Biomod/2011/Slovenia/BioNanoWizards/ideaproteinaddons: Difference between revisions

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  style="color: black; font-weight: bold;">Protein add-ons</span></big></big></big></big><br>
  style="color: black; font-weight: bold;">Protein add-ons</span></big></big></big></big><br>
<br>
<br>
<span style="font-family: Arial;">Protein
<span style="font-family: Arial;"><br>Protein
functionalization of DNA has so far utilized a limited number of
functionalization of DNA has so far utilized a limited number of
orthogonal approaches, using nucleic acid-protein conjugates (Wilner,
orthogonal approaches, using nucleic acid-protein conjugates (Wilner,
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  style="font-family: Arial;">
   </li>
   </li>
</ul>
</ul><br><br>
<table
<table
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  style="margin: 3px 0px 20px 20px; width: 444px; height: 50px; float: right;"
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       <td style="text-align: center;"><img
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  alt="" src="http://openwetware.org/images/d/d7/ShemaZNFdolg.jpg"></td>
  alt="" src="http://openwetware.org/images/d/d7/ShemaZNFdolg.jpg"></td>
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     </tr>
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<br>
<br>
<br>
<br>
<big style="font-family: Arial;"><big><big><big><span
<big style="font-family: Arial; text-align: left"><big><big><big><span
  style="color: black; font-weight: bold;">A DNA origami
  style="color: black; font-weight: bold;">A DNA origami
add-on approach proposed by BioNanoWizards</span></big></big></big></big>
add-on approach proposed by BioNanoWizards</span></big></big></big></big>
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     <tr>
     <tr>
       <td style="text-align: center;"><img
       <td style="text-align: center;"><img
  style="font-family: Arial; width: 890px; height: 663px;" alt=""
  style="font-family: Arial; width: 890px; height: 663px; padding: 0 0 8px 0;" alt=""
  title="Beach house"
  title="Beach house"
  src="http://openwetware.org/images/c/c5/Slika8.png"></td>
  src="http://openwetware.org/images/c/c5/Slika8.png"></td>
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might be also used for structural purposes, e.g. to combine several DNA
might be also used for structural purposes, e.g. to combine several DNA
nanostructures via protein tethers, containing ZFPs, which is described
nanostructures via protein tethers, containing ZFPs, which is described
in the next section.</span><br style="font-family: Arial;">
in the next section.</span><br style="font-family: Arial;"><br>
<hr style="width: 100%; height: 2px;"><span
<hr style="width: 100%; height: 2px;"><span
  style="font-family: Arial;"></span><br>
  style="font-family: Arial;"></span><br>
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Acids Res</span>. in press
Acids Res</span>. in press
<br>
<br>
<br>
 
He Y, Tian Y, Ribbe AE, Mao C (2006) Antibody Nanoarrays with a pitch
He Y, Tian Y, Ribbe AE, Mao C (2006) Antibody Nanoarrays with a pitch
of 20 nanometers <span style="font-style: italic;">J. Am.
of 20 nanometers <span style="font-style: italic;">J. Am.
Chem. Soc</span>. 128: 12664-12665.
Chem. Soc</span>. 128: 12664-12665.
<br>
<br>
<br>
 
Kuzuya A, Kimura M, Numajiri N, Koshi N, Ohnishi T, Okada F, Komiyama M
Kuzuya A, Kimura M, Numajiri N, Koshi N, Ohnishi T, Okada F, Komiyama M
(2009) Precisely programmed and robust 2D streptavidin nanoarrays by
(2009) Precisely programmed and robust 2D streptavidin nanoarrays by
Line 643: Line 643:
10: 1811-1815.
10: 1811-1815.
<br>
<br>
<br>
 
Rinker S, Ke Y, Liu Y, Chhabra R (2008) Self-assembled DNA
Rinker S, Ke Y, Liu Y, Chhabra R (2008) Self-assembled DNA
nanostructures for distance-dependent multivalent ligand-protein
nanostructures for distance-dependent multivalent ligand-protein
Line 649: Line 649:
3: 418-422.
3: 418-422.
<br>
<br>
<br>
 
Sacca B, Meyer R, Erkelenz M, Kiko K, Arndt A, Schroeder H, Rabe KS,
Sacca B, Meyer R, Erkelenz M, Kiko K, Arndt A, Schroeder H, Rabe KS,
Niemeyer CM (2010) Orthogonal protein decoration of DNA origami. <span
Niemeyer CM (2010) Orthogonal protein decoration of DNA origami. <span
Line 655: Line 655:
9378-83.
9378-83.
<br>
<br>
<br>
 
Voight NV, Torring T, Rotaru A, Jacobsen MF, Ravnsbaek JB, Subramani R,
Voight NV, Torring T, Rotaru A, Jacobsen MF, Ravnsbaek JB, Subramani R,
Mamdouh W, Kjems J, Mokhir A, Besenbacher F, Gothelf KV (2010) Single
Mamdouh W, Kjems J, Mokhir A, Besenbacher F, Gothelf KV (2010) Single
Line 662: Line 662:
5:200-203.
5:200-203.
<br>
<br>
<br>
 
