עבודה זו מומנה על ידי משרד הצי צעיר מחקר תכנית פרס חוקר N000141110914, משרד המחקר של צי גרנט N000141010827, NSF פרס קריירת CCF1054898, פרס ממציא ניו 1DP2OD007292 של מנהל ה- NIH ומכון Wyss לפקולטה להנדסת הפעלת קרן בהשראה ביולוגית (לPY) ו צינג-פקינג מרכז למדעי חיים הפעלת קרן (לBW).

<ol>
	<li>Seeman, N. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nucleic+acid+junctions+and+lattices.">Nucleic acid junctions and lattices.</a> J. Theor. Biol. 99 (2), 237-247 (1982).</li><li>Fu, T. J., Seeman, N. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA+double-crossover+molecules.">DNA double-crossover molecules.</a> Biochemistry. 32 (13), 3211-3220 (1993).</li><li>Winfree, E., Liu, F., Wenzler, L. A., Seeman, N. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Design+and+self-assembly+of+two-dimensional+DNA+crystals.">Design and self-assembly of two-dimensional DNA crystals.</a> Nature. 394 (6693), 539-544 (1998).</li><li>Yan, H., Park, S. H., Finkelstein, G., Reif, J. H., LaBean, T. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA-templated+self-assembly+of+protein+arrays+and+highly+conductive+nanowires.">DNA-templated self-assembly of protein arrays and highly conductive nanowires.</a> Science. 301 (5641), 1882-1884 (2003).</li><li>Rothemund, P. W. K., Papadakis, N., Winfree, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Algorithmic+self-assembly+of+DNA+Sierpinski+triangles.">Algorithmic self-assembly of DNA Sierpinski triangles.</a> PLoS Biol. 2 (12), e424 (2004).</li><li>Shih, W., Quispe, J., Joyce, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+1.7-kilobase+single-stranded+DNA+that+folds+into+a+nanoscale+octahedron.">A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron.</a> Nature. 427 (6975), 618-621 (2004).</li><li>Chworos, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Building+programmable+jigsaw+puzzles+with+RNA.">Building programmable jigsaw puzzles with RNA.</a> Science. 306 (5704), 2068-2072 (2004).</li><li>Park, S. H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Finite-size,+fully-addressable+DNA+tile+lattices+formed+by+hierarchical+assembly+procedures.">Finite-size, fully-addressable DNA tile lattices formed by hierarchical assembly procedures.</a> Angew. Chem. Int. Ed. 45 (5), 735-739 (2006).</li><li>Rothemund, P. W. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Folding+DNA+to+create+nanoscale+shapes+and+patterns.">Folding DNA to create nanoscale shapes and patterns.</a> Nature. 440 (7082), 297-302 (2006).</li><li>Schulman, R., Winfree, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Synthesis+of+crystals+with+a+programmable+kinetic+barrier+to+nucleation.">Synthesis of crystals with a programmable kinetic barrier to nucleation.</a> Proc. Natl Acad. Sci. USA. 104 (39), 15236-15241 (2007).</li><li>He, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hierarchical+self-assembly+of+DNA+into+symmetric+supramolecular+polyhedra.">Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra.</a> Nature. 452 (7184), 198-201 (2008).</li><li>Yin, P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Programming+DNA+tube+circumferences.">Programming DNA tube circumferences.</a> Science. 321 (5890), 824-826 (2008).</li><li>Sharma, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Control+of+self-assembly+of+DNA+tubules+through+integration+of+gold+nanoparticles.">Control of self-assembly of DNA tubules through integration of gold nanoparticles.</a> Science. 323 (5910), 112-116 (2009).</li><li>Douglas, S. M., Dietz, H., Liedl, T., H&#246;gberg, B., Graf, F., Shih, W. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Self-assembly+of+DNA+into+nanoscale+three-dimensional+shapes.">Self-assembly of DNA into nanoscale three-dimensional shapes.</a> Nature. 459 (7245), 414-418 (2009).</li><li>Andersen, E. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Self-assembly+of+a+nanoscale+DNA+box+with+a+controllable+lid.">Self-assembly of a nanoscale DNA box with a controllable lid.</a> Nature. 459 (7243), 73-76 (2009).</li><li>Dietz, H., Douglas, S. M., Shih, W. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Folding+DNA+into+twisted+and+curved+nanoscale+shapes.">Folding DNA into twisted and curved nanoscale shapes.