Team:Harvard/Test Page 6

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Gene therapy is a powerful approach for the treatment of disease, and holds great potential for success. While gene therapy has progressed significantly since its conception, much of its projected potential remains untapped, while existing therapeutic advancements are still fraught with serious problems. Many of these roadblocks to existing therapies are caused by non-specific gene insertion (as through viral vectors), which hinders therapeutic viability and can lead to unintended side effects including cancer. In recent attempts to overcome this obstacle, however, one particular approach has shown much promise. This approach utilizes engineered zinc finger proteins, which have been shown to edit the genome with dramatically increased accuracy (Perez et al 2008, Li et al 2011).Zinc finger proteins are naturally-occurring protein domains composed of multiple individual zinc finger subdomains. Although the individual subdomains (“fingers”) occur in a variety of structural motifs, the classic Cys<sub>2</sub>His<sub>2</sub> (C<sub>2</sub>H<sub>2</sub>) motif is among the best characterized and can be observed in a variety of transcription factors. The C<sub>2</sub>H<sub>2</sub> motif consists of a beta-sheet conjugated to an alpha helix, and it is structurally coordinated through interactions between two cysteine and two histidine residues with a single zinc ion. Many eukaryotic transcription factors utilize C<sub>2</sub>H<sub>2</sub> zinc finger domains, which possess a unique capacity to bind to specific DNA sequences. Zinc finger proteins have received increasing attention in recent research for their DNA-binding ability and specificity, which offers a solution to non-specificity in gene therapy and could thus bring the scientific community a step closer to realizing many novel therapeutic applications. Recent studies, for instance have demonstrated that DNA-binding zinc fingers coupled with Type IIS restriction endonucleases such as Fok1 can be harnessed as effective tools to genetically treat hemophilia and confer HIV resistance in mouse models (Perez et al 2008, Li et al 2011).
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While many different natural zinc finger proteins can be employed for synthetic biology-based tasks, engineered zinc finger proteins are most commonly composed of an array of three zinc fingers based on Zif268. Zif268 is a well-characterized mammalian early response transcription factor also known as EGR-1 that was discovered in mice. Zif268 has three C<sub>2</sub>H<sub>2</sub> finger subunits, and each finger binds a specific 3-nucleotide base pair (bp) triplet on a DNA strand. Composed of an array of three fingers, Zif268 binds to three consecutive DNA triplets that in total comprise a 9-bp binding site.  This 3-finger domain, 9-bp specificity is a commonly occurring theme in zinc finger literature, although it is by no means a rule. Natural and engineered zinc finger arrays may contain fewer or more zinc fingers and bind DNA sequences of corresponding length and specificity. While any given zinc finger might bind a certain 3-bp DNA sequence with exquisite specificity, even the most specific 3-bp binding event is of little practical value for gene therapy, as a given 3-bp sequence may appear countless times within a given genome. Thus, for practical use in drug delivery or gene therapy, zinc fingers must be engineered to bind more specifically to DNA sequences. Such increased specificity can be achieved through the creation of multi-finger arrays that bind to specific 9-bp sequences. With this in mind, research has focused on creating modular zinc finger subunits, which can be combined into multi-finger arrays. Three-finger arrays, for instance, are tailored to bind to a specific 9-bp sequence through the selection of appropriate zinc fingers to bind to each DNA triplet.