Williams BAR, Lund K, Liu Y, Yan H, Chaput JC (2007) Self-assembled
Williams BAR, Lund K, Liu Y, Yan H, Chaput JC (2007) Self-assembled
peptide nanoarrays: an approach to studying protein-protein
peptide nanoarrays: an approach to studying protein-protein
Line 668: Line 668:
119: 3111-3114.
119: 3111-3114.
<br>
<br>
<br>
 
Wilner OI, Weizmann Y, Gill R, Lioubashevski O, Freeman R, Willner I
Wilner OI, Weizmann Y, Gill R, Lioubashevski O, Freeman R, Willner I
(2009) Enzyme cascades activated on topologically programmed DNA
(2009) Enzyme cascades activated on topologically programmed DNA
Line 674: Line 674:
4: 249-254.
4: 249-254.
<br>
<br>
<br>
 
Yan H, Park SH, Finkelstein G, Reif JH, LaBean TH (2003) Design and
Yan H, Park SH, Finkelstein G, Reif JH, LaBean TH (2003) Design and
construction of double-decker tile as a route to three-dimensional
construction of double-decker tile as a route to three-dimensional

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</ul> <!-- End PureCSSMenu.com MENU --> </div> </div> </div> <!-- end #header --> <div id="page" class="container"> <div id="content"> <div class="post"> <div class="entry"><big><big><big><big><span 

style="color: black; font-weight: bold;">Protein add-ons</span></big></big></big></big><br>

<br> <span style="font-family: Arial;"><br>Protein functionalization of DNA has so far utilized a limited number of orthogonal approaches, using nucleic acid-protein conjugates (Wilner, 2009), aptamer-protein interactions (Rinker, 2008), antibody-antigen interactions (He, 2006; Williams, 2007) and streptavidin-biotin system (Yan, 2003; Kuzuya, 2009; Voight, 2010). Sacca and co-workers demonstrated the use of three different protein tags at the same time: biotin-streptavidin interaction and two suicide ligands for their specific enzymes (Sacca, 2010). These systems are based mainly on incorporation of specifically labeled oligonucleotides.</span><br 

style="font-family: Arial;">

<br style="font-family: Arial;"> <span style="font-family: Arial;"> We proposed a more general approach for position-specific protein binding to the surface of DNA origami, which has to comply with several criteria:<br> </span> <ul> 

 <li>strong binding affinities (Kd preferably in the nanomolar

or subnanomolar range),</li> 

 <li><span style="font-family: Arial;">simultaneous

binding of several molecules using the same approach and reaction conditions,</span></li> 

 <li><span style="font-family: Arial;">technological

feasibility in terms of cost and technology used.</span><br 

style="font-family: Arial;">
 </li>

</ul><br><br> <table 

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     <td style="text-align: justify;">Figure 1: Schematic

representation of six-finger ZFP to its binding DNA. <span 

style="font-weight: normal;"> Each zinc finger motif

composed of ββα fold binds specifically to 3 bp of DNA.</span></td> 

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</table> <span style="font-family: Arial;">Last year <a 

href="http://2010.igem.org/Team:Slovenia">Team Slovenia at

iGEM2010</a> competition proposed a scaffold-assisted biosynthetic pathway utilizing linear dsDNA as a program and zinc finger proteins as binding domains. This approach increased production of trans-resveratrol in bacteria 5-fold in the presence of DNA program which arranged the enzymes in the correct order (Conrado, 2011).</span><br 

style="font-family: Arial;">

<br style="font-family: Arial;"> <span style="font-family: Arial;"><span 

style="font-weight: bold;">Zinc finger proteins (ZFPs)</span>

are the most widespread and best characterized DNA-binding protein domains to date. These small structural motifs form coordination bonds with zinc cations to stabilize their ββα fold. Each zinc finger recognizes and <span style="font-weight: bold;">binds three consecutive base pairs</span> of a double stranded DNA in a sequence-dependent manner (<span style="font-weight: bold;">Figure 1</span>). Their specificity is based on interactions between amino acid side chains of the zinc finger α-helix and the DNA.</span><br 

style="font-family: Arial;">

<br style="font-family: Arial;"> <span style="font-family: Arial;">Moreover, zinc finger proteins can be designed by direct protein fusion of several successive zinc fingers which gives us access to an almost <span 

style="font-weight: bold;">unlimited</span> pool of

proteins (at least 700 well characterized in the ZiFDB database), which specifically and predictably target distinct DNA sequences. <span 

style="font-weight: bold;">Binding

affinity</span> of such zinc finger proteins to their target DNA sequences depends mainly on the number of successive zinc fingers used. Therefore, six finger proteins had been reported to have subnanomolar and even <span style="font-weight: bold;">picomolar</span> binding affinities.</span><br style="font-family: Arial;"> <br> <br> <big style="font-family: Arial; text-align: left"><big><big><big><span 

style="color: black; font-weight: bold;">A DNA origami

add-on approach proposed by BioNanoWizards</span></big></big></big></big> <br> <span style="font-family: Arial;"></span><br> <table 

