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The DNA Discovery KitThe DNA Discovery Kit©©

The Guided Discovery Approach The Guided Discovery Approach && Teacher Notes Teacher Notes

www.3dmoleculardesigns.com � 3D Molecular Designs Copyright 2013

All rights reserved on DNA Discovery Kit©. US Patent 6,471,520 B1

Photos by Sean Ryan

The Guided Discovery ApproachThe Guided Discovery Approach �� Teacher NotesTeacher Notes

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Contents of The Guided Discovery ApproachContents of The Guided Discovery Approach

Contents of The DNA Discovery KitContents of The DNA Discovery Kit©© �� 2 Base Pair Kit2 Base Pair Kit

Contents of the DNA Discovery Kit©12 Base Pair Kit . . . . . . . . . . . . . . . . . . . .2

Contents of the DNA Discovery Kit©2 Base Pair Kit . . . . . . . . . . . . . . . . . . . . .2

Assembly Instructions . . . . . . . . . . . . . . . . .3The DNA Backbone . . . . . . . . . . . . . . . . . .6The Four Deoxyribonucleotides . . . . . . . . .8Purines and Pyrimidines . . . . . . . . . . . . . . .9Important Features of DNA . . . . . . . . . . . .9

Discovering the Structure of DNA . . . . . .10Mini-Toober DNA . . . . . . . . . . . . . . . . . . .14Three Frequently Asked Questions . . . . .16Student Handout . . . . . . . . . . . . . . . . . . . .19Transparency Templates

Chemical Structures . . . . . . . . . . . . . . .22Information Available to

Watson & Crick in 1953 . . . . . . . . . . .24

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

1 Each: Adenosine, Guanine, Thymine andCytosine Nucleotides

8 Nucleotide Labels

Assembly Instructions

Contents & Introduction PDF�sDNA Discovery Kit© IntroductionDNA Contents & Assembly Directions

DNA Activities & Teacher Notes PDF�sThe Discovery ApproachThe Guided Discovery ApproachStudent HandoutThree Frequently Asked Questions

Watson & Crick Papers PDF�sWatson & Crick � April 1953Watson & Crick � May 1953Annotated Version of Watson & CrickPaper

DNA Resource Information Read Me FirstTeacher NotesStudent WorksheetStudent Answer Sheet

DNA Websites Additional DNA Resources

Contents of The DNA Discovery KitContents of The DNA Discovery Kit©© �� 12 Base Pair Kit12 Base Pair Kit

6 each of Adenosine, Thymine, Guanineand Cytosine Nucleotides

48 Nucleotide Labels2 Mini-ToobersBlack Helix Guide

Black RodBlack BaseAssembly Instructions

3D Molecular Designs Copyright 2013The Guided Discovery Approach

The Guided Discovery Approach The Guided Discovery Approach �� Teacher NotesTeacher Notes

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DNA Discovery KitDNA Discovery Kit©© �� Assembly InstructionsAssembly Instructions

Nucleotides AssembledNucleotides AssembledThe nucleotides are preassembled.

You have the option of using labeled or unlabeled nucleotides. To label anucleotide, peel a letter from its protectivebacking and press it into the depressionon a corresponding base. After placingthe label on one side, flip the base overand repeat with another label. Use thephoto to correctly place the labels on thenucleotides. (Labels only fit inside thelarger depression on the Adenosine andGuanine nucleotides.)

The nucleotide models have magnets embedded in them to

simulate the spontaneousbonding that occurs between

complementary base pairs(hydrogen bonds) and between

the phosphate group of onenucleotide 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.

Magnets

Phosphodiester BondMagnets Simulate BondingMagnets Simulate Bonding

Hydrogen Bonds

3D Molecular Designs Copyright 2013 The Guided Discovery Approach


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We encourage you toleave the DNADiscovery Kit© piecesout on a table for yourstudents to explore intheir free time.

