Biomod/2013/Aarhus/Supplementary/References

From OpenWetWare
Jump to: navigation, search

<html> <style> /* ul.menu li.</html>Supplementary/References<html> a {

 color: cyan;

}

  • /
  1. toc {

display: none; }

  1. mytoc {

background: none; width: 200px; }

.toc { border: 0px solid; }

  1. toc ul ul,.toc ul ul {

margin: 0 0 0 1em; }

table.toc { background-color: #f0f4f4; }

  1. mytoc a,#mytoc a:visited {

font-size: normal; color: #222222; }

  1. mytoc a:hover {

font-color: #009ee0; /* text-decoration: underline; */ }

  1. wiki-toc {

width: 200px; margin-top: 6px; float: left; }

  1. wiki-body {

margin-left: 200px; padding-left: 12px; padding-right: 35px; }

  1. toc #toctitle,.toc #toctitle,#toc .toctitle,.toc .toctitle {

text-align: left; }

  1. toc h2,.toc h2 {

font-weight: normal; font-size: 17px; }

/*

  1. wiki-contents A {

color: #00aeef; }

  1. wiki-contents A:HOVER {

color: #00aeef; }

  • /
  1. toctitle span {

display: none; }

/*

  1. wiki-body p,#wiki-body li,#wiki-body dd,div.thumbcaption {

font-size: medium; }

  • /

/* required to avoid jumping */

  1. tocScrolWrapper {

/* left: 450px; */ position: absolute; /* margin-left: 35px; width: 280px; */ }

  1. tocScrol {

position: absolute; top: 0; /* just used to show how to include the margin in the effect */ /*margin-top: 20px; */ /* border-top: 1px solid purple; */ /*padding-top: 19px;*/ }

  1. tocScrol.fixed {

position: fixed; top: 0; }

  1. editPageTxt {

text-align: left; padding-left: 15px; }

  1. editPageTxt P {

clear: both; }

  1. toPageTop {

float: left; position: relative; top: 18px; left: 13px; color: #d13f31; } </style>

<script type="text/javascript"> $(document).ready(function() { var parentTable = $("#toc").parent(); $('#mytoc').append($("#toc").first());

$('#mytoc').find("#toc").attr("id", ""); parentTable.closest('table').remove(); });

$(document).ready( function() { var top = $('#tocScrol').offset().top - parseFloat($('#tocScrol').css('marginTop').replace( /auto/, 0)); var nav = $('#tocScrol'); var max = $('#indexing').offset().top - nav.height();

$(window).scroll(function(event) { // what the y position of the scroll is var y = $(this).scrollTop();

if (y > top) { // && signs are html decoded thus this construction if (y >= max) { nav.removeClass('fixed'); nav.css({ position : 'absolute', top : max - top }); } else { nav.addClass('fixed'); nav.removeAttr('style'); } } else { nav.removeClass('fixed'); nav.removeAttr('style'); } }); }); </script> <html> <html> <div id="wiki-contents"> <div id="tocScrolWrapper"> <div id="tocScrol"> <div id="wiki-toc"> <a id="toPageTop" href="#">&#x25B2;</a> <table id="mytoc" class="toc" summary="Contents"> </table> <div id="editPageTxt"> <p> [<a href="http://openwetware.org/index.php?title=Biomod/2013/Aarhus/</html>Supplementary/References<html>&action=edit">edit this page</a>] </p> </div> </div> </div> </div> <div id="wiki-body"> </html>

