base. Before correctly placing the Guanine - Cytosine base pairs around the rod, look carefully at the models. You will see that the Guanine model has two hydrogen that are longer than the third hydrogen. (See photo at right and refer to the page 2 photo labeled, Hydrogen Bonds.) The Cytosine model has one hydrogen that is longer and two shorter hydrogen. Adenosine and Thymine each have one longer hydrogen and one shorter hydrogen. The Guanine - Cytosine base pair should be placed so that the rod is between the longer and the shorter hydrogen (photos above). The Adenosine - Thymine base pair should be placed so that the rod is between the two hydrogen (one is longer and one is shorter). As each base pair is placed on the rod, rotate it until it forms the phosphodiester bond with the previous base pair. Four base pairs fit above each disk.

Making Mini-Toober DNA Black Helix Guide Place two Mini-Toobers side-by- side, so the red end cap on one is even with the blue end cap on the other. Next, line them up with the first two grooves in the black helix guide. Begin wrapping the Mini- Toobers around the guide following the grooves. Once the Mini-Toobers are wound around the guide, you can remove them by twisting the guide as though you are unscrewing it from the Mini-Toobers. Then loosen and separate the coils by gently unwinding and pulling them apart.

(See the Activities and Teacher Notes at 3dmoleculardesigns.com/resources.php for information on this activity.)

The Guided Discovery Approach requires that students manipulate the DNA Discovery Kit© model pieces to discover the structure of DNA, but in a series of lessons that are more structured than those described in the Discovery Approach. The blue italic text in yellow boxes provides questions you can use to stimulate your students exploration of the structure of DNA. Each question is followed by a brief description of the concepts that students should discover in their exploration and the ensuing discussion.

The DNA Backbone

Divide the deoxyribose and phosphate models evenly between groups of students. You may connect the deoxyribose to the Phosphate phosphate prior to this exercise or let the students discover this connection themselves.

These molecules have a special property. Can you discover what this special property is?

First, your students should discover that the phosphate and sugar subunits can be connected together using the trapezoid-shaped snap connections.

Second, students should discover that the magnets allow them to Deoxyribose assemble the sugar-phosphate molecules into a chain. The deoxyribose of one subunit attaches to the phosphate of the next subunit. When your students put three or four subunits together the angles of the subunits enable the assembled (backbone) structure to begin to form a turn. When additional subunits are added, (if you have the 12 Base-Pair DNA Discovery Kit©), your students will begin to see a helix forming.

What else do you notice about this structure? For example, do you see a way for this molecule to encode information?

No. This backbone is a repetitive structure that does not encode information.

Let’s take a closer look at the repeating molecules. Can you describe the structure in more detail?

Students may notice the cyclic structure of deoxyribose (a 5- carbon sugar), and the star-shaped structure of the phosphate group. - The chemical structure for the molecule we are examining is on O Base the right. (On page 22, you’ll find a larger image of the two - 5’ P O CH chemical drawings on this page. They can be printed on O 2 transparency film for overhead use.) O O 4’ 1’ In CPK Coloring — which is used in molecular modeling — H H H H carbon is gray or black; nitrogen is blue; oxygen is red; and 3’ 2’ phosphorous is yellow. Have your students compare the DNA OH H model pieces with the chemical structure. (Most of the hydrogen atoms have been eliminated from the models in order to more clearly reveal the underlying structure.)

The polymer that you created is known as the sugar- 5’ phosphate backbone of DNA. It consists of alternating deoxyribose (sugar) molecules and phosphate groups. In this backbone, a phosphate group joins two consecutive 3’ sugars together via a covalent phosphodiester bond. Can you identify which carbon atoms on the deoxyribose are covalently linked to oxygen in the phosphodiester linkage?

One oxygen atom is attached to the 5' carbon of one deoxyribose, and the second oxygen atom is attached to the 3’ carbon of the next sugar molecule.

