Please contact us if any parts are missing or damaged. DNA Backbone

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1 DNA Starter Kit Contents 1-Group Set Contents 12 Red Foam Adenine Bases (DNASK-R-A) 12 Blue Foam Cytosine Bases (DNASK-R-C) 12 Green Foam Guanine Bases (DNASK-R-G) 12 Yellow Foam Thymine Bases (DNASK-R-T) 3 White Foam Uracil Bases (DNASK-R-U) 48 Orange Phosphate Pieces (DNASK-R-P) 48 Orange Connector Pieces (DNASK-R-C) 4 Gray Foam DNA Backbone Pieces (DNASK-R-Backbone) 1 Bag with 24 Blue, 24 Yellow and 6 White Bands (DNASK-R-Bands) 24 Gray Sugar-Phosphate DNA Backbone Pieces (DNASK-R-GSP) 12 Purple Sugar-Phosphate RNA Backbone Pieces (DNASK-R-PSP) Please contact us if any parts are missing or damaged. Replacement Parts Available Order replacement parts with the item number in parentheses from the above list in our catalog or online at DNA Backbone Adenine Guanine Sugar-Phosphate DNA Backbone Thymine Cytosine Uracil Sugar-Phosphate RNA Backbone Phosphate Connector! WARNING: CHOKING HAZARD -- This product contains small parts and should be kept out of the reach of children under the age of 3, because the parts or their pieces may present a choking hazard to small children. CAUTION: This is a science education product, not a toy. It is not intended for children under 8 years old North Market Street, Suite CC130A, Milwaukee, WI Phone Fax dmoleculardesigns.com

2 Assembly To complete your pyrimidine bases (blue cytosine, yellow thymine & white uracil) you will attach the sticky-backed foam bands to each side of the base as shown at left. (Please remove the paper backing on the bands first.) The prongs of the pyrimidine bases should be completely covered by the stickybacked bands. These sticky-backed bands provide stability for the model and reduce confusion between base pairs. Narrow Wide Match the shape of the band to the shape of the base. Note the angle cut on the bands. Place the narrow end at the outside of the prongs. See photo. Note: If over time the bands on the pyrimidines become loose, or are not sticking to the foam base, use super glue to re-attach them. Powder Bases Before Using The adhesive on the bands makes joining and separating the base pairs difficult. This stickiness can be eliminated with talcum powder. Dip the purines exposed prongs into the talcum powder provided. Insert the purine into the complementary pyrimidine. The bases should easily attach and detach. Care & Maintenance The foam will tear if too much force is used. Encourage your students to be careful. Wash with a damp cloth or, if necessary, a mild dishwashing detergent. Misconception Caution Models are powerful teaching tools, but can cause misconceptions. With this DNA model, students might develop the misconception that DNA is made by simply adding the four DNA bases (A,T,G,C) to a pre-formed sugar-phosphate backbone. To avoid this misconception, we encourage you to explain that a nucleotide consists of a base, deoxyribose sugar and a phosphate group. You can use the individual sugar phaosphate pieces joined to the base to help your students visualize the individual nucleotides. Individual nucleotide units are then joined together by phosphodiester bonds to build up the alternating sugar-phosphate backbone of DNA as it is synthesized by DNA polymerase enzymes in the cell. Page 1

3 Introduction DNA Starter Kit Pilot Study Pilot Study Thank you for purchasing the Pilot Study Version of the DNA Starter Kit! We value your insights on how this kit may be used to help your students learn important concepts about DNA. You will have two venues in which to share your input. Share Your Comments & Lessons Online The MSOE Center for BioMolecular Modeling is hosting an interactive website for the Pilot Study. 3D Molecular Designs is posting photos and other resources. You will be able to post your lesson plans, photos, comments, feedback and/or suggestions, and view materials developed by other teachers. While posting is optional, we hope you will be willing to share your ideas with us. Survey Within a month of receiving the kit(s), you will receive an with a link to a survey. The first 100 people to complete the survey will receive replacement parts/kits for every kit purchased. DNA Structure Build your DNA model with either the long continuous backbone, or the individual sugarphosphate pieces. Remember, the base always attaches to the sugar (deoxyribose or ribose). Create half of your model by attaching 12 bases to the backbone. Then attach the complementary bases to either the long backbone or individual pieces. Note: Pull the base through the DNA backbone hole until flared ends pop through. To remove a base from the DNA backbone, squeeze the flared ends until they To create the double helix, rotate the bases so that fit through the hole. they are vertical instead of horizontal, as shown left. With your right hand on the top base pair and left on the bottom twist your hands in opposite directions. (Your right hand should twist counterclockwise and your left hand clockwise). Twist until the DNA backbones touch each other in a tight coil. Release the bases and allow the model to relax into its double-helical shape. Page 2

4 Using the DNA Starter Kit Deoxyribonucleotide Triphosphates (dntps) DNA (RNA) Synthesis* We include deoxyribonucleotide triphosphates in the DNA Starter Kit to help students understand that during the process of DNA replication (or RNA transcription) these nucleotide triphosphates serve as the substrates (monomeric subunits) that are joined together by DNA polymerase (or RNA polymerase) to create the complementary strand of DNA (or RNA). A significant fraction of the cell s metabolism is devoted to maintaining an adequate supply of these nucleotide triphosphates for DNA replication and/or RNA transcription. As the nucleotide triphosphate is added to the growing chain, a high energy phosphate bond joining the three phosphate groups together is cleaved by the polymerase releasing a pyrophosphate (PP i ) and incorporating the nucleotide monophosphate into the growing chain. Energy Metabolism* As an added benefit, students can construct models of ATP (adenosine -triphosphate) as they consider this universal currency of cellular energy. ATP is generated by ATP synthase as it binds both ADP (adenosine -diphosphate) and P i and then forms the final high energy phosphate bond to create ATP. This key reaction in the cell is powered by the high proton concentration that is built up in the inter-membrane space of the mitochondria, as a result of oxidative respiration. *Depending on the level of your students you may not use this information and/or the phosphate pieces. Replication Start with your DNA Starter Kit model in its ladder shape and unzip the base pairs at one end of the DNA. the two strands of complementary DNA should be antiparallel. Begin by adding complementary deoxyribonucleotide triphosphates (dntps) to the end of the single-stranded DNA (the end with the point of the arrow). Page 3

5 Replication Continued Each time another dntp is added: break the phosphate bond between the first and second phosphate group set the resulting pyrophosphate aside (the orange PP i ) form the phosphodiester bond to the previous nucleotide by slipping the hole in the remaining phosphate over the peg in the deoxyribose. Note that to replicate the opposite strand of DNA, you would have to start at the replication fork and join complementary dntps together as you move along the opposite strand toward the unzipped end. In this way, both replicated double-stranded DNAs will be anti-parallel. This idea may be too sophisticated for younger students who could simply replicate one strand of the DNA in an anti-parallel manner and then replicate the opposite strand once it is completely freed from the original double-stranded DNA. Transcription RNA can be transcribed from either of the two DNA strands in much the same way as DNA was replicated. But rather than unzipping the DNA from one end, we suggest that you create a transcription bubble by separating several base pairs in the middle of the DNA model. And then as you begin transcribing one of the two strands of DNA by adding ribonucleotide triphosphates together, splitting off a pyrophosphate at each step be sure that the RNA strand that you are making is anti-parallel to the template strand of DNA. Page 4 You might also want to point out to students that only one of the two strands of a gene is transcribed into mrna. Transcription of the opposite strand would result in an RNA that would encode an entirely different sequence of amino acids.