Contents


References

  1. Han, D.R. et al. DNA Origami with Complex Curvatures in Three-Dimensional Space. Science 332, 342-346 (2011) [1] [Han]
  2. Y. Ke et al. Multilayer DNA Origami Packed on a Square Lattice. J. Am. Chem. Soc. 131, 15903-15908 (2009). [1] [Ke]
  3. Douglas, S.M. et al. Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Res. 37, 5001-5006 (2009) [1] [Douglas]
  4. Zhang, Z. et al. Self-assembly of DNA origami and single-stranded tile structures at room temperature. Angew. Chem. Int. Ed. Engl. 52, 9219-23 (2013) [1] [Zhang]
  5. Kim, D. N. et al. Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures. Nucleic Acids Res. 40, 2862-2868 (2012). [1] [Kim]
  6. Kim, K. N. et al. Comparison of methods for orienting and aligning DNA origami. Soft Matter 7, 4636-4643 (2011). [1] [KimKN]
  7. Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297-302 (2006)[1] [Rothemund]
  8. Teruya, K. et al. Semisynthesis of a protein with cholesterol at the C-terminal, targeted to the cell membrane of live cells. K. Protein J. 29, 493–500 (2010). [1] [Teruya]
  9. Pedersen, B. W. et al. Single Cell Responses to Spatially-Controlled Photosensitized Production of Extracellular Singlet Oxygen. Photochem. Photobiol. 87, 1077-1091 (2011) [1] [Pedersen]
  10. O. Mendes et al. MMP2 role in breast cancer brain metastasis development and its regulation by timp2 and erk1/2. Clin. Exp. Metastasis, 24, 341-351 (2007). [1] [Mendes]
  11. D. E. Kleiner et al. Matrix metalloproteinases and metastasis. Cancer. Chemother. Pharmacol., 43, 42-51 (1999). [1] [Kleiner]
  12. R. Visse et al. Matrix metalloproteinases and tissue inhibitors of metalloproteinases: Structure, function, and biochemistry. Circ. Res., 92, 827-839 (2003). [1] [Visse]
  13. E. Morgunova et al. Structural insight into the complex formation of latent matrix metalloproteinase 2 with tissue inhibitor of metalloproteinase 2. Proc. Natl. Acad. Sci. USA, 99, 7414-7419 (2002). [1] [Morgunova]
  14. E. I. Chen et al. Smith. A unique substrate recognition profile for matrix metalloproteinase-2. J. Biol. Chem., 277, 4485-4491 (2002). [1] [Chen]
  15. J. N. Zadeh et al. Nucleic acid sequence design via efficient ensemble defect optimization. J. Comput. Chem., 32, 439-452 (2011). [1] [Zadeh]
  16. T. Moriguchi et al. Synthesis and properties of aminoacylamido-amp chemical optimization for the construction of an n-acyl phosphoramidate linkage. J. Org. Chem., 65, 8229-8238 (2000). [1] [Moriguchi]
  17. J. Robles et al. Peptide-oligonucleotide hybrids with n-acylphosphoramidate linkages. J. Org. Chem., 60, 4856-4861 (1995). [1] [Robles]
  18. Langecker, M. et al. Synthetic lipid membrane channels formed by designed DNA nanostructures. Science 338, 932–936 (2012)[1] [Langecker]
  19. Simeone, L. et al. Cholesterol-based nucleolipid-ruthenium complex stabilized by lipid aggregates for antineoplastic therapy. Bioconjugate Chem. 23, 758–770 (2012) [1] [Simeone]