Look at your backbone chain again. - O 5’ end Base Do you see a difference between the two ends? - 5’ 5’ O P O CH2 O O At the beginning there is a free phosphate group attached to 4’ 1’ H H the 5' carbon (5' end). At the end there is a free hydroxyl H H 3’ 2’ group attached to the 3' carbon of deoxyribose (3' end). O H

(Note: In the model the hydroxyl group is represented by the Base - 5’ O P O CH magnet attached to the 3' carbon.) The deoxyribose- 2 O O phosphate backbone shown in the above photo is oriented in 4’ 1’ H H the 5’ end (upper left) to 3’ end (lower right). 3’ H H 3’ 2’ 3’ end OH H

The Four Deoxyribonucleotides

The Sequence of DNA A G T C T Shorthand nomenclatures have been developed, so we can avoid drawing the complex structure of DNA. The notation to the right represents a DNA molecule and 3' 3' 3' 3' 3' shows the nucleotide single letter abbreviations, the P P P P P OH phosphodiester links, and the 5' phosphate and 3' 5' 5' 5' 5' 5' hydroxyl. If the 3' - 5' designation for the phosphodiester links is removed the same molecule can be represented as: 5' pApGpTpCpT 3' Finally, because it is understood that the phosphodiester linkage is between each base we can write the most compact form, which shows only the nucleotide 5' AGTCT 3' sequence in the DNA. By convention the sequence is always written in the 5' - 3' direction:

As we discussed earlier, the sugar-phosphate backbone of DNA is repetitive and does not encode information. However, DNA includes another functional group called a base. Can you incorporate these groups into your sugar-phosphate backbone? Can you determine the sequence of bases in your DNA? How might these groups allow DNA to encode information?

PhosphatesDeoxyribose Nitrogenous Bases

Students should quickly discover that the bases attach to the backbone via the half-circle snap connection. Different groups will most likely assemble the bases in different orders. The different order, or sequence, of the bases is how information is encoded in DNA.

Purines and Pyrimidines The nitrogenous bases are of two types, purines and pyrimidines. In DNA the purines are adenine (A) and guanine (G) and the pyrimidines are cytosine (C) and thymine (T). Purines are attached to deoxyribose molecules through nitrogen 9, and pyrimidines are attached through nitrogen 1. Once attached to the deoxyribose subunit a base is called a nucleoside. A nucleoside doesnt contain a phosphate group. Monomer unites containing a phosphate group (a 5'-phosphorylated deoxyribose sugar) and a base are called nucleotides. Since DNA can be considered a polymer of nucleotides, a stretch of DNA is also known by the generic name polynucleotide. Small polymers of only a few nucleotides are called oligonucleotides.

Important Features of DNA Genetic information is encoded in the sequence of bases attached to the deoxyribose groups of a polynucleotide chain. A polynucleotide chain has a sense of direction, provided by the backbone. The phosphodiester linkage is always between the 5' carbon of one nucleotide and the 3' carbon of the next. When a sequence of nucleotides in DNA is reported, by convention, they are read in the 5 - 3 direction (written left to right).

The Double Helix

Discovering the Structure of DNA Discuss what was known about DNA at the time Watson and Crick determined its structure. Each student should have a copy of the Student Handout (begins on page 19), and refer to page 2 of the Student Handout (page 20 in this document). (Key points of the Information Available to Watson and Crick in 1953, (on page 24), can be printed on transparency film for overhead use. The Student Handout is also available as a separate document at 3dmoleculardesigns.com/resources.php) If they havent done so, ask your students to separate each backbone strand into its phosphate, deoxyribose and nitrogenous subunits. Then let your students see if they can discover the double stranded structure of DNA.

You can see a summary of what was known about the structure of DNA in the early 1950s, in your handout. Using your molecular models, see if you can discover the structure of double- stranded DNA. Remember that your model must fit all of the experimental observations listed on your handout (page 2.)

Correct Pairing for Forming Double Helix

As your students assemble A-T and G-C base pairs, remind them that the deoxyribose-phosphate groups are on the outside, forming the backbone of DNA. The nitrogenous bases are on the inside of the base pairs. If your students have difficulty building an accurate DNA double helix, you can use the following questions to guide them.

Use your models to build the individual nucleotides (base + deoxyribose + phosphate). What you can discover about how the nucleotides might interact with each other? What general feature of these nucleotide pairs do you see?

Remember that the crystallographic data indicated DNA was a helix made up of two strands. Using what we learned previously about the primary structure of DNA, and what youve just discovered about pairs of nucleotides, can you build a helix made up of two strands of DNA?