</a> Science. 325 (5941), 725-730 (2009).</li><li>Zheng, J. P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=From+molecular+to+macroscopic+via+the+rational+design+of+self-assembled+3D.">From molecular to macroscopic via the rational design of self-assembled 3D.</a> DNA crystal. Nature. 461 (7260), 74-77 (2009).</li><li>Han, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA+origami+with+complex+curvatures+in+three-dimensional+space.">DNA origami with complex curvatures in three-dimensional space.</a> Science. 332 (6024), 342-346 (2011).</li><li>Liu, W., Zhong, H., Wang, R., Seeman, N. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Crystalline+two-dimensional+DNA+origami+arrays.">Crystalline two-dimensional DNA origami arrays.</a> Angew. Chem. Int. Ed. 50 (1), 264-267 (2011).</li><li>Zhao, Z., Liu, Y., Yan, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Organizing+DNA+origami+tiles+into+larger+structures+using+preformed+scaffold+frames.">Organizing DNA origami tiles into larger structures using preformed scaffold frames.</a> Nano Lett. 11 (7), 2997-3002 (2011).</li><li>Woo, S., Rothemund, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Programmable+molecular+recognition+based+on+the+geometry+of+DNA+nanostructures.">Programmable molecular recognition based on the geometry of DNA nanostructures.</a> Nat. Chem. 3 (8), 620-627 (2011).</li><li>Delebecque, C. J., Lindner, A. B., Silver, P. A., Aldaye, F. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Organization+of+intracellular+reactions+with+rationally+designed+RNA+assemblies.">Organization of intracellular reactions with rationally designed RNA assemblies.</a> Science. 333 (6041), 470-474 (2011).</li><li>Lin, C., Liu, Y., Rinker, S., Yan, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA+tile+based+self-assembly:+building+complex+nanoarchitectures.">DNA tile based self-assembly: building complex nanoarchitectures.</a> ChemPhysChem. 7 (8), 1641-1647 (2006).</li><li>Seeman, N. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nanomaterials+based+on+DNA.">Nanomaterials based on DNA.</a> Annu. Rev. Biochem. 79 (1), 65-87 (2010).</li><li>Voigt, N. V., Nangreave, J., Yan, H., Gothelf, K. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA+origami:+a+quantum+leap+for+self-assembly+of+complex+structures.">DNA origami: a quantum leap for self-assembly of complex structures.</a> Chem. Soc. Rev. 40 (12), 5636-5646 (2011).</li><li>Wei, B., Dai, M., Yin, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Complex+Shapes+self-assembled+from+single+stranded+DNA+tiles.">Complex Shapes self-assembled from single stranded DNA tiles.</a> Nature. 485 (7400), 623-626 (2012).</li><li>Wei, B., Wang, Z., Mi, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Uniquimer:+software+of+de+novo+DNA+sequence+generation+for+DNA+self-assembly:+an+introduction+and+the+related+applications+in+DNA+self-assembly.">Uniquimer: software of de novo DNA sequence generation for DNA self-assembly: an introduction and the related applications in DNA self-assembly.</a> J. Comput. Theor. Nanosci. 4 (1), 133-141 (2007).</li><li>Seeman, N. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=De+novo+design+of+sequences+for+nucleic+acid+structural+engineering.">De novo design of sequences for nucleic acid structural engineering.</a> J. Biomol. Struct. Dyn. 8 (3), 573-581 (1990).</li><li>Hansma, H. G., Laney, D. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA+binding+to+mica+correlates+with+cationic+radius:+assay+by+atomic+force+microscopy.">DNA binding to mica correlates with cationic radius: assay by atomic force microscopy.</a> Biophys. J. 70 (4), 1933-1939 (1996).</li><li>Seelig, G., Soloveichik, D., Zhang, D. Y., Winfree, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Enzyme-free+nucleic+acid+logic+circuits.">Enzyme-free nucleic acid logic circuits.</a> Science. 314 (5805), 1585-1588 (2006).</li><li>Yin, P., Choi, H. M. T., Calvert, C. R., Pierce, N. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Programming+biomolecular+self-assembly+pathways.">Programming biomolecular self-assembly pathways.</a> Nature. 451 (7176), 318-322 (2008).</li></ol>