  20. Cló, E. et al. DNA-programmed control of photosensitized singlet oxygen production. J. Am. Chem. Soc. 128, 4200–4201 (2006).[1] [Clo]
  21. Kochevar, I. E. et al. Singlet Oxygen , but not Oxidizing Radicals , Induces Apoptosis in HL-60 Cells. Photochem. Photobiol. 72, 548–553 (2000). [1] [Kochevar]
  22. Mitsunaga, M. et al.' Cancer cell-selective in vivo near infrared photoimmunotherapy targeting specific membrane molecules. Nat. Med. 17, 1685–1691 (2011). [1] [Mitsunaga]
  23. Frost, C. G. et al. Selectivity in Palladium Catalysed Allylic Substitution. Tetrahedron: Asymmetry. 3, 1089-1122 (1992)[1] [Frost]
  24. Funder, E. et al. Synthesis of Dopamine and Serotonin Derivatives for Immobilization on a Solid Support. J. Org. Chem. 77, 3134-3142 (2012)[1] [Funder]
  25. Jahn, K. et al. Functional patterning of DNA origami by parallel enzymatic modification. Bioconjugate Chem. 22, 819–823 (2011).[1] [Jahn]
  26. Asakura, J. et al. Cerium (IV) catalyzed iodination at C5 uracil nucleosides. Tetrahedron Lett. 29, 2855–2858 (1988).[1] [Asakura]
  27. Tahmassebi, D. et al. Substituent Effects on the Stability of Sulfenes. Phosphorus, Sulfur Silicon Relat. Elem. 181, 2745–2755 (2006).[1] [Tahmassebi]
  28. Jäger, S. et al. A versatile toolbox for variable DNA functionalization at high density. J. Am. Chem. Soc. 127, 15071–15082 (2005). [1] [Jager]
  29. Caton-Williams, J. et al. Protection-Free One-Pot Synthesis of 2’-Deoxynucleoside 5'-Triphosphates and DNA Polymerization. Org. Lett. 13, 4156–4159 (2011).[1] [Caton-Williams]
  30. Patel, L. N. et al. Cell penetrating peptides: Intracellular pathways and pharmaceutical perspectives. Pharm. Res. 24, 1977-92 (2007). [1] [Patel]
  31. Dempsey, C. E. et al. The actions of melittin on membranes. Biochim. Biophys. Acta 1031, 143-61 (1990) [1] [Dempsey]
  32. Li, W. et al. GALA: A designed synthetic pH-responsive amphipathic peptide with applications in drug and gene delivery. Adv. Drug Deliv. 56, 967-85 (2004) [1]. [Li]
  33. Veronese, F. M. et al. PEGylation, successful approach to drug delivery. Drug Discov. Today '21, 1451-8 (2005) [1] [Veronese]
  34. Bramsen, J. B. et al. Improved silencing properties using small internally segmented interfering RNAs. Nucleic Acids Res. 35, 5886-97 (2007). [1]. [Bramsen]
  35. Oleinick, N. L. et al. The role of apoptosis in response to photodynamic therapy: what, where, why, and how. Photochem. Photobiol. Sci. 1, 1-21 (2002).[1] [Oleinick]
  36. H. E. Gottlieb et al. NMR Chemical Shifts of Common Laboratory Solvents as Trace Impurities. J. Org. Chem. 62 7512-7515 (1997). [1] [Gottlieb]
  37. H. A. Behanna et al. Coassembly of amphiphiles with opposite peptide polarities into nanofibers. J. Am. Chem. Soc. 127, 1193-1200 (2005). [1] [Behanna]
  38. Z. J. Gartner et al. Expanding the reaction scope