You can also easily display or store the fullyassembled double helixby setting up the blackbase and black rod that are included inthe 12 Base Pair DNA Discovery Kit©.

Or you can hang the double helix from a ceiling by threading a strong cordthrough the eyelet at the top of the rod.Do not use the black base when hangingthe DNA.

NucleotidesNucleotides SeparateSeparate IntoInto Component PartsComponent PartsEach nucleotide separates into its three component parts �the nitrogenous base, deoxyribose group and phosphategroup.

To separate the pieces, pull the three pieces apart as shown in the photos. Be sure to pull the pieces apart with astraight motion. The attachment posts can break if atwisting or bending motion is used.

Three Ways to Display DNA Discovery KitThree Ways to Display DNA Discovery Kit©©

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Place two Mini-Toobers side-by-side, so the red end cap on one iseven with the blue end cap on theother. Next, line them up with thefirst two grooves in the black helixguide. Begin wrapping the Mini-Toobers around the guide following thegrooves.

Once the Mini-Toobers are wound around the guide, you can remove them by twistingthe guide as though you are unscrewing itfrom the Mini-Toobers. Then loosen andseparate the coils by gently unwinding andpulling them apart.

(See the Activities and Teacher Notes at3dmoleculardesigns.com/resources.php forinformation on this activity.)

Setting Up Base & Rod to Display DNASetting Up Base & Rod to Display DNA

Push the bottom of the rod (end without the eyelet) into theblack base. Press down firmly so it rests securely in thebase. The lowest disk will restabout 3/4 inch above the base.

Before correctly placing the Guanine - Cytosine base pairsaround the rod, look carefully at the models. You will see thatthe Guanine model has two hydrogen that are longer than the third hydrogen. (See photo at rightand refer to the page 2 photo labeled, Hydrogen Bonds.) The Cytosine model has one hydrogenthat is longer and two shorter hydrogen. Adenosine and Thymine each have one longer hydrogenand 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 thatthe rod is between the two hydrogen (one is longer and one is shorter). As each base pair isplaced on the rod, rotate it until it forms the phosphodiester bond with the previous base pair. Fourbase pairs fit above each disk.

MakingMaking MiniMini--TooberToober DNADNA

Eyelet for Hanging DNA on Rod

Black Helix Guide


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Divide the deoxyribose and phosphate models evenly betweengroups of students. You may connect the deoxyribose to thephosphate prior to this exercise or let the students discover thisconnection themselves.

The DNA BackboneThe DNA Backbone

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


The Guided Discovery ApproachThe Guided Discovery Approach requires that students manipulate the DNA Discovery Kit© modelpieces to discover the structure of DNA, but in a series of lessons that are more structured than thosedescribed in the Discovery Discovery ApproachApproach. The blue italic text in yellow boxes provides questions you can useto stimulate your student�s exploration of the structure of DNA. Each question is followed by a briefdescription of the concepts that students should discover in their exploration and the ensuing discussion.

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

First, your students should discover that the phosphate and sugarsubunits can be connected together using the trapezoid-shaped snapconnections.

Second, students should discover that the magnets allow them to assemble the sugar-phosphate molecules into a chain. Thedeoxyribose of one subunit attaches to the phosphate of the nextsubunit. When your students put three or foursubunits together the angles of the subunits enablethe assembled (backbone) structure to begin to forma turn. When additional subunits are added, (if youhave the 12 Base-Pair DNA Discovery Kit©), yourstudents 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?

Deoxyribose

Phosphate


The Guided Discovery Approach The Guided Discovery Approach –– Teacher NotesTeacher Notes

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Students may notice the cyclic structure of deoxyribose (a 5-carbon sugar), and the star-shaped structure of the phosphategroup.

The chemical structure for the molecule we are examining is on the right. (On page 22, you’ll find a larger image of the twochemical drawings on this page. They can be printed ontransparency film for overhead use.)