The authors declare competing financial interests.

בשלב היווצרות מבנה, חשוב לשמור על ריכוז מתאים של קטיונים מגנזיום (למשל., 15 מ&quot;מ) בתערובת גדיל DNA לDNA ננו העצמי להרכיב. כמו כן, בשלב אפיון agarose ג&#39;ל / טיהור, חשוב לשמור על ריכוז קטיון מגנזיום מתאים (למשל., 10 מ&quot;מ) בג&#39;ל וחיץ ריצת ג&#39;ל לשמור DNA ננו במהלך אלקטרופור...

עבודת הרכבה עצמית קודמת חומצות גרעין 1-25 הובילה לבנייה המוצלחת של מגוון רחב של מבנים מורכבים, לרבות DNA 2 - 5,8,10 - 13,17,23 או RNA 7,22 3,4,7 תקופתי, 22 ו -5 דו ממדים אלגוריתמיים חסימה, סרטים 10,12 וצינורות 4,12,13, גבישי 3D 17, פאונים 11 וסופיים, 2D מעצב 7,8. שיטה יעילה במיוחד היא מלווה בתמיכת אוריגמי DNA, לפיה גדיל פיגום אחת מקופל על ידי רב גדילי מצרך עזר קצרים ליצירת צורה מורכבת 9,14 - 16,18 - 21,25. לאחרונה דיווחו שיטה לבניית ננו הדיסקרטי עם צורות 2D נקבעו באמצעות אריחים חד-גדילים (SST), והפגינו מבנים עם מורכבות דומה לאוריגמי DNA 26. articl זהדואר הוא עיבוד של העבודה הקודמת שלנו 26 ומתאר מפורט פרוטוקולים להסדרת טמפרטורת פני הים מיעון בנפרד לצורות 2D סופיות מתוחכמות עם ממדים שנקבעו בדיוק (רוחב ואורך) ומורפולוגיות. יתרון מרכזי אחד של שיטת SST הוא המודולריות שלה. כל SST המרכיב של מבנה משמש כיחידת בנייה מודולרית בהרכבה, וקבוצות משנה שונות של טמפרטורת פני הים אלה לייצר צורות שונות. כך, הקמנו פלטפורמה כללית לבניית ננו עם גדלים וצורות שנקבעו מגדילי דנ&quot;א קצרים, סינטטיים. טמפרטורת פני הים מכילים ארבעה תחומים, כל אחת (איור 1 א) באורך 10 או 11 נוקלאוטידים. טמפרטורת פני הים להיקשר כך שהסלילים המקבילים שלהם ליצור סריג DNA מוחזק ביחד על ידי קשרים מוצלבים. כל מוצלב הוא פוספט בין תחומים 2 ו -3 פוספט נמתח באופן מלאכותי בתרשימים לבהירות חזותית. הצלבות מרווחים שני סיבובי סליל (21 בסיסים) מזה (&lt;1B strong&gt; איור). המלבנים מרוכבים מכונים על ידי ממדיהם במספר הסלילים וסיבובי סליל. לדוגמא, מלבן שרוחבו שישה סלילים ושמונה סליל הופך ארוך הפניה כ6H × מלבן 8T. ניתן להשאיר את טמפרטורת פני ים החוצה, הוסיפו, או מחדש בדרך אחרת כדי ליצור מבנים של צורות וגדלים (איור 1 ג) שרירותיות. לדוגמא, עיצוב מלבני ניתן התגלגל לתוך צינור באורך רצוי ורדיוס (1D איור). לחלופין, סריג SST המלבני ניתן לראות כבד מולקולרי המורכב מפיקסלים SST, כל ננומטר 3 על ידי 7 ננומטר. במחקר זה, אנו משתמשים בבד מולקולרי של 310 טמפרטורת פני הים פנימית באורך מלא, 24 טמפרטורת פני הים באורך מלא המרכיבות את גבולות ימין ועל השמאל, וטמפרטורת פני ים 28 חצי אורך להרכיב את הגבולות העליונים ותחתונים. יש הבד 24 סלילים כפולים מקושרים על ידי הצלבות וכל סליל מכיל 28 סיבובי סליל (294 בסיסים), ולכן הוא מכונה24H × בד מלבני 28T. 24H × בד 28T יש משקל מולקולרי דומה לזה של מבנה אוריגמי DNA שנוצר מפיגום הפאג M13.