    of dna-templated synthesis. Angew. Chem. Int. Ed, 41, 1796-1800 (2002). [1]

    [Gartner]
  39. Hussey, S. L. et al.. Synthesis of chimeric 7α-substituted estradiol derivatives linked to cholesterol and cholesterylamine. Org. Lett. 4, 415–418 (2002). [1] [Hussey]
  40. Horwitz, J. P. et al. Nucleosides. IX. The formation of 2’,3'-unsaturated pyrimidine nucleosides via a novel beta-elimination reaction. J. Org. Chem. 121, 205–211 (1966). [1] [Horwitz]
  41. Trybulski, E. J. et al. The synthesis and biochemical pharmacology of enantiomerically pure methylated oxotremorine derivatives. J. Med. Chem. 36, 3533–3541 (1993).[1] [Trybulski]
  42. Arian, D. et al. A nucleic acid dependent chemical photocatalysis in live human cells. Chem. Eur. J. 16, 288–295 (2010).[1] [Arian]
  43. Wang, H.M. et al. Chemical constituents from the leaves of Nelumbo nucifera Gaertn. cv. Rosa-plena. Chem. Nat Comp. 47, 316-318 (2011)[1] [Wang]
  44. McGuigan, C. et al. Discovery of a new family of inhibitors of human cytomegalovirus (HCMV) based upon lipophilic alkyl furano pyrimidine dideoxy nucleosides: action via a novel non-nucleosidic mechanism. J. Med. Chem. 47, 1847–1851 (2004). [1] [McGuigan]
  45. Geisse, N. A. et al. AFM and Combined Optical Techniques. Mater. Today 12, 40–45 2009. [1]. [Geisse]
  46. Sinha, N. D. et al. Polymer support oligonucleotide synthesis. XVIII: use of β-cyanoethyl-N,N-dialkylamino-/N-morpholino phosphoramidite of deoxynucleosides for the synthesis of DNA fragments simplifying deprotection and isolation of the final product. Nucl. Acids Res. 12, 4539–4557 (1984).[1] [Sinha]
  47. van Meerloo, J. et al. Cell sensitivity assays: The MTT assay. Methods Mol. Biol. 731, 237-45 (2011)[1] [VanMeerloo]
  48. H. C. Kolb, et al. Click Chemistry: Diverse Chemical Function from a Few Good Reactions. Angew. Chem. Int. Ed 40, 2004–2021 (2001). [Kolb]
  49. Bloomfield, V. A. et al. Static and dynamic light scattering from aggregating particles. Biopolymers 54, 168-172 (2000). [Bloomfield]
  50. Dalby, B. et al. Advanced transfection with Lipofectamine 2000 reagent: Primary neurons, siRNA, and high-throughput applications. Methods 33, 95-103 (2004). [1] [Dalby]
  51. Ford, S. R. et al. Improvements in the application of firefly luciferase assays. Methods Mol. Biol. 102, 3-20 (1998). [1] [Ford]
  52. Merrifield, R. B. Solid-phase peptide synthesis. Adv. Enzymol. Relat. Areas. Mol. Biol. 32 221-296 (1969). [Merrifield]
  53. Harris, D. C. Quantitative Chemical Analysis Ch. 21. (W. H. Freeman and Company, New York, 2010). [HarrisLCMS]
  54. Friebolin, H. Basic One- and Two-Dimensional NMR Spectroscopy (Wiley Verlag GMBH & Ci. KGaA., Weinheim, 2005) [Friebolin]
  55. Delarue, M. et al. Crystal structures of a template-independent DNA polymerase: murine terminal deoxynucleotidyltransferase. EMBO J. 21, 427-439 (2002). [1] [Delarue]
  56. Prasad, P. N. Bioimaging: Principles and Techniques, in Introduction to Biophotonics. (John Wiley & Sons, Inc., Hoboken, NJ, USA., 2004) [1] [Prasad]
  57. Thuring, R. W. J. et al. A freeze-squeeze method for recovering long DNA from agarose gels. Anal. Biochem. 66, 213-220 (1975). [1] [Thuring]
  58. Harris, D. C. Quantitative Chemical Analysis Ch. 24. (W. H. Freeman and Company, New York, 2010). [HarrisHPLC]
  59. Harris, D. C. Quantitative Chemical Analysis Ch. 17. (W. H. Freeman and Company, New York, 2010). [HarrisSpectro]
  60. Shapiro, D. J. Quantitative ethanol precipitation of nanogram quantities of DNA and RNA. Anal. Biochem. 110, 229-231 (1981). [1] [Shapiro]


<html></div></div></html> <html> <head> <style>

  1. indexing {

/* float: left; position: center; */ background-color: #222; border-top: 2px solid #d13f31; color: #006e9c; margin: 0px; padding: 0px 0px 10px 0px; width: 100%; text-align: center; }