In CPK Coloring — which is used in molecular modeling —carbon is gray or black; nitrogen is blue; oxygen is red; andphosphorous is yellow. Have your students compare the DNAmodel pieces with the chemical structure. (Most of thehydrogen atoms have been eliminated from the models in order to more clearly reveal theunderlying structure.)

One oxygen atom is attached to the 5' carbon of onedeoxyribose, and the second oxygen atom is attached to the3’ carbon of the next sugar molecule.

At the beginning there is a free phosphate group attached tothe 5' carbon (5' end). At the end there is a free hydroxylgroup attached to the 3' carbon of deoxyribose (3' end).(Note: In the model the hydroxyl group is represented by themagnet attached to the 3' carbon.) The deoxyribose-phosphate backbone shown in the above photo is oriented inthe 5’ end (upper left) to 3’ end (lower right).

5’

3’

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

The polymer that you created is known as the sugar-sugar-phosphate backbonephosphate backbone of DNA. It consists of alternatingdeoxyribose (sugar) molecules and phosphate groups. Inthis backbone, a phosphate group joins two consecutivesugars together via a covalent phosphodiester bond.

Can you identify which carbon atoms on the deoxyribose are covalently linked to oxygen in the phosphodiester linkage?

Look at your backbone chain again. Do you see a difference between the two ends?


CH2

HH

H

HH

H

O-

O-

P

O

OO

O

5’

4’

Base

3’ 2’

1’

5’ end

3’ end3’

CH2

CH2

H HH H

H

HH

H

HH

H

O-

O-

O-

OP

P

OO

O

O

OO

O

5’ 5’

5’

4’

4’

Base

Base

3’

3’

2’

2’

1’

1’


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The Sequence of DNAThe Sequence of DNA

Shorthand nomenclatures have been developed, so wecan avoid drawing the complex structure of DNA. Thenotation to the right represents a DNA molecule andshows the nucleotide single letter abbreviations, thephosphodiester links, and the 5' phosphate and 3'hydroxyl.

If the 3' - 5' designation for the phosphodiester links is removed the same molecule can be represented as:

Finally, because it is understood that the phosphodiesterlinkage is between each base we can write the mostcompact form, which shows only the nucleotidesequence in the DNA. By convention the sequence isalways written in the 5' - 3' direction:

5'

3'

A

5'

3'

G

5'

3'

T

5'

3'

C

OH

5'

3'

T

PP P P P

5'

3'

A

5'

3'

G

5'

3'

T

5'

3'

C

OH

5'

3'

T

PPPPP PPP PPP PPP

5' pApGpTpCpT 3'

5' AGTCT 3'

Students should quickly discover that the bases attach tothe backbone via the half-circle snap connection. Differentgroups will most likely assemble the bases in differentorders. The different order, or sequence, of the bases ishow information is encoded in DNA.

As we discussed earlier, the sugar-phosphate backbone of DNA is repetitive and doesnot 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?

The Four DeoxyribonucleotidesThe Four Deoxyribonucleotides

Phosphates Nitrogenous BasesDeoxyribose



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Purines and PyrimidinesPurines and PyrimidinesThe 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, andpyrimidines are attached through nitrogen 1.

Once attached to the deoxyribose subunit a base is called a nucleoside. A nucleoside doesn�t contain a phosphate group. Monomer unites containing a phosphate group (a5'-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 nucleotidesare called oligonucleotides.

Important Features of DNAImportant Features of DNA

� Genetic information is encoded in the sequence of bases attached to the deoxyribose groups of apolynucleotide chain.

� A polynucleotide chain has a sense of direction, provided by the backbone. The phosphodiester linkage isalways 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).



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Discovering the Structure of DNADiscuss 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 2of the Student Handout (page 20 in this document). (Key points of the Information Available toWatson 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 at3dmoleculardesigns.com/resources.php)

If they haven�t 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 doublestranded structure of DNA.

The Double HelixThe Double Helix

You can see a summary of what was known about the structure of DNA in the early 1950�s, inyour 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 listedon your handout (page 2.)