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Different studies have suggested different models of binding and varying levels of success for zinc finger modularity. Thus, through an approach utilizing data-mining, binding models, and comprehensive bioinformatics, in conjunction with next-generation oligo synthesis technology, we hope to develop a method for engineering zinc finger proteins that can bind to any arbitrarily-selected DNA sequence. The success of such an engineering method would, in turn, facilitate clinical advancements by promoting highly-specific, targeted gene therapies, and would promote personalized medicine by allowing the production of zinc finger-based therapies tailored to unique genomic sequences.
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<h2 class="title">Mentors</h2>
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                  <img src="https://static.igem.org/mediawiki/2011/e/e5/HARVMentors.jpg"></div>
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<h2 class="title">Dan</h2>
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<p><h3> Daniel Goodman</h3><br><br>
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                                PhD Candidate in the Medical Engineering and Medical Physics Program, MIT/HMS/HST<br> 
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                                <br>Church Laboratory</p>     
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<h2 class="title">Vatsan</h2>
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                                <p><h3> Srivatsan Raman, PhD</h3><br><br>
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                                Postdoctoral Fellow<br> 
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                                <br>Church Laboratory</p>     
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<h2 class="title">Joyce</h2>
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                                <p><h3> Joyce Yang</h3><br><br>
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                                PhD Candidate in the Biomedical and Biological Science Program, Harvard Medical School<br> 
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                                <br>Church Laboratory</p>     
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<h2 class="title">Jamie</h2>
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<p><h3> Jamie Rodgers</h3><br><br>
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                                PhD student<br> </p>
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<h2 class="title">Noah</h2>
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<p><h3> Noah Taylor</h3><br><br>
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                                PhD student<br> </p>
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<h2 class="title">Jun</h2>
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<p><h3> Jun Li</h3><br><br>
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                                PhD student<br> </p>
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<h2 class="title">Jagesh</h2>
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<p><h3> Jagesh Shah, PhD</h3><br><br>
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                                Assistant Professor of Systems Biology, Harvard Medical School<br> </p>
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<h2 class="title">Alain</h2>
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<p><h3> Alain Viel, PhD</h3><br><br>
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                                Director of Undergraduate Research, Department of Molecular and Cellular Biology<br>
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                                Senior Lecturer in Molecular and Cellular Biology<br> </p>
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<h2 class="title">Andy</h2>
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<p><h3> Andrew Cumming</h3><br> Laboratory Technician <br> </p>
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==References==
 