.footer-section { padding: 10px; display: table-cell; text-align: left; }

.footer-section-title { font-size: 20px; }

  1. footer-contents {

color: #006e9c; display: inline-table; }

.footer-section A { color: #006e9c; text-decoration: none; }

.footer-section A:HOVER { color: #00aeef; }

.footer-section ul { list-style-type: square; }

  1. sitemapTitle {

margin-top: 20px; font-size: 24px; }

  1. editFooter {

float: right; margin-top: -28px; margin-right: 5px; }

  1. editFooter A {

color: #006e9c; text-decoration: none; }

.cf:before,.cf:after { content: " "; /* 1 */ display: table; /* 2 */ }

.cf:after { clear: both; }

  1. bodyContent a[href^="mailto:"], .link-mailto {
   background: url() no-repeat scroll right center transparent;
   padding-right: 0px;
   color: #006e9c;

}

</style> </head> <body> <div id="indexing"> <div id="sitemap"> <p id="sitemapTitle">SITEMAP | BIOMOD 2013 NANO CREATORS | Aarhus University</p> <div id="footer-contents"> <div class="footer-section"> <p class="footer-section-title">INTRODUCTION</p> <ul> <li><a href="/wiki/Biomod/2013/Aarhus">Home, abstract, animation and video</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Introduction">Introduction</a></li </ul> </div> <div class="footer-section"> <p class="footer-section-title">RESULTS AND DISCUSSION</p> <ul> <li><a href="/wiki/Biomod/2013/Aarhus/Results_And_Discussion/Origami">Origami</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Results_And_Discussion/Peptide_lock">Peptide lock</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Results_And_Discussion/Chemical_Modification">Chemical modification</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Results_And_Discussion/sisiRNA">sisiRNA</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Results_And_Discussion/System_In_Action">System in action</a></li> </ul> </div> <div class="footer-section"> <p class="footer-section-title">MATERIALS AND METHODS</p> <ul> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/Origami">Origami</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/Peptide_lock">Peptide lock</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/Chemical_Modification">Chemical modification</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/sisiRNA">sisiRNA</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/System_In_Action">System in action</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/Methods">Methods</a></li> </ul> </div> <div class="footer-section"> <p class="footer-section-title">SUPPLEMENTARY</p> <ul> <li><a href="/wiki/Biomod/2013/Aarhus/Supplementary/Team_And_Acknowledgments">Team and acknowledgments</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Supplementary/Optimizations">Optimizations</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Supplementary/Supplementary_Data">Supplementary data</a></li>

                                               <li><a

href="/wiki/Biomod/2013/Aarhus/Supplementary/Supplementary_Informations">Supplementary informations</a> <li><a href="/wiki/Biomod/2013/Aarhus/Supplementary/References">References</a></li> </ul> </div> </div> <div> <p id="copyright">Copyright (C) 2013 | BIOMOD Team Nano Creators @ Aarhus University | Programming by: <a href="mailto:pvskaarup@gmail.com?Subject=BIOMOD 2013:">Peter Vium Skaarup</a>.</p> </div> </div>

<!-- Sponsers --> <div> <img alt="Sigma - Aldrich" src="http://openwetware.org/images/3/39/Sigmaaldrich-logo%28transparant%29.png" width="300px" height="154px"> <img alt="VWR International" src="http://openwetware.org/images/2/28/Vwr_logo.png" width="300px" height="61px"> <img alt="Promega" src="http://openwetware.org/images/7/72/Promega.png" width="175px" height="105px" style="padding-right: 5px; padding-left: 5px;"> <img alt="kem-en-tec" src="http://openwetware.org/images/3/3a/Kementec.png" width="130px" height="129px"> <img alt="Centre For Dna Nanotechnology" src="http://openwetware.org/images/4/4f/CDNA_logo.png" width="420px" height="90px"> <img alt="Dansk Tennis Fond" src="http://openwetware.org/images/9/9a/Dansk_tennis.png" width="250px" height="53px"> </div> <div id="editFooter"> [<a href="http://openwetware.org/index.php?title=Template:Biomod/2013/Aarhus/Nano_Creators/footer&action=edit">edit sitemap</a>] </div> </div> </body> </html>