Students who build the correct A - T and G - C Incorrect Pairing for Forming Double Helix base pairs should also discover that they can build the double helix by forming the correct bonds between the 5' phosphates and the 3' hydroxyl groups. They may also find they can form incorrect C - C and G - G base pairs using only two of the three hydrogen bonds, or A - A and T - T base pairs. (Note photo on right.) When the phosphate-deoxyribose is added to the incorrectly paired bases, your students will not be able to add them to correctly paired A - T or G - C base pairs to form a double helix. (Note photo below. Both of the phosphate-sugar groups have a downward orientation. Now note the similar photo on the previous page.) Ask your students if they can discover alternative base pairing that will allow them to put two base pairs together. You may want to explain that in a natural environment, nitrogenous bases can form incorrect bonds, but the bonds will be unstable and break apart since they wont be able to bond with correctly paired A - T or Incorrect Pairing for Forming Double Helix G - C base pairs and form the stable double helix structure.

After students explore base pairing, have them disassemble the nucleotides and then form a two-nucleotide chain as was done in the first exercise. Then ask the students to use what they learned about base pairing to add two nucleotides to the structure so that they build a helix with two strands as was suggested by the crystallographic data. The students should discover that the only way to build a double helix is by following the A - T, G - C base pairing rule.

The 5' phosphate of one strand is opposite the 3' hydroxyl of the opposite strand, and vice versa. Note that the two DNA strands run in the opposite directions. As a result, one strand is oriented in the 5' - 3' direction, while the opposite strand is orientated in the 3' - 5'. The two strands are said to be anti-parallel due to the different directions.

Looking at your double helix model of DNA, can you identify the 5' phosphate and 3' hydroxyl of each strand? Where are they in relation to each other on the two strands? The DNA sequence is always read in the 5' - 3' direction. Can you write the sequence of each strand in your DNA model?

Check to make sure the sequences are read in the 5' - 3' direction. At this point, it would be useful for your students to assemble all 12 base pairs into the double helix.

Lets examine the full DNA model to see if we satisfied all of the experimental predictions. Is it a polymer?

Yes.

Does it form a double stranded helix with 10 residues per turn as predicted from the x-ray crystallography?

Yes. Starting with the 5' phosphate at the top of the model, count down 10 residues. The tenth 5' phosphate will line up directly under the first 5' phosphate.

What do you notice about the location of the phosphate molecules and the bases?

The phosphate molecules, which are negatively charged, are on the outside where they interact with the aqueous environment. The bases are stacked on top of one another with the planes of the bases nearly perpendicular to the helix axis.

How does the base paring in the model explain Chargaffs Rules?

While the overall nucleotide composition (percentage of G - C pairs and percentage of A - T pairs) of the DNA of different organisms can vary, the concentration of A always equals the concentration of T, and G is always equal to C. This is a direct consequence of Chargaffs Rules, which state that A is always paired with T, and G is always paired with C.

How does this organization of DNA's bases, deoxyriboses and phosphates make DNA a stable molecule? In other words, what forces make this a stable structure?

The ribose subunits in the backbone are connected by covalent phosphodiester bonds. The backbone is connected to the nitrogenous bases by covalent bonds. The nucleotide base pairs are formed by hydrogen bonding. A-T base pairs form two hydrogen bonds and are less stable than G-C base pairs, which form three hydrogen bonds. Hydrophobic interactions between the base pairs provide additional stability to the double helix.

Reviewing Bonds A covalent bond forms when two atoms share two electrons. A covalent bond is an intra- molecular bond within one molecule. Covalent bonds can be either polar (which have partially charged atoms) or non-polar (without charged atoms). A hydrogen bond is an intermolecular force between the two molecules where a positively charged hydrogen atom interacts with a negatively charged fluorine, nitrogen, or oxygen atom in a second molecule. An ionic bond is the complete transfer of an electron between two atoms resulting in one positively and one negatively charged atom. Ionic bonds are intra-molecular bonds within one molecule. Ions are charged atoms that have gained or lost electrons as a result of an ionic bond.