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     <td style="text-align: justify;"><span
style="font-weight: bold;">Figure 2:&nbsp; Position

specific functionalization of DNA origami with selected protein functions. </span>Step 1: Desired functional protein domains are combined with any of the characterized 700 ZFPs into chimeric proteins. Step 2: Staples at selected positions on DNA origami are replaced with staples with added hairpin that incorporates the recognition sequence of the ZFPs selected in step 1, DNA origami with modified staples is annealed. Step 3: ZFP-functional domain chimeras are added to DNA origami and bind to the selected positions.</td> 

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</table> <span style="font-family: Arial;">Full potential of zinc fingers could be realized by fusion to selected functional protein domains, e.g. nucleases, recombinases and others, which have already been used to engineer genomes. In such systems zinc finger proteins serve for targeting functional domains to specific sites on DNA. This idea set the foundation for <span style="font-weight: bold;">protein DNA origami add-ons</span>. By inserting DNA hairpins into staple strands at specific positions on DNA origami, one can easily direct binding of such functional domains through zinc finger protein-target DNA interactions. Such an approach offers immediate <span style="font-weight: bold;">high-tech applications</span> such as <a 

href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/applabonchip">lab-on-a-nanochip</a>,

<a 

href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/appbiosensors">nanobiosensors</a>,

sequential biosynthetic route setups or <a 

href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/appbiosynthteticcompartments">construction

of biosynthetic organelles</a>.</span><br 

style="font-family: Arial;">

<br style="font-family: Arial;"> <span style="font-family: Arial;">DNA binding proteins might be also used for structural purposes, e.g. to combine several DNA nanostructures via protein tethers, containing ZFPs, which is described in the next section.</span><br style="font-family: Arial;"><br> <hr style="width: 100%; height: 2px;"><span 

style="font-family: Arial;"></span><br>

<span style="font-family: Arial;"><small> Conrado RJ, Wu GC, Boock JT, Xu H, Chen SY, Lebar T, Turnšek J, Tomšič N, Avbelj M, Gaber R, Koprivnjak T, Mori J, Glavnik V, Vovk I, Benčina M, Hodnik V, Anderluh G, Dueber JE, Jerala R, DeLisa MP (2011) DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency. <span style="font-style: italic;">Nucleic Acids Res</span>. in press <br>

He Y, Tian Y, Ribbe AE, Mao C (2006) Antibody Nanoarrays with a pitch of 20 nanometers <span style="font-style: italic;">J. Am. Chem. Soc</span>. 128: 12664-12665. <br>

Kuzuya A, Kimura M, Numajiri N, Koshi N, Ohnishi T, Okada F, Komiyama M (2009) Precisely programmed and robust 2D streptavidin nanoarrays by using periodical nanometer-scale wells embedded in DNA origami assembly <span style="font-style: italic;">ChemBioChem</span> 10: 1811-1815. <br>

Rinker S, Ke Y, Liu Y, Chhabra R (2008) Self-assembled DNA nanostructures for distance-dependent multivalent ligand-protein binding <span style="font-style: italic;">Nat. Nanotech</span>. 3: 418-422. <br>

Sacca B, Meyer R, Erkelenz M, Kiko K, Arndt A, Schroeder H, Rabe KS, Niemeyer CM (2010) Orthogonal protein decoration of DNA origami. <span 

style="font-style: italic;">Angew. Chem</span>. 49:

9378-83. <br>

Voight NV, Torring T, Rotaru A, Jacobsen MF, Ravnsbaek JB, Subramani R, Mamdouh W, Kjems J, Mokhir A, Besenbacher F, Gothelf KV (2010) Single molecule chemical reactions on DNA origami <span 

style="font-style: italic;">Nat. Nanotechnol</span>.

5:200-203. <br>

Williams BAR, Lund K, Liu Y, Yan H, Chaput JC (2007) Self-assembled peptide nanoarrays: an approach to studying protein-protein interactions <span style="font-style: italic;">Angew. Chem</span>. 119: 3111-3114. <br>

Wilner OI, Weizmann Y, Gill R, Lioubashevski O, Freeman R, Willner I (2009) Enzyme cascades activated on topologically programmed DNA scaffolds <span style="font-style: italic;">Nat. Nanotech</span>. 4: 249-254. <br>

Yan H, Park SH, Finkelstein G, Reif JH, LaBean TH (2003) Design and construction of double-decker tile as a route to three-dimensional periodic assembly of DNA <span style="font-style: italic;">Science</span> 301: 1882-1884.</small> </span> </div> </div> </div> <!-- end #content --> <div style="clear: both;">&nbsp;</div> </div> <!-- end #page --></div> <div id="footer-content" class="container"> <div id="footer-bg"> <table 

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