As your students assemble A-T and G-Cbase pairs, remind them that thedeoxyribose-phosphate groups are on theoutside, forming the backbone of DNA.The nitrogenous bases are on the inside ofthe base pairs.

If your students have difficulty building anaccurate DNA double helix, you can usethe 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?

Correct Pairing for Forming Double Helix



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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 you�ve 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 - Cbase pairs should also discover that they canbuild the double helix by forming the correctbonds 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 ofthe three hydrogen bonds, or A - A and T - Tbase 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 - Tor G - C base pairs to form a double helix. (Note photo below. Both of the phosphate-sugargroups have a downward orientation. Now note the similar photo on the previous page.) Askyour students if they can discover alternative base pairing that will allow them to put two basepairs together. You may want to explain that in a natural environment, nitrogenous bases canform incorrect bonds, but the bonds will be unstable and break apart since they won�t be able to

bond with correctly paired A - T orG - C base pairs and form thestable double helix structure.

Incorrect Pairing for Forming Double Helix

Incorrect Pairing for Forming Double Helix

After students explore base pairing, have them disassemblethe nucleotides and then form a two-nucleotide chain as wasdone in the first exercise. Then ask the students to use whatthey learned about base pairing to add two nucleotides to thestructure so that they build a helix with two strands as wassuggested by the crystallographic data. The students shoulddiscover that the only way to build a double helix is byfollowing the A - T, G - C base pairing rule.


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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?

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 inthe 5' - 3' direction, while the opposite strand is orientated in the 3' - 5'. The two strands are said tobe anti-parallel due to the different directions.

Yes.

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.

Let�s examine the full DNA model to see if we satisfied all of the experimental predictions.

Is it a polymer?

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

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, countdown 10 residues. The tenth 5' phosphate will line up directlyunder the first 5' phosphate.

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

How does the base paring in the model explain Chargaff�s 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 concentrationof T, and G is always equal to C. This is a direct consequence of Chargaff�s Rules, which statethat A is always paired with T, and G is always paired with C.


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� 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.

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?

Reviewing BondsReviewing BondsA 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 partiallycharged atoms) or non-polar (without charged atoms).

A hydrogen bond 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 atomin a second molecule.

An ionic bond 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 onemolecule.

Ions are charged atoms that have gained or lost electrons as a result of an ionic bond.

Watson and Crick DNA PapersWatson and Crick DNA PapersAfter your students discover the structure of DNA by putting the model together, they should readthe classic paper published by Watson and Crick in Nature, April 23, 1953. You can download thePDF at 3dmoleculardesigns.com/resources.php (an annotated version of the paper is included asa teacher resource.) Watson and Crick published a second paper in the next issue of Nature thatexpanded on the significance of their proposed structure. This paper provides an interestingdescription of what was known and unknown at that time, and sets the stage for the constructionof 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 Crick�s second paper concerns the way in which the two strands of DNA wrap around each other. Watson andCrick clearly understood the topological problem this structure presents, even though they did notunderstand at that time how the cell would deal with it. To help your students better understandthat 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 12Base-Pair DNA Discovery Kit©. Instructions and photos follow on the next two pages.


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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(abovephoto). (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. Onceclass starts ask one of your students to put the two strands together in the

Place two Mini-Toobers side-by-side,so the red end cap onone is even with theblue end cap on theother. Next, line themup 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 completely wound aroundthe guide, you can remove the Mini-Toobers by twistingthe guide as though you are unscrewing it from the Mini-Toobers. Then loosen and separate the coils by gently unwinding andpulling them apart.

Making a Mini-Toober Model of DNAMaking a Mini-Toober Model of DNA

You just made a right-handed doublehelix DNA model. How do you knowif your helix is right-handed?

Imagine the helix is a spiral staircase. As you walk up, one of your handsrests on the outside rail of the staircase.If it is your right hand, then you arewalking up a right-handed helix.

The structure of DNA is always a right-handed double helix.