<table border="0" cellpadding="0" cellspacing="0" width="919">
	<tbody>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Name of Material/ Equipment</td>
			<td style="width:183px;">Company</td>
			<td style="width:119px;">Catalog Number</td>
			<td style="width:401px;">Comments/Description</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">DNA Strands&#160;</td>
			<td style="width:183px;">Integrated DNA Technology</td>
			<td style="width:119px;"></td>
			<td>Section 3.1</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">SYBR Safe DNA gel stain</td>
			<td style="width:183px;">Invitrogen</td>
			<td style="width:119px;">S33102</td>
			<td>Section 3.4.2</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Freeze&#39;N Squeeze DNA Gel Extraction Spin Columns</td>
			<td style="width:183px;">BIO-RAD</td>
			<td style="width:119px;">731-6166</td>
			<td>Section 3.6</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Bruker&#39;s Sharp Nitride Lever Probes</td>
			<td style="width:183px;">Bruker AFM Probes</td>
			<td style="width:119px;">SNL10</td>
			<td>Section 4.3</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Safe Imager 2.0 Blue Light Transilluminator</td>
			<td style="width:183px;">Invitrogen</td>
			<td style="width:119px;">G6600</td>
			<td>Section 3.6</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Centrifuge 5430R</td>
			<td style="width:183px;">Eppendorf</td>
			<td style="width:119px;">5428 000.414</td>
			<td>Section 3.6</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Transmission Electron Microscope&#160;</td>
			<td style="width:183px;">Jeol</td>
			<td style="width:119px;">Jem 1400</td>
			<td>Section 7.4</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Multimode 8</td>
			<td style="width:183px;">Veeco</td>
			<td style="width:119px;"></td>
			<td>Section 4</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Typhoon FLA 9000 Laser Scanner</td>
			<td style="width:183px;">GE Heathcare Life Sciences</td>
			<td style="width:119px;">28-9558-08</td>
			<td>Section 3.5</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Ultrapure Distilled water</td>
			<td style="width:183px;">Invitrogen</td>
			<td style="width:119px;">10977-023</td>
			<td>Section 3.7.1</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Mica disk</td>
			<td style="width:183px;">SPI Supplies</td>
			<td style="width:119px;">12001-26-2</td>
			<td>Section 4.1</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Steel mounting disk</td>
			<td style="width:183px;">Ted Pella, Inc.</td>
			<td style="width:119px;">16218</td>
			<td>Section 4.1</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">carbon coated copper grid for TEM</td>
			<td style="width:183px;">Electron Microscopy Sciences</td>
			<td style="width:119px;">FCF400-Cu</td>
			<td>Section 7.2</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">tweezers</td>
			<td style="width:183px;">Dumont</td>
			<td>0203-N5AC-PO</td>
			<td>Section 7.31</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">glow discharge system</td>
			<td style="width:183px;">Quorum Technologies</td>
			<td style="width:119px;">K100X</td>
			<td>Section 7.2</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">DNA Engine Tetrad 2 Peltier Thermal Cycler</td>
			<td style="width:183px;">BIO-RAD</td>
			<td>PTC&#8211;0240G</td>
			<td>Section 3.3</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Owl Easycast B2 Mini Gel Electrophoresis Systems</td>
			<td style="width:183px;">ThermoScientific</td>
			<td>B2</td>
			<td>Section 3.4.3</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Seekam LE Agarose 500G</td>
			<td style="width:183px;">Lonza</td>
			<td style="width:119px;">50004</td>
			<td>Section 3.4.1</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">GeneRuler 1kb Plus DNA Ladder, Ready-To-Use 75-20000bp</td>
			<td style="width:183px;">ThermoScientific</td>
			<td style="width:119px;">SM1333</td>
			<td>Section 3.4.4</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Nanodrop 2000c UV-vis Spectrophotometer</td>
			<td style="width:183px;">ThermoScientific</td>
			<td style="width:119px;"></td>
			<td>Section 3.7</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">0.2 um filter</td>
			<td style="width:183px;">Corning Inc.</td>
			<td style="width:119px;">431219</td>
			<td>Section 7.1.2</td>
		</tr>
	</tbody>
</table>

self-assembly of complex two-dimensional shapes from single-stranded dna tiles

Current methods in DNA nano-architecture have successfully engineered a variety of 2D and 3D structures using principles of self-assembly. In this article, we describe detailed protocols on how to fabricate sophisticated 2D shapes through the self-assembly of uniquely addressable single-stranded DNA tiles which act as molecular pixels on a molecular canvas. Each single-stranded tile (SST) is a 42-nucleotide DNA strand composed of four concatenated modular domains which bind to four neighbors during self-assembly. The molecular canvas is a rectangle structure self-assembled from SSTs. A prescribed complex 2D shape is formed by selecting the constituent molecular pixels (SSTs) from a 310-pixel molecular canvas and then subjecting the corresponding strands to one-pot annealing. Due to the modular nature of the SST approach we demonstrate the scalability, versatility and robustness of this method. Compared with alternative methods, the SST method enables a wider selection of information polymers and sequences through the use of de novo designed and synthesized short DNA strands.

