User:Adamsr

Rebecca Adams

Synthetic Biology, Summer 2007

Initial Ideas: 6/4-6/8

Having looked at BrainPOP for a number of different science topics, I have found that movies are approximately 2-3 minutes in length. The metamorphosis video was less than 2 minutes and it was too short. I was left with questions unanswered and it felt almost truncated. The movies in general are very packed with information and the quizzes are very helpful to enumerate what the main points were. It was a little difficult for me, someone who understands the concepts, to separate or identify all of them. Maybe longer movies would be more appropriate. I can understand how younger children could enjoy the two characters, but I found the robot distracting and the male’s voice very robotic itself. I hope that our animations feel more interactive.

My older sister, she just finished her B.A. in Philosophy at Bates College, and found the comic book interesting but made a couple of important comments: she found it difficult to follow the frames because they were different sizes, she enjoyed the explanations (she knows little about DNA and nothing about synthetic biology) and found they were complete enough. Reading the comic book sparked a good conversation about restriction sites, gene manipulation, and such. This made me excited. This is our goal, right? Interest those who don’t know that much about (synthetic) biology.

The two books that Natalie let me borrow, The Cartoon Guide to Chemistry and DNA for Beginners, are good for reference and I think they could be used for our topics under the heading of “Basic.” Both books present their topic in an interesting and concise manner. I think we should try to do the same. We will lose high school students if we create animations that are not interesting enough. I think we can build animations that have enough content, but not too much. I don’t want an information overload, because these are animations and hopefully will be fun and interesting, not just two characters basically reading out of a text book.

Week 2

Uploaded are the topics which I have delved into more.

DNA File:DNA.doc

20.109

20.109 “For Next Time” of 2-9-07 Due 2-14-07

1.

Italics: reengineering ideas

Gene I 3196-4242 Overlaps with Gene 11 Makes the pour for the protein to leave the bacteria Seems necessary. Why change it? Gene II 8268-831 Overlaps with Gene 10 Initiates single-stranded DNA again Gene III 1579-2853 No overlap At the blunt end of the phage, coats the DNA Attaches to F Pilus of E. Coli Pinches off phage after it leaves the host cell Can it enter another way? Could we make it enter better/more often? Gene IV 4220-5500 Overlaps with Genes 11 and 1 Makes pour for M13 to leave bacteria Gene V 843-1106 No overlap Protecting protein. Binds to single stranded DNA to ensure that it is not degraded by bacteria cell Removed as the DNA leaves the host cell Gene VI 2856-3194 No overlap Coats DNA at blunt end, “hidden” Find a way to see the usefulness/necessity of this “hidden” protein. Gene VII 1108-1209 Overlaps with Gene 9 Coats DNA at rounded end, secondary to 9 Gene VIII 1301-1522 Overlaps with Gene 9 Main gene to code for the protein coat. P8 travels length of phage Replaces P5 after DNA exits host cell Gene IX 1206-1304 Overlaps with Genes 7 and 8 Makes 5 copies of P9 to as the coat on the rounded end of the phage Gene X 496-831 Overlaps Gene 2 Regulates “the number of double stranded genomes in the bacterial host” Ensures + stands accumulate Make this better? Make more + strands? More phage? Gene XI 3916-4242 Overlaps Genes 1 and 4 Makes pour for the exiting phage

Generals reengineering ideas: something to change the pour/exit process through genes 4, 11, and 1.

2. P8 If the C-terminus were not negatively charged, I do not believe it would be able to create the massive chain necessary to coat the entire DNA strand. (Assuming the N-terminus is positively charged) The protein can make ionic bonds between each other for the length of the phage.

If all Leucines were encoded by CTA instead of CTG, there may be problems in reading other aspects of the nucleotides other than just codon/anticodon match up. One example is specific sites which are used for cutting, such as the palindromes which are needed for enzymes recognition. These do not read codons, but the nucleotides themselves.

Because the number of P8 proteins varies depended on the number necessary to coat the length of the phage, I do not believe if the size doubled, it would have a big impact. I think that there would just be a smaller number necessary. Since the phage can detect how many is necessary, I do not feel there would be a problem, assuming the phage “knew” that P8 had doubled in size.

P3 If the C-terminus of P3 were neutral instead of negatively charged, I feel this would again have an impact. I do not think it would be able to tolerate such a change. The interactions among ions verses not charged pieces of proteins or molecules are huge. Suddenly any repulsion or attraction would not occur and would have disastrous effects.

I believe the same would happen with P3 that I thought for P8 with a change in nucleotides for coding Leucine.

Because the end size of the phage is set and the number of P3s necessary to coat this blunt end is exact and much smaller than the number of P8 necessary, if the size of the protein were to double, I believe it would be problematic. There may be too much clutter at the end. Also the exiting of the phage from the bacteria may have problems because the P3 is the last site of contact and if they are twice as long, there may be problems exiting the host cell. One possibility is that the protein coat may not close properly and the DNA may be exposed directly to the gel or whatever the medium in which the bacteria is held.

2b. Transcriptional terminators that are 2x stronger/weaker, I would assume would still work, although not optimally, because otherwise this would probably have evolved in such a way to have these stronger or weaker terminators. 100x in either direction would be too far off from the norm to encode correctly. If it were stronger some things may be transcribed too much while others were not affected quite as much and then there would not be the appropriate ratio of RNA and subsequently proteins. If it were 100x weaker, this may be too weak for sections of DNA, then there may be missing information for the rest of the central dogma sequence to continue correctly.

3. Two related single-stranded phages are f1 and fd (http://tools.neb.com/wolbachia/labsite/protocols/M13.htm)

They are both single-stranded phages, like M13. They can infect E. Coli cells

(On another site, it appeared that the three were written as different names for the same phage.)

4. You’ve been cc’ed.

For next time due 2-28-07 My refactored section is M31971. It is also listed above. The major work was to remove repeated sections once the genome was separated. I did this by changing the wobble position in the gene that was overlapping, which stopped the repeat but kept the amino acid sequence the same. I added two restriction sites between each gene. And created what I call ‘gene units.’ The unit is the two restriction sites at either end, the promoter (if available), the RBS, and the gene itself. Different sites ensure that the refactored gene (if one is reengineering a specific gene) will enter in the correct orientation. Although I am not completely sure if two sites are necessary, it allows an entity to be created for each gene unit without any sharing, even restriction sites. I worked on paper and on the computer in order to organize my thoughts and those papers are attached.