Watson and Crick DNA Papers After your students discover the structure of DNA by putting the model together, they should read the classic paper published by Watson and Crick in Nature, April 23, 1953. You can download the PDF at 3dmoleculardesigns.com/resources.php (an annotated version of the paper is included as a teacher resource.) Watson and Crick published a second paper in the next issue of Nature that expanded on the significance of their proposed structure. This paper provides an interesting description of what was known and unknown at that time, and sets the stage for the construction of the Central Dogma of Molecular Biology, which was developed in the following years. One interesting feature of the DNA structure that is addressed in Watson and Cricks second paper concerns the way in which the two strands of DNA wrap around each other. Watson and Crick clearly understood the topological problem this structure presents, even though they did not understand at that time how the cell would deal with it. To help your students better understand that the two strands of DNA are intertwined and to appreciate the problem this intertwining poses, we have included the supplies to create a Mini-Toober model of double-stranded DNA,with the 12 Base-Pair DNA Discovery Kit©. Instructions and photos follow on the next two pages.

Making a Mini-Toober Model of DNA

Place two Mini- Toobers side-by-side, so the red end cap on one is even with the blue end cap on the other. Next, line them up with the first two grooves in the black helix guide. Begin wrapping the Mini- Toobers around the guide following the grooves. You just made a right-handed double helix DNA model. How do you know if your helix is right-handed? Imagine the helix is a spiral staircase. As you walk up, one of your hands rests on the outside rail of the staircase. If it is your right hand, then you are walking up a right-handed helix.

Once the Mini-Toobers are completely wound around The structure of DNA is always a the guide, you can remove the Mini-Toobers by twisting right-handed double helix. the guide as though you are unscrewing it from the Mini- Toobers. Then loosen and separate the coils by gently unwinding and pulling them apart.

Carefully position each strand of DNA to show the major and minor grooves (right photo). Then, holding the DNA horizontally by only one strand, demonstrate that the two strands are wrapped around each other(above photo). (The term used to describe this property of DNA is plectonemeic.) Another way to show that DNA is plectonemeic is to separate the two strands of Mini-Toober DNA, by unwinding one strand from the other (Photo top of next page). Separate the Mini-Toobers before class. Once class starts ask one of your students to put the two strands together in the

same way that the double stranded DNA fits together. After a few false starts your student will probably try winding one of the strands into the second strand.

How do you think the cell separates the two strands of DNA for replication and transcription, when they are wound around each other?

Watson and Crick realized the problem intertwined DNA poses for DNA replication and RNA transcription. In their May 1953 paper, published in Nature (see Watson & Crick PDFs online at 3dmoleculardesigns.com/resources.php), they wrote,Since the two chains in our model are intertwined, it is essential for them to untwist if they are to separate. As they make one complete turn around each other in 34 A, there will be about 150 turns per million molecular weight, so that whatever the precise structure of the chromosome, a considerable amount of uncoiling would be necessary. It is well known from microscopic observation that much coiling and uncoiling occurs during mitosis, and though this is on a much larger scale it probably reflects similar processes on a molecular level. Although it is difficult at the moment to see how these processes occur without everything getting tangled, we do not feel that this objection will be insuperable. We now know that the solution is provided by a family of proteins known as topoisomerases. These enzymes function to unwind or wind double-stranded DNA by: Cleaving a phosphodiester bond in the backbone of one strand of DNA Effectively unwinding the free end one turn around the other DNA strand Re-forming the phosphodiester bond. In this way DNA can be unwound one turn at a time. You can simulate the result but not the mechanism of this localized unwinding by grasping the toober model with both hands spaced about 6 inches apart. Then unwind the double-helix to form the replication bubble shown above.

Discussion Opportunity Csompare the DNA Discovery Kits plastic model with its Mini-Toober DNA model. What are the advantages and disadvantages of each? Compare them to textbook drawings and illustrations of DNA. (Drawings appear on the next page. Larger images that can be printed on transparency film for overhead use appear on page 20.)

How do these models compare with the chemical drawings of nucleotides in my textbook?

As your students become familiar with DNA’s phosphate groups, deoxyribose groups and bases, by handling the models, the 2-D drawings of DNA’s chemical structure will be more meaningful. When your students compare the models with the chemical drawings in textbooks, it is important that they understand that most of the hydrogen atoms have been eliminated from the models in order to more clearly reveal the underlying structure. A direct comparison of the physical models with typical chemical drawings of the nucleotide structures is provided below.