ההרכבה העצמית של טמפרטורת פני הים (איור 1) תניב 24H × מלבן 28T, כפי שמודגם באיור 2. רצפי DNA לטמפרטורת פני הים השונים יכולים להיות שונה / מותאם כדי לאפשר תיוג streptavidin (איור 3 ו -4), את הפיכתו של מלבן לתוך צינור (איור 5), הרכבה העצמית הני...

Watch this Scientific Journal Video about Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles at JoVE.com

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles

DNA tiling is an effective approach to make programmable nanostructures. We describe the protocols to construct complex two-dimensional shapes by the self-assembly of single-stranded DNA tiles.

עצמי הרכבה של צורות דו-ממדיות מורכבות מחד-גדילי דנ&quot;א אריחים

Current methods in DNA nano-architecture have successfully engineered a variety of 2D and 3D structures using principles of self-assembly. In this ...

self-assembly-complex-two-dimensional-shapes-from-single-stranded-dna

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11.5K Views.  Tsinghua University. DNA tiling is an effective approach to make programmable nanostructures. We describe the protocols to construct complex two-dimensional shapes by the self-assembly of single-stranded DNA tiles.

Video: Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles

Origami Inspired Self-assembly of Patterned and Reconfigurable Particles

There are numerous techniques such as photolithography, electron-beam lithography and soft-lithography that can be used to precisely pattern two dimensional (2D) structures. These technologies are mature, offer high precision and many of them can be implemented in a high-throughput manner. We leverage the advantages of planar lithography and combine them with self-folding methods1-20 wherein physical forces derived from surface tension or residual stress, are used to curve or fold planar structures into three dimensional (3D) structures. In doing so, we make it possible to mass produce precisely patterned static and reconfigurable particles that are challenging to synthesize.
In this paper, we detail visualized experimental protocols to create patterned particles, notably, (a) permanently bonded, hollow, polyhedra that self-assemble and self-seal due to the minimization of surface energy of liquefied hinges21-23 and (b) grippers that self-fold due to residual stress powered hinges24,25. The specific protocol described can be used to create particles with overall sizes ranging from the micrometer to the centimeter length scales. Further, arbitrary patterns can be defined on the surfaces of the particles of importance in colloidal science, electronics, optics and medicine. More generally, the concept of self-assembling mechanically rigid particles with self-sealing hinges is applicable, with some process modifications, to the creation of particles at even smaller, 100 nm length scales22, 26 and with a range of materials including metals21, semiconductors9 and polymers27. With respect to residual stress powered actuation of reconfigurable grasping devices, our specific protocol utilizes chromium hinges of relevance to devices with sizes ranging from 100 &mu;m to 2.5 mm. However, more generally, the concept of such tether-free residual stress powered actuation can be used with alternate high-stress materials such as heteroepitaxially deposited semiconductor films5,7 to possibly create even smaller nanoscale grasping devices.

We describe experimental details of the synthesis of patterned and reconfigurable particles from two dimensional (2D) precursors. This methodology can be used to create particles in a variety of shapes including polyhedra and grasping devices at length scales ranging from the micro to centimeter scale.

אוריגמי השראה עצמית הרכבה של חלקיקים בדוגמת וReconfigurable

There are numerous techniques such as photolithography, electron-beam lithography and soft-lithography that can be used to precisely pattern two ...

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

In nature, complex functional structures are formed by the self-assembly of biomolecules under mild conditions. Understanding the forces that control self-assembly and mimicking this process in vitro will bring about major advances in the areas of materials science and nanotechnology. Among the available biological building blocks, peptides have several advantages as they present substantial diversity, their synthesis in large scale is straightforward, and they can easily be modified with biological and chemical entities1,2. Several classes of designed peptides such as cyclic peptides, amphiphile peptides and peptide-conjugates self-assemble into ordered structures in solution. Homoaromatic dipeptides, are a class of short self-assembled peptides that contain all the molecular information needed to form ordered structures such as nanotubes, spheres and fibrils3-8. A large variety of these peptides is commercially available.
This paper presents a procedure that leads to the formation of ordered structures by the self-assembly of homoaromatic peptides. The protocol requires only commercial reagents and basic laboratory equipment. In addition, the paper describes some of the methods available for the characterization of peptide-based assemblies. These methods include electron and atomic force microscopy and Fourier-Transform Infrared Spectroscopy (FT-IR). Moreover, the manuscript demonstrates the blending of peptides (coassembly) and the formation of a &#34;beads on a string&#34;-like structure by this process.9 The protocols presented here can be adapted to other classes of peptides or biological building blocks and can potentially lead to the discovery of new peptide-based structures and to better control of their assembly.