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#Li H, Haurigot V, Doyon Y, Li T, Wong SY, Bhagwat AS, Malani N, Anguela XM, Sharma R, Ivanciu L, Murphy SL, Finn JD, Khazi FR, Zhou S, Paschon DE, Rebar EJ, Bushman FD, Gregory PD, Holmes MC, High KA (2011). In vivo genome editing restores haemostasis in a mouse model of haemophilia. ''Nature'', doi: 10.1038/nature10177 [Epub ahead of print].
 
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#Perez EE, Wang J, Miller JC, Jouvenot Y, Kim KA, Liu O, Wang N, Lee G, Bartsevich VV, Lee YL, Guschin DY, Rupniewski I, Waite AJ, Carpenito C, Carroll RG, Orange JS, Urnov FD, Rebar EJ, Ando D, Gregory PD, Riley JL, Holmes MC, June CH (2008). Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases. ''Nature Biotechnology'', 26(7), 808-16.
 
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=Clinical Applications=
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<h2 class="title">Team</h2>
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                  <img src="https://static.igem.org/mediawiki/2011/1/1e/HARVteam_picture.jpg"></div>
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<h2 class="title">Kristin</h2>
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<p><table style="background:transparent"><tr><td><h3> Kristin Barclay</h3><br><br>
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                                  <b>Concentration:</b>  Physics and Astrophysics <br><br>
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                                  <b>Year:</b> 2014<br><br>
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                                  <b>Team Affiliation:</b>  Bioinformatics, Web Design <br><br>
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                                  <b>Other Hobbies:</b> Stargazing, ASOIAF, Battlestar Galactica <br><br>
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                                  <b>Favourite YouTube Video:</b> <a href="http://www.youtube.com/watch?v=WGoi1MSGu64"> The Humans Are Dead</a>          <br><br>
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                                  <b>Way to Pass Time While Waiting for PCR:</b> Strike a heroic pose while  staring dreamily into the distance.  </td><td><img src="https://static.igem.org/mediawiki/2011/b/b5/Kristin_test.jpg"></td></tr></table></p>
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<h2 class="title">Justin</h2>
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<p><table style="background:transparent"><tr><td><h3>Justin Chew</h3><br><br>
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                                  <b>Concentration:</b> Folklore and Mythology <br><br>
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                                  <b>Year:</b> 2011 <br><br>
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                                  <b>Team Affiliation:</b>  Bioinformatics, ZF <br><br>
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                                  <b>Other Hobbies:</b> Odin worship, lightning bolts, swordfighting, and carving art out of bones <br><br>
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                                  <b>Favourite YouTube Video:</b> <a href="http://www.youtube.com/watch?v=nRoVIpczcrY"> Sansa sees beheaded father Ned (Game of Thrones, HBO)</a> <br><br>
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                                  <b>Way to Pass Time While Waiting for PCR:</b> Sacrifice a gel to Thor.  <br></td><td><img src="https://static.igem.org/mediawiki/2011/8/8f/HARVJustin.png"></td></tr></table></p>
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<h2 class="title">Sarah</h2>
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<p><table style="background:transparent"><tr><td><h3> Sarah Cloudhury</h3><br><br>
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                                  <b>Concentration:</b> Linguistics<br><br>
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                                  <b>Year:</b> 2012 <br><br>
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                                  <b>Team Affiliation:</b>  Wet Lab, TolC <br><br>
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                                  <b>Other Hobbies:</b> Studies of Latin, Greek, Ancient Greek, Russian, Swedish, Swahilli, and !Kung, among many others <br><br>
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                                  <b>Favourite YouTube Video:</b> <a href="http://www.youtube.com/watch?v=0Kx9NVVOU88"> Geek Love Song </a> <br><br>
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                                  <b>Way to Pass Time While Waiting for PCR:</b> Tell it to go faster - I speak DNA (both template and amplify dialects.  <br></td><td><img src="https://static.igem.org/mediawiki/2011/4/45/HARVSarah.png"></td></tr></table></p>
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<h2 class="title">Hello!</h2>
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<p><table style="background:transparent"><tr><td><h3> Will Clerx</h3><br><br>
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                                  <b>Concentration:</b> Molecular & Cellular/Organismic & Evolutionary Biology <br><br>
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                                  <b>Year:</b> 2014 <br><br>
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                                  <b>Team Affiliation:</b>  Wet Lab, Web Design <br><br>
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                                  <b>Other Hobbies:</b> Cross country, track, musics, playing with zinc fingers <br><br>
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                                  <b>Favourite YouTube Video:</b> <a href="http://www.youtube.com/watch?v=MahTKZDHXaA"> Harry Potter and the Deathly Hallows Trailer Parody </a> <br><br>
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                                  <b>Way to Pass Time While Waiting for PCR:</b> Do another PCR. Or, write an iGEM song.    <br></td><td><img src="https://static.igem.org/mediawiki/2011/6/60/HARVWill.jpg"></td></tr></table></p>
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<h2 class="title">Naomi</h2>