O HN H

C C H N - C NH N C O H C O - C C C C O OH H N P N NH O N H H O O C C P H O O H O H C C C G C C C O C H O C C H H H OH

H NH O H H C N C C - N HN C O C H H C O C P - OH H C C C O O N N H O N H C C H O O O P H C H O C C C C C A T H H O O C C H H OH

A larger version of these drawings and photos appears on page 23. It can be printed on transparency film for overhead use.

How does the model show that the two strands of DNA are anti-parallel?

One powerful feature of this model is that it clearly demonstrates that the two strands of DNA are running in opposite directions. Look at the photo shown below, and focus on the red oxygen atom found in the two deoxyribose groups. Notice how the oxygen of the deoxyribose on the left is below the plane of the base pair, while the oxygen of the deoxyribose on the right is above the plane. This is a clear indication that the polarity of the nucleotides in the two strands are opposite each other.

3 5

Now focus your students attention on the phosphate groups from each nucleotide. Again, one of these phosphates will be below the plane of the base pair while the other will be above the plane. And since the phosphate group is attached to the 5carbon of the deoxyribose group, the DNA chain on the right of the double helix shown in the photo above is said to run 5 to 3 from the top of the photo to the bottom while to other strand is running 5 to 3, from the bottom to the top.

Can incorrect base pairs be formed with the model pieces?

Yes, non-standard base pairs (other than the A - T and G - C that form the double helix) can be formed by this model just as these base pairs can form in solution with real nucleotides. Four of these non-standard base pairs are shown below. However, these non-standard base pairs are not compatible with double helical DNA, for two reasons. Base pairs formed with two purines or two pyrimidines will have a different diameter than standard A - T and G - C base pairs that consist of one purine paired with one pyrimidine. Therefore, the non-standard base pairs shown below cannot be assembled into a double helical model with a uniform diameter. Encourage your students to discover these non-standard base pairs -- and then determine for themselves why these base pairs are not consistent with the model proposed by Watson and Crick.

For the non-standard hydrogen bonded base pairs to form, the polarity of the two strands of DNA must be parallel, not anti-parallel. Therefore, notwithstanding the problem with the diameter of these non-standard base pairs (see above paragraph), it is not possible to accommodate these parallel base pairs in the Watson-Crick model of DNA.

TheThe DiscoveryDiscovery ofof DNADNA

On April 25, 1953, a one-page paper entitled, A Structure for Deoxyribonucleic Acid, appeared in the British journal, Nature. The authors of this paper were James Watson, a young American post-doctoral candidate who had recently received a Ph.D. from the University of Illinois, and Francis Crick, a physicist who was completing his doctoral dissertation at Cambridge University, England. The paper began; "We wish to suggest a structure for the salt of deoxyribose nucleic acid (D. N. A.). This structure has novel features which are of considerable biological interest." This initial description of the structure of DNA marked a major milestone in the development of molecular biology. In addition to reporting the correct structure of DNA, the paper also contained their classic understatement in scientific literature: "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material." Their paper serves as an excellent example of what has become a recurring theme in the molecular biosciences Forms Follows Function. That is, the structure of a macromolecule often explains the macromolecules function (how the macromolecule) works. Watson and Crick's achievement is notable in several ways, including the fact that they determined the structure of DNA without performing a single experiment. They used the information from numerous other scientists who were investigating various properties of DNA. Modeling was the major approach Watson and Crick used. Using paper cut-outs of the shapes of the four nitrogenous bases (A,T, G and C), they were able to combine all of the different facts that had accumulated to that date into a plausible model for the structure of DNA.