This paper describes the formation of highly ordered peptide-based structures by the spontaneous process of self-assembly. The method utilizes commercially available peptides and common lab equipment. This technique can be applied to a large variety of peptides and may lead to the discovery of new peptide-based assemblies.

היווצרות של מבני Biomolecular הוזמנו על ידי ההרכבה העצמית של פפטידים קצרים

In nature, complex functional structures are formed by the self-assembly of biomolecules under mild conditions. Understanding the forces that control ...

Folding and Characterization of a Bio-responsive Robot from DNA Origami

The DNA nanorobot is a hollow hexagonal nanometric device, designed to open in response to specific stimuli and present cargo sequestered inside. Both stimuli and cargo can be tailored according to specific needs. Here we describe the DNA nanorobot fabrication protocol, with the use of the DNA origami technique. The procedure initiates by mixing short single-strand DNA staples into a stock mixture which is then added to a long, circular, single-strand DNA scaffold in presence of a folding buffer. A standard thermo cycler is programmed to gradually lower the mixing reaction temperature to facilitate the staples-to-scaffold annealing, which is the guiding force behind the folding of the nanorobot. Once the 60 hr folding reaction is complete, excess staples are discarded using a centrifugal filter, followed by visualization via agarose-gel electrophoresis (AGE). Finally, successful fabrication of the nanorobot is verified by transmission electron microscopy (TEM), with the use of uranyl-formate as negative stain.

DNA origami is a powerful method for fabricating precise nanoscale objects by programming the self-assembly of DNA molecules. Here we describe a protocol for the folding of a bio-responsive robot from DNA origami, its purification and negative staining for transmission electron microscopic imaging (TEM).

מתקפל ואפיון של רובוט ביו-תגובה מה- DNA אוריגמי

The DNA nanorobot is a hollow hexagonal nanometric device, designed to open in response to specific stimuli and present cargo sequestered inside. Both ...

Synthesis of a Water-soluble Metal&#8211;Organic Complex Array

We demonstrate a method for the synthesis of a water-soluble multimetallic peptidic array containing a predetermined sequence of metal centers such as Ru(II), Pt(II), and Rh(III). The compound, named as a water-soluble metal-organic complex array (WSMOCA), is obtained through 1) the conventional solution-chemistry-based preparation of the corresponding metal complex monomers having a 9-fluorenylmethyloxycarbonyl (Fmoc)-protected amino acid moiety and 2) their sequential coupling together with other water-soluble organic building units on the surface-functionalized polymeric resin by following the procedures originally developed for the solid-phase synthesis of polypeptides, with proper modifications. Traces of reactions determined by mass spectrometric analysis at the representative coupling steps in stage 2 confirm the selective construction of a predetermined sequence of metal centers along with the peptide backbone. The WSMOCA cleaved from the resin at the end of stage 2 has a certain level of solubility in aqueous media dependent on the pH value and/or salt content, which is useful for the purification of the compound.

Synthesis of a Water-soluble Metal&amp;#8211;Organic Complex Array

A potential general method for the synthesis of water-soluble multimetallic peptidic arrays containing a predetermined sequence of metal centers is presented.

סינתזה של מערך מורכב מתכת-אורגנית נמס במים

We demonstrate a method for the synthesis of a water-soluble multimetallic peptidic array containing a predetermined sequence of metal centers such as ...

Grafting Multiwalled Carbon Nanotubes with Polystyrene to Enable Self-Assembly and Anisotropic Patchiness

We demonstrate a straightforward protocol to graft pristine multiwalled carbon nanotubes (MWCNTs) with polystyrene (PS) chains at the sidewalls through a free-radical polymerization strategy to enable the modulation of the nanotube surface properties and produce supramolecular self-assembly of the nanostructures. First, a selective hydroxylation of the pristine nanotubes through a biphasic catalytically mediated oxidation reaction creates superficially distributed reactive sites at the sidewalls. The latter reactive sites are subsequently modified with methacrylic moieties using a silylated methacrylic precursor to create polymerizable sites. Those polymerizable groups can address further polymerization of styrene to produce a hybrid nanomaterial containing PS chains grafted to the nanotube sidewalls. The polymer-graft content, amount of silylated methacrylic moieties introduced and hydroxylation modification of the nanotubes are identified and quantified by Thermogravimetric Analysis (TGA). The presence of reactive functional groups hydroxyl and silylated methacrylate are confirmed by Fourier Transform Infrared Spectroscopy (FT-IR). Polystyrene-grafted carbon nanotube solutions in tetrahydrofuran (THF) provide wall-to-wall collinearly self-assembled nanotubes when cast samples are analyzed by transmission electron microscopy (TEM). Those self-assemblies are not obtained when suitable blanks are similarly cast from analogous solutions containing non-grafted counterparts. Therefore, this method enables the modification of the nanotube anisotropic patchiness at the sidewalls which results into spontaneous auto-organization at the nanoscale.