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<p><table style="background:transparent"><tr><td><h3> Naomi Genuth</h3><br><br>
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                                  <b>Concentration:</b> Molecular & Cellular/Organismic & Evolutionary Biology <br><br>
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                                  <b>Year:</b> 2014 <br><br>
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                                  <b>Team Affiliation:</b>  Wet Lab, Wolfe  <br><br>
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                                  <b>Other Hobbies:</b> Reading, running, hiking, piano <br><br>
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                                  <b>Favourite YouTube Video:</b> <a href="http://www.youtube.com/watch?v=E6h1KsWNU-A"> America's Funniest Home Videos - Funny Cats</a> <br><br>
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                                  <b>Way to Pass Time While Waiting for PCR:</b> Set up another reaction. Or two. Or three.  <br></td><td><img src="https://static.igem.org/mediawiki/2011/6/69/HARVnaomi.jpg"></td></tr></table></p>
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<h2 class="title">Brandon</h2>
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<p><table style="background:transparent"><tr><td><h3> Brandon Gerberich</h3><br><br>
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                                  <b>Concentration:</b> Chemistry <br><br>
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                                  <b>Year:</b> 2014 <br><br>
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                                  <b>Team Affiliation:</b>  Bioinformatics, Wolfe <br><br>
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                                  <b>Other Hobbies:</b> Trumpet, Board Games, Wind Surfing <br><br>
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                                  <b>Favourite YouTube Video:</b> <a href="http://www.youtube.com/watch?v=JkxieS-6WuA"> Imagining the Tenth Dimension</a> <br><br>
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                                  <b>Way to Pass Time While Waiting for PCR:</b> 1) Just use the 6th dimension for instant PCR results, or 2) Remain in the 3rd dimension and build ice snowmen.  <br></td><td><img src="https://static.igem.org/mediawiki/2011/0/00/HARVBrandon.jpg"></td></tr></table></p>
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<h2 class="title">Mark</h2>
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<p><table style="background:transparent"><tr><td><h3> Mark Kopelman</h3><br><br>
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                                  <b>Concentration:</b> Human Evolutionary Biology <br><br>
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                                  <b>Year:</b> 2012 <br><br>
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                                  <b>Team Affiliation:</b>  Wet Lab,  ToIC, Web Design <br><br>
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                                  <b>Other Hobbies:</b> Winning <br><br>
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                                  <b>Favourite YouTube Video:</b> <a href="http://www.youtube.com/watch?v=Ey-VNes5YQs&feature=related"> Friday</a> <br><br>
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                                  <b>Way to Pass Time While Waiting for PCR:</b> ...Run another PCR, duh.  <br></td><td><img src="https://static.igem.org/mediawiki/2011/6/6d/HARVMark.png"></td></tr></table></p>
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<h2 class="title">Matt</h2>
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<p><table style="background:transparent"><tr><td><h3> Matt Lunati </h3><br><br>
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                                  <b>Concentration:</b> Studies of Women, Gender, and Sexuality <br><br>
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                                  <b>Year:</b> 2012 <br><br>
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                                  <b>Team Affiliation:</b>  Wet Lab, ToIC <br><br>
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                                  <b>Other Hobbies:</b> Picket lines, making signs, bumper stickers  <br><br>
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                                  <b>Favourite YouTube Video:</b> <a href="http://www.youtube.com/watch?v=Ljur6v7-yoc&feature=fvwrel"> Hitler Finds Out Pokemon Aren't Real</a> <br><br>
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                                  <b>Way to Pass Time While Waiting for PCR:</b> Campaign for pipette equality.  <br></td><td><img src="https://static.igem.org/mediawiki/2011/8/81/HARVMatt.png"></td></tr></table></p>
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<h2 class="title">Nida</h2>
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<p><table style="background:transparent"><tr><td><h3> Nida Naushad</h3><br><br>
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                                  <b>Concentration:</b> Mathematics and Philosophy <br><br>
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                                  <b>Year:</b> 2014 <br><br>
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                                  <b>Team Affiliation:</b>  Bioinformatics, ZF <br><br>
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                                  <b>Other Hobbies:</b> Marx, Einstein, assorted dead Russian authors  <br><br>
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                                  <b>Favourite YouTube Video:</b> <a href="http://www.youtube.com/watch?v=R_w4HYXuo9M"> How To Turn a Sphere Inside Out</a> <br><br>
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                                  <b>Way to Pass Time While Waiting for PCR:</b> Contemplate the possibility of sentient bacteria in all possible worlds.  <br></td><td><img src="https://static.igem.org/mediawiki/2011/0/0f/HARVNida.jpg"></td></tr></table></p>
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==Colorblindness==
 