...The structure has two helical chains coiled around the same axis (see diagram). We have made the usual chemical assumptions, namely, that each chain consists of phosphate diester groups joining B-D-deoxyribofuranose residues with 3',5' linkages. The two chains (but not their bases) are related by a dyad perpendicular to the fibre axis. Both chains follow right-handed helices, but owing to the dyad the sequences of the atoms in the two chains run in opposite direction. Watson, J.D. and Crick, F.H.C., Nature, 171, 737-738 (1953)

(Page 1 of Student Handout)

The DNA Student Challenge Your challenge today is to see if you can discover the correct structure of double-stranded DNA, just as Watson and Crick did over 50 years ago. Your model should satisfy all of the pieces of experimental information that was known in 1953, as noted in the blue box below. Rather than using paper cut-outs to represent the DNA bases, you will use plastic models of the four deoxyribonucleotides whose 3D structures are based on known atomic coordinates of the B-form DNA. In these nucleotide models, magnets are used to represent both: the phosphodiester bonds that link the nucleotide units together into a long, linear polymer the hydrogen bonds that bond one base to another.

Information Available to Watson and Crick in 1953

DNA is a Polymer: Previous studies identified DNA as the genetic material of cells, and that DNA was a polymer consisting of three components: A nitrogenous base A pentose (5-carbon) sugar called deoxyribose A phosphate group.

Moreover, experiments suggested that the DNA molecule was unbelievably large, with molecular weights ranging from 25 x 106 to 3 x 109 daltons. (Since each nucleotide has a mass of 330 daltons, DNA molecules were believed to be composed of between 76,000 and 9,000,000 nucleotides.)

DNA is more dense than protein. At a density of 1.6 gm/cm3, DNA was known to be more dense than protein (1.3gm/cm3). This suggested that DNA was a densely packed structure.

Chargaff's Rules: In 1947, Erwin Chargaff demonstrated that while the four nucleotides were not present in equal amounts in the DNA from different organisms, the amount of adenine was the same as thymine, and the amount of guanine was the same as cytosine. This became known as Chargaff's Rules: The proportion of A always equals that of T, and the proportion of G always equals that of C. Thus, A = T and G = C.

X-ray Crystallography Data: In the laboratory of Maurice Wilkins, Rosalind Franklin used X-ray diffraction to analyze fibers of DNA. The pattern of spots on the X-ray diffraction pattern suggested that: Phosphate was on the outside, nitrogenous bases were on the inside. DNA was a double helix, made up of two strands. The two strands of DNA run in opposite directions (anti-parallel). There are 10 base pairs per turn of the double helix.

(Page 2 of Student Handout)

PhosphatesDeoxyribose Nitrogenous Bases

Each group of students should have physical models of the four nucleotides, separated into their component parts. These include: Phosphate group which is negatively charged Deoxyribose group which is a cyclic ring structure Four nitrogenous bases (A, G, C and T) Each component of the nucleotides is color coded according to atom type, following the standard CPK coloring scheme: Oxygen is RED Nitrogen is BLUE Phosphorus is YELLOW Carbon is GRAY Hydrogen is WHITE

(Page 3 of Student Handout)

- O Base - 5’ O P O CH2 O Di-Nucleotide O 4’ 1’ (Two Deoxyribibonucleotides H H joined by H H a phosphoddiiester bond) 3’ 2’ OH H

- O 5’ end Base - 5’ 5’ O P O CH2 O O 4’ 1’ H H H H 3’ 2’ O H

Base - 5’ O P O CH2 O O 4’ 1’ H H 3’ H H 3’ 2’ 3’ end OH H

Transparency Template of Chemical Structure of DNA. See page 7.

C C H N - C NH N C O H C O - C C C C O OH H N P N NH O N H H O O C C P H O O H O H C C C G C C C O C H O C C H H H OH

H NH O H H C N C C - N HN C O C H H C O C P - OH H C C C O O N N H O N H C C H O O O P H C H O C C C C C A T H H O O C C H H OH

Transparency Template of Comparison of Models to Textbook Drawings of Nucleotides. See page 16.

DNA is the genetic information of cells DNA is a Polymer A nitrogenous base A pentose (5-carbon) sugar called deoxyribose A phosphate group.

DNA molecule is unbelievably large DNA is more dense than protein

Chargaffs Rules The proportion of A always equals that of T The proportion of G always equals that of C A = T and G = C

X-ray Crystallography Data The phosphate is on the outside; nitrogenous base is on the inside. DNA is a double helix, made up of two strands. The two strands of DNA run in opposite directions (anti-parallel). There are 10 base pairs per turn of the double helix.

Transparency Template of Information Available to Watson & Crick. See pages 10 and 20.