A procedure for the synthesis of polystyrene-grafted multiwalled carbon nanotubes using successive chemical modification steps to selectively introduce the polymer chains to the sidewalls and their self-assembly via anisotropic patchiness is presented.

הרכבה Multiwalled פחמן עם פוליסטירן כדי לאפשר הרכבה עצמית, Patchiness אנאיזוטרופי

We demonstrate a straightforward protocol to graft pristine multiwalled carbon nanotubes (MWCNTs) with polystyrene (PS) chains at the sidewalls through a ...

Liquid-cell Transmission Electron Microscopy for Tracking Self-assembly of Nanoparticles

Drying a nanoparticle dispersion is a versatile way to create self-assembled structures of nanoparticles, but the mechanism of this process is not fully understood. We have traced the trajectories of individual nanoparticles using liquid-cell transmission electron microscopy (TEM) to investigate the mechanism of the assembly process. Herein, we present the protocols used for liquid-cell TEM studies of the self-assembly mechanism. First, we introduce the detailed synthetic protocols used to produce uniformly sized platinum and lead selenide nanoparticles. Next, we present the microfabrication processes used to produce liquid cells with silicon nitride or silicon windows and then describe the loading and imaging procedures of the liquid-cell TEM technique. Several notes are included to provide helpful tips for the entire process, including how to manage the fragile cell windows. The individual motions of nanoparticles tracked by liquid-cell TEM revealed that changes in the solvent boundaries caused by evaporation affected the self-assembly process of nanoparticles. The solvent boundaries drove nanoparticles to primarily form amorphous aggregates, followed by flattening of the aggregates to produce a 2-dimensional (2D) self-assembled structure. These behaviors are also observed for different nanoparticle types and different liquid-cell compositions.

Here we introduce experimental protocols for the real-time observation of a self-assembly process using liquid-cell transmission electron microscopy.

במיקרוסקופ אלקטרונים הילוכים נוזלי-תא לצורך מעקב הרכבה עצמית של חלקיקים

Drying a nanoparticle dispersion is a versatile way to create self-assembled structures of nanoparticles, but the mechanism of this process is not fully ...

Fabrication of Spherical and Worm-shaped Micellar Nanocrystals by Combining Electrospray, Self-assembly, and Solvent-based Structure Control

Micellar nanocrystals (micelles with encapsulated nanocrystals) have become an emerging major class of nanobiomaterials. We describe a method of fabricating micellar nanocrystals based on combining top-down electrospray, bottom-up self-assembly, and solvent-based structure control. This method involves first using electrospray to generate uniform ultrafine liquid droplets, each of which functions as a micro-reactor in which self-assembly reaction occurs forming micellar nanocrystals, with the structures (micelle shape and nanocrystal encapsulation) controlled by the organic solvent used. This method is largely continuous and produces high quality micellar nanocrystal products with an inexpensive structure control approach. By using a water-miscible organic solvent tetrahydrofuran (THF), worm-shaped micellar nanocrystals can be produced due to solvent-induced/facilitated micelle fusion. Compared with the common spherical micellar nanocrystals, worm-shaped micellar nanocrystals can offer minimized non-specific cellular uptake, thus enhancing biological targeting. By co-encapsulating multiple nanocrystals into each micelle, multifunctional or synergistic effects can be achieved. Current limitations of this fabrication method, which will be part of the future work, primarily include imperfect encapsulation in the micellar nanocrystal product and the incompletely continuous nature of the process.

The present work describes a method to fabricate micellar nanocrystals, an emerging major class of nanobiomaterials. This method combines top-down electrospray, bottom-up self-assembly, and solvent-based structure control. The fabrication method is largely continuous, can produce high quality products, and possesses an inexpensive means of structure control.

ייצור של כדוריות, בצורת תולעת Nanocrystals Micellar על-ידי שילוב ספקטרומטריית Electrospray, הרכבה עצמית ובקרת מבנה ממס מבוסס

Micellar nanocrystals (micelles with encapsulated nanocrystals) have become an emerging major class of nanobiomaterials. We describe a method of ...