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=Technological Applications=
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*The novel methods we employed in our project have the potential to revolutionize synthetic biology practices, and the way that future iGEM competitions are conducted. To learn more about the technological applications of our project, please see our [https://2011.igem.org/Team:Harvard/Technology '''Technology'''] page
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</div>
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<div class="whitebox">
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=Helpful Zinc Finger Links=
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*Predicting DNA Recognition by C2H2 Zinc Finger Proteins: http://compbio.cs.princeton.edu/zf/
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**An SVM useful for predicting how well a given amino acid sequence will bind to a given DNA sequence
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*The Zinc Finger Consortium: http://www.zincfingers.org/default2.htm
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**Information & helpful resources for zinc fingers
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*Joung Lab: http://www.jounglab.org/
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**Information about Dr. Joung's extensive work with zinc fingers
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</div>
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Revision as of 18:17, 2 August 2011

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Team

Kristin

Kristin Barclay



Concentration: Physics and Astrophysics

Year: 2014

Team Affiliation: Bioinformatics, Web Design

Other Hobbies: Stargazing, ASOIAF, Battlestar Galactica

Favourite YouTube Video: The Humans Are Dead

Way to Pass Time While Waiting for PCR: Strike a heroic pose while staring dreamily into the distance.

Justin

Justin Chew



Concentration: Folklore and Mythology

Year: 2011

Team Affiliation: Bioinformatics, ZF

Other Hobbies: Odin worship, lightning bolts, swordfighting, and carving art out of bones

Favourite YouTube Video: Sansa sees beheaded father Ned (Game of Thrones, HBO)

Way to Pass Time While Waiting for PCR: Sacrifice a gel to Thor.

Sarah

Sarah Cloudhury



Concentration: Linguistics

Year: 2012

Team Affiliation: Wet Lab, TolC

Other Hobbies: Studies of Latin, Greek, Ancient Greek, Russian, Swedish, Swahilli, and !Kung, among many others

Favourite YouTube Video: Geek Love Song

Way to Pass Time While Waiting for PCR: Tell it to go faster - I speak DNA (both template and amplify dialects.

Hello!

Will Clerx



Concentration: Molecular & Cellular/Organismic & Evolutionary Biology

Year: 2014

Team Affiliation: Wet Lab, Web Design

Other Hobbies: Cross country, track, musics, playing with zinc fingers

Favourite YouTube Video: Harry Potter and the Deathly Hallows Trailer Parody

Way to Pass Time While Waiting for PCR: Do another PCR. Or, write an iGEM song.

Naomi

Naomi Genuth



Concentration: Molecular & Cellular/Organismic & Evolutionary Biology

Year: 2014

Team Affiliation: Wet Lab, Wolfe

Other Hobbies: Reading, running, hiking, piano

Favourite YouTube Video: America's Funniest Home Videos - Funny Cats

Way to Pass Time While Waiting for PCR: Set up another reaction. Or two. Or three.

Brandon

Brandon Gerberich



Concentration: Chemistry

Year: 2014

Team Affiliation: Bioinformatics, Wolfe

Other Hobbies: Trumpet, Board Games, Wind Surfing

Favourite YouTube Video: Imagining the Tenth Dimension

Way to Pass Time While Waiting for PCR: 1) Just use the 6th dimension for instant PCR results, or 2) Remain in the 3rd dimension and build ice snowmen.

Mark

Mark Kopelman



Concentration: Human Evolutionary Biology

Year: 2012

Team Affiliation: Wet Lab, ToIC, Web Design

Other Hobbies: Winning

Favourite YouTube Video: Friday

Way to Pass Time While Waiting for PCR: ...Run another PCR, duh.

Matt

Matt Lunati



Concentration: Studies of Women, Gender, and Sexuality

Year: 2012

Team Affiliation: Wet Lab, ToIC

Other Hobbies: Picket lines, making signs, bumper stickers

Favourite YouTube Video: Hitler Finds Out Pokemon Aren't Real

Way to Pass Time While Waiting for PCR: Campaign for pipette equality.

Nida

Nida Naushad



Concentration: Mathematics and Philosophy

Year: 2014

Team Affiliation: Bioinformatics, ZF

Other Hobbies: Marx, Einstein, assorted dead Russian authors

Favourite YouTube Video: How To Turn a Sphere Inside Out

Way to Pass Time While Waiting for PCR: Contemplate the possibility of sentient bacteria in all possible worlds.

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