1. Are the objective and introduction written in an engaging way? Yes No     If 'No' please explain. characters left 2. Is the difficulty level accurate? Yes No     If 'No' please explain. characters left 3. Were the materials easily obtained? Yes No     If 'No' please explain. characters left 4. Was the procedure clear? Yes No      If 'No' please explain. characters left 5. Were all safety measures included? Yes No      If 'No' please explain. characters left 6. Did you obtain clear, unambiguous results? Yes No     If 'No' please explain. characters left 7. How much time did you spend on the project? Choose One... A day or less Several days About one week A couple weeks Several weeks to months 8. How much did the project cost? Choose One... Less than $20 $20 - $50 $50 - $100 $100 - $150 $150+ Optional:  Do you have any suggestions to improve this project? characters left Optional:  Attach a picture of your project (JPG, JPEG, GIF, PNG only) Optional:  Caption for picture characters left Thank you for your feedback! * Note: This is an abbreviated project idea, without notes to start your background research or a procedure for how to do the experiment. You can identify abbreviated project ideas by the asterisk at the end of the title. If you want a project idea with full instructions, please pick one without an asterisk. Abstract Some sequences of RNA can catalyze biochemical reactions, much like protein enzymes. These catalytic RNA sequences are called ribozymes. The function of a ribozyme depends upon the primary sequence of the RNA which folds into a 3-D structure. How do different ribozyme sequences fold? You can search for ribozyme sequences using Entrez BLAST (NCBI, 2006). Then you can use a program like MFOLD (http://bioweb.pasteur.fr/seqanal/interfaces/mfold-simple.html) to submit your sequence for an analysis of its predicted 3-D structures based upon thermodynamics (Zuker, 2006; Zuker, 2003). Compare the different predicted structures and see if they are similar or different. If possible, compare the predicted structures to a published crystal structure. How close was the predicted structure to the crystal structure? Can you identify primary sequence elements in your molecule that contribute to parts of the structure? For example, palindromic stretches can form stem-loop structures. You can also mutate the sequence and submit the new sequence to MFOLD. How does this alter the 3-D structure? Can you use this computational method to identify potentially important nucleotides? Bibliography National Center for Biotechnology Information. (2006). Entrez PubMed. Retrieved March 25, 2006, from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db. Variations For more science project ideas in this area of science, see Biotechnology Techniques Project Ideas. Last edit date: 2008-11-10 15:10:22

I Did This Project! Tell us about your experience with this science project. What was the most important thing you learned? characters left What problems did you encounter? (Enter "none" if you had none.) characters left Can you suggest any improvements or ideas? (Enter "no" if you have none.) characters left How do you rate this project? Poor OK Good Very Good Excellent Optional:  Attach a picture of your project (JPG, JPEG, GIF, PNG only) Optional:  Caption for picture characters left Thank you for your feedback! Related Links Science Fair Project Guide Projects Involving Human Subjects Project Summary Difficulty  10  Time required Long (a couple of weeks) to Very Long (several weeks to months) Prerequisites Advanced biology course, or willingness to read up on such topics extensively. Material Availability A computer with Internet access is necessary for this project. Cost Very Low (under $20) Safety No issues Share this Project Idea! Donate to Science Buddies Sponsor Sponsored by generous grants from Bio-Rad and its Biotechnology Explorer program Inspiring minds want to know. Unravel the mysteries of biotech explorer.bio-rad.com

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