3D Molecular Designs Copyright 2013 The Guided Discovery Approach 15

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

Watson and Crick realized the problem intertwined DNA poses for DNA replication and RNAtranscription. In their May 1953 paper, published in Nature (see Watson & Crick PDF�s online at3dmoleculardesigns.com/resources.php), they wrote,�Since the two chains in our model areintertwined, it is essentialfor them to untwist if theyare to separate. As theymake one complete turnaround each other in 34 A,there will be about 150turns per million molecularweight, so that whateverthe precise structure of thechromosome, aconsiderable amount ofuncoiling would benecessary. It is well known from microscopic observation that much coiling and uncoiling occursduring mitosis, and though this is on a much larger scale it probably reflects similar processes on amolecular level. Although it is difficult at the moment to see how these processes occur withouteverything 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 spacedabout 6 inches apart. Then unwind the double-helix to form the replication bubble shown above.

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

Discussion Opportunity Csompare the DNA Discovery Kit�s plastic model with its Mini-Toober DNA model. Whatare 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 useappear on page 20.)

Three Frequently Asked QuestionsThree Frequently Asked Questions

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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, byhandling 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 tomore clearly reveal the underlying structure. A direct comparison of the physical models with typicalchemical drawings of the nucleotide structures is provided below.

A larger version of these drawingsand photos appears on page 23.It can be printed on transparency

film for overhead use.


H

HG C

H

H

H HP

H

HH

H

O

O OO

O

O

ON

N

N

NH

NH

HN

N

NC

C

CC

C C

CC

C

CC C

CCH

H

C

HOH

OC

C C

C

H

O-

OO

O

P

O-

H

H

H

A T

H

H

H

H

HH

H

HHH

H

H

H

P

P

O-

O-

HO

C

N

N

N N

N

N

N C

CC

C C C

C C

CC

C

C

CCC

OO

HOHC C

CCO

O

O

OO

O

OO


17

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 arerunning in opposite directions. Look at the photo shown below, and focus on the red oxygen atomfound in the two deoxyribose groups. Notice how the oxygen of the deoxyribose on the left is belowthe plane of the base pair, while the oxygen of the deoxyribose on the right is above the plane. Thisis a clear indication that the �polarity� of the nucleotides in the two strands are opposite each other.

Now focus your students attention on the phosphate groupsfrom each nucleotide. Again, one of these phosphates will bebelow the plane of the base pair while the other will be abovethe plane. And since the phosphate group is attached to the5�carbon of the deoxyribose group, the DNA chain on the rightof 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 otherstrand is running 5� to 3�, from the bottom to the top.

5�

3�

3�

5�



18

Yes, non-standard base pairs (other than the A - T and G - C that form the doublehelix) can be formed by this model � just as these base pairs can form in solutionwith 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 diameterthan standard A - T and G - C base pairs that consist of one purine paired with onepyrimidine. Therefore, the non-standard base pairs shown below cannot beassembled 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 modelproposed by Watson and Crick.

Can incorrect base pairs be formed with the model pieces?

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


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The Discovery of DNA The Discovery of DNA

On April 25, 1953, a one-page paper entitled, AStructure for Deoxyribonucleic Acid, appeared in theBritish journal, Nature. The authors of this paper wereJames Watson, a young American post-doctoralcandidate who had recently received a Ph.D. from theUniversity of Illinois, and Francis Crick, a physicist whowas completing his doctoral dissertation at CambridgeUniversity, England. The paper began; "We wish tosuggest a structure for the salt of deoxyribose nucleicacid (D. N. A.). This structure has novel features whichare 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 thecorrect structure of DNA, the paper also contained their classic understatement in scientificliterature: "It has not escaped our notice that the specific pairing we have postulated immediatelysuggests a possible copying mechanism for the genetic material." Their paper serves as anexcellent example of what has become a recurring theme in the molecular biosciences � FormsFollows Function. That is, the structure of a macromolecule often explains the macromolecule�sfunction (how the macromolecule) works. Watson and Crick's achievement is notable in several ways, including the fact that they determinedthe structure of DNA without performing a single experiment. They used the information fromnumerous other scientists who were investigating various properties of DNA.Modeling was the major approach Watson and Crick used. Using paper cut-outsof the shapes of the four nitrogenous bases (A,T, G and C), they were able tocombine all of the different facts that had accumulated to that date into aplausible model for the structure of DNA.