Negative Additive Manufacturing of Complex Shaped Boron Carbides

Boron carbide (B4C) is one of the hardest materials in existence. However, this attractive property also limits its machineability into complex shapes for high wear, high hardness, and lightweight material applications such as armors. To overcome this challenge, negative additive manufacturing (AM) is employed to produce complex geometries of boron carbides at various length scales. Negative AM first involves gelcasting a suspension into a 3D-printed plastic mold. The mold is then dissolved away, leaving behind a green body as a negative copy. Resorcinol-formaldehyde (RF) is used as a novel gelling agent because unlike traditional hydrogels, there is little to no shrinkage, which allows for extremely complex molds to be used. Furthermore, this gelling agent can be pyrolyzed to leave behind ~50 wt% carbon, which is a highly effective sintering aid for B4C. Due to this highly homogenous distribution of in situ carbon within the B4C matrix, less than 2% porosity can be achieved after sintering. This protocol highlights in detail the methodology for creating near fully dense boron carbide parts with highly complex geometries.

A method called negative additive manufacturing is used to produce near fully dense complex shaped boron carbide parts of various length scales. This technique is possible via the formulation of a novel suspension involving resorcinol-formaldehyde as a unique gelling agent that leaves behind a homogenous carbon sintering aid after pyrolysis.

הייצור מוספים שלילי של קומפלקס בצורת Carbides בורון

Boron carbide (B4C) is one of the hardest materials in existence. However, this attractive property also limits its machineability into complex shapes for ...

Exfoliation and Analysis of Large-area, Air-Sensitive Two-Dimensional Materials

We describe methods for producing and analyzing large, thin flakes of air-sensitive two-dimensional materials. Thin flakes of layered or van der Waals crystals are produced using mechanical exfoliation, in which layers are peeled off a bulk crystal using adhesive tape. This method produces high-quality flakes, but they are often small and can be hard to find, particularly for materials with relatively high cleavage energies such as black phosphorus. By heating the substrate and the tape, two-dimensional material adhesion to the substrate is promoted, and the flake yield can be increased by up to a factor of ten. After exfoliation, it is necessary to image or otherwise analyze these flakes but some two-dimensional materials are sensitive to oxygen or water and will degrade when exposed air. We have designed and tested a hermetic transfer cell to temporarily maintain the inert environment of a glovebox so that air-sensitive flakes can be imaged and analyzed with minimal degradation. The compact design of the transfer cell is such that optical analysis of sensitive materials can be performed outside of a glovebox without specialized equipment or modifications to existing equipment.

A method for exfoliating large thin flakes of air sensitive two-dimensional materials and safely transporting them for analysis outside of a glovebox is presented.

קילוף עור וניתוח של גדולים-אזור, חומרים מימדי רגיש אוויר

We describe methods for producing and analyzing large, thin flakes of air-sensitive two-dimensional materials. Thin flakes of layered or van der Waals ...

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules

This article presents a detailed protocol for synthesis of small circular DNA molecules, annealing of circular DNA motifs, and construction of 1D and 2D DNA nanostructures. Over decades, the rapid development of DNA nanotechnology is attributed to the use of linear DNAs as the source materials. For example, the DAO (double crossover, antiparallel, odd half-turns) tile is well-known as a building block for construction of 2D DNA lattices; the core structure of DAO is made from two linear single-stranded (ss) oligonucleotides, like two ropes making a right hand granny&#160;knot. Herein, a new type of DNA tiles called cDAO (coupled DAO) are built using a small circular ss-DNA of c64nt or c84nt (circular 64 or 84 nucleotides) as the scaffold strand and several linear ss-DNAs as the staple strands. Perfect 1D and 2D nanostructures are assembled from cDAO tiles: infinite nanowires, nanospirals, nanotubes, nanoribbons; and finite nano-rectangles. Detailed protocols are described: 1) preparation by T4 ligase and purification by denaturing PAGE (polyacrylamide gel electrophoresis) of small circular oligonucleotides, 2) annealing of stable circular tiles, followed by native PAGE analysis, 3) assembling of infinite 1D nanowires, nanorings, nanospirals, infinite 2D lattices of nanotubes and nanoribbons, and finite 2D nano-rectangles, followed by AFM (Atomic Force Microscopy) imaging. The method is simple, robust, and affordable for most labs.

This article presents a detailed protocol for T4 ligation and denaturing PAGE purification of small circular DNA molecules, annealing and native PAGE analysis of circular tiles, assembling and AFM imaging of 1D and 2D DNA nanostructures, as well as agarose gel electrophoresis and centrifugation purification of finite DNA nanostructures.

המוטיבים אן יציב, 1 י ו- 2D Nanostructures בנוי מולקולות DNA מעגלי קטן

This article presents a detailed protocol for synthesis of small circular DNA molecules, annealing of circular DNA motifs, and construction of 1D and 2D ...