...where molecules become realTM

...The structure has two helical chains coiled around the same axis (seediagram). We have made the usual chemical assumptions, namely, that eachchain consists of phosphate diester groups joining B-D-deoxyribofuranoseresidues with 3',5' linkages. The two chains (but not their bases) are relatedby a dyad perpendicular to the fibre axis. Both chains follow right-handedhelices, but owing to the dyad the sequences of the atoms in the two chainsrun in opposite direction.

� Watson, J.D. and Crick, F.H.C., Nature, 171, 737-738 (1953)

(Page 1 of Student Handout)


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The DNA Student ChallengeThe DNA Student ChallengeYour challenge today is to see if you can discover the correct structure of double-stranded DNA, justas Watson and Crick did over 50 years ago. Your model should satisfy all of the pieces of experimental information that was known in 1953, asnoted in the blue box below. Rather than using paper cut-outs to represent the DNA bases, you willuse plastic models of the four deoxyribonucleotides whose 3D structures are based on knownatomic coordinates of the B-form DNA. In these nucleotide models, magnets are used to representboth:

� the phosphodiester bonds that link the nucleotide units together into a long, linear polymer� the hydrogen bonds that bond one base to another.

Student HandoutStudent Handout

Information Available to Watson and Crick in 1953Information 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, withmolecular weights ranging from 25 x 106 to 3 x 109 daltons. (Since each nucleotidehas a mass of 330 daltons, DNA molecules were believed to be composed of between76,000 and 9,000,000 nucleotides.)

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

Chargaff's Rules: In 1947, Erwin Chargaff demonstrated that while the fournucleotides 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 thesame 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, RosalindFranklin used X-ray diffraction to analyze fibers of DNA. The pattern of spots on theX-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.



21

Background information for studentsBackground information for students

Each group of students Each group of students should have physical models of the four nucleotides, separatedinto 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 thestandard CPK coloring scheme:

Oxygen is RED Nitrogen is BLUE Phosphorus is YELLOWCarbon is GRAY Hydrogen iis WWHITE

Phosphates Nitrogenous BasesDeoxyribose



22

Single DeoxyribonucleotideSingle Deoxyribonucleotide

Di-NucleotideDi-Nucleotide(Two Deoxyribonucleotides(Two Deoxyribonucleotides

joined by joined by a phosphodiester bond)a phosphodiester bond)

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


5’ end

3’ end3’

CH2

CH2

H HH H

H

HH

H

HH

H

O-

O-

O-

OP

P

OO

O

O

OO

O

5’ 5’

5’

4’

4’

Base

Base

3’

3’

2’

2’

1’

1’

CH2

HH

H

HH

H

O-

O-

P

O

OO

O

5’

4’

Base

3’ 2’

1’

23

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


H

H

H

A T

H

H

H

H

HH

H

HHH

H

H

H

P

P

O-

O-

HO

C

N

N

N N

N

N

N C

CC

C C C

C C

CC

C

C

CCC

OO

HOHC C

CCO

O

O

OO

O

OO

H

HG C

H

H

H HP

H

HH

H

O

O OO

O

O

ON

N

N

NH

NH

HN

N

NC

C

CC

C C

CC

C

CC C

CCH

H

C

HOH

OC

C C

C

H

O-

OO

O

P

O-

24

Information Available to Watson and Crick in 1953

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

Chargaff�s 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.


the dna discovery kit - 3d molecular designs...2013/05/16 · the dna discovery kit© 4 we...

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