Please check out the papers mentioned in the webinar - you can find a list here: www.oligotherapeutics.org/advances-in-selex-technologies-for-aptamer-selection/
No problem - if you still have questions after reading the papers you could try asking your questions on our twitter feed @OTSociety or emailing the authors of the papers or the webinar presenters.
@@MyRandomVideos09 Was OTS cut off by the Great Wall of China? Here are all the paper references: Selection and Biosensor Application of Aptamers for Small Molecules. Pfeiffer F, Mayer G. Front Chem. 2016 Jun 15;4:25. By-product formation in repetitive PCR amplification of DNA libraries during SELEX. Tolle F, Wilke J, Wengel J, Mayer G. PLoS One. 2014 Dec 9;9(12):e114693. In vitro selection of structure-switching signaling aptamers. Nutiu R, Li Y. Angew Chem Int Ed Engl. 2005 Feb 4;44(7):1061-5. Capture-SELEX: Selection of DNA Aptamers for Aminoglycoside Antibiotics. Stoltenburg R, Nikolaus N, Strehlitz B. J Anal Methods Chem. 2012;2012:415697. Synthetic genetic polymers capable of heredity and evolution. Pinheiro VB, Taylor AI, Cozens C, Abramov M, Renders M, Zhang S, Chaput JC, Wengel J, Peak-Chew SY, McLaughlin SH, Herdewijn P, Holliger P. Science. 2012 Apr 20;336(6079):341-4. A synthetic genetic polymer with an uncharged backbone chemistry based on alkyl phosphonate nucleic acids. Arangundy-Franklin S, Taylor AI, Porebski BT, Genna V, Peak-Chew S, Vaisman A, Woodgate R, Orozco M, Holliger P. Nat Chem. 2019 Jun;11(6):533-542. In vivo selection of tumor-targeting RNA motifs. Mi J, Liu Y, Rabbani ZN, Yang Z, Urban JH, Sullenger BA, Clary BM. Nat Chem Biol. 2010 Jan;6(1):22-4. Targeting hormone refractory prostate cancer by in vivo selected DNA libraries in an orthotopic xenograft mouse model. Civit L, Theodorou I, Frey F, Weber H, Lingnau A, Gröber C, Blank M, Dambrune C, Stunden J, Beyer M, Schultze J, Latz E, Ducongé F, Kubbutat MHG, Mayer G. Sci Rep. 2019 Mar 21;9(1):4976. Poly-ligand profiling differentiates trastuzumab-treated breast cancer patients according to their outcomes. Domenyuk V, Gatalica Z, Santhanam R, Wei X, Stark A, Kennedy P, Toussaint B, Levenberg S, Wang J, Xiao N, Greil R, Rinnerthaler G, Gampenrieder SP, Heimberger AB, Berry DA, Barker A, Quackenbush J, Marshall JL, Poste G, Vacirca JL, Vidal GA, Schwartzberg LS, Halbert DD, Voss A, Magee D, Miglarese MR, Famulok M, Mayer G, Spetzler D. Nat Commun. 2018 Mar 23;9(1):1219. Fluorescence-activated cell sorting for aptamer SELEX with cell mixtures. Mayer G, Ahmed MS, Dolf A, Endl E, Knolle PA, Famulok M. Nat Protoc. 2010 Dec;5(12):1993-2004. Robotic assisted generation of 2′-deoxy-2′-fluoro-modifed RNA aptamers - High performance enabling strategies in aptamer selection. Breuers S, Bryant LL, Legen T, Mayer G. Methods. 2019 May 15;161:3-9. Aptamer-based multiplexed proteomic technology for biomarker discovery. Gold L, Ayers D, Bertino J, Bock C, Bock A, Brody EN, Carter J, Dalby AB, Eaton BE, Fitzwater T, Flather D, Forbes A, Foreman T, Fowler C, Gawande B, Goss M, Gunn M, Gupta S, Halladay D, Heil J, Heilig J, Hicke B, Husar G, Janjic N, Jarvis T, Jennings S, Katilius E, Keeney TR, Kim N, Koch TH, Kraemer S, Kroiss L, Le N, Levine D, Lindsey W, Lollo B, Mayfield W, Mehan M, Mehler R, Nelson SK, Nelson M, Nieuwlandt D, Nikrad M, Ochsner U, Ostroff RM, Otis M, Parker T, Pietrasiewicz S, Resnicow DI, Rohloff J, Sanders G, Sattin S, Schneider D, Singer B, Stanton M, Sterkel A, Stewart A, Stratford S, Vaught JD, Vrkljan M, Walker JJ, Watrobka M, Waugh S, Weiss A, Wilcox SK, Wolfson A, Wolk SK, Zhang C, Zichi D. PLoS One. 2010 Dec 7;5(12):e15004. Aptamer-based multiplexed proteomic technology for biomarker discovery. Gold L, Ayers D, Bertino J, Bock C, Bock A, Brody EN, Carter J, Dalby AB, Eaton BE, Fitzwater T, Flather D, Forbes A, Foreman T, Fowler C, Gawande B, Goss M, Gunn M, Gupta S, Halladay D, Heil J, Heilig J, Hicke B, Husar G, Janjic N, Jarvis T, Jennings S, Katilius E, Keeney TR, Kim N, Koch TH, Kraemer S, Kroiss L, Le N, Levine D, Lindsey W, Lollo B, Mayfield W, Mehan M, Mehler R, Nelson SK, Nelson M, Nieuwlandt D, Nikrad M, Ochsner U, Ostroff RM, Otis M, Parker T, Pietrasiewicz S, Resnicow DI, Rohloff J, Sanders G, Sattin S, Schneider D, Singer B, Stanton M, Sterkel A, Stewart A, Stratford S, Vaught JD, Vrkljan M, Walker JJ, Watrobka M, Waugh S, Weiss A, Wilcox SK, Wolfson A, Wolk SK, Zhang C, Zichi D. PLoS One. 2010 Dec 7;5(12):e15004. Nucleic Acid Ligands With Protein-like Side Chains: Modified Aptamers and Their Use as Diagnostic and Therapeutic Agents. Rohloff JC, Gelinas AD, Jarvis TC, Ochsner UA, Schneider DJ, Gold L, Janjic N. Mol Ther Nucleic Acids. 2014 Oct 7;3:e201. Customised nucleic acid libraries for enhanced aptamer selection and performance. Pfeiffer F, Rosenthal M, Siegl J, Ewers J, Mayer G. Curr Opin Biotechnol. 2017 Dec;48:111-118. In vitro selection with artificial expanded genetic information systems. Sefah K, Yang Z, Bradley KM, Hoshika S, Jiménez E, Zhang L, Zhu G, Shanker S, Yu F, Turek D, Tan W, Benner SA. Proc Natl Acad Sci U S A. 2014 Jan 28;111(4):1449-54. Identification and characterization of nucleobase-modified aptamers by click-SELEX. Pfeiffer F, Tolle F, Rosenthal M, Brändle GM, Ewers J, Mayer G. Nat Protoc. 2018 May;13(5):1153-1180. Aptamers against Cells Overexpressing Glypican 3 from Expanded Genetic Systems Combined with Cell Engineering and Laboratory Evolution. Zhang L, Yang Z, Le Trinh T, Teng IT, Wang S, Bradley KM, Hoshika S, Wu Q, Cansiz S, Rowold DJ, McLendon C, Kim MS, Wu Y, Cui C, Liu Y, Hou W, Stewart K, Wan S, Liu C, Benner SA, Tan W. Angew Chem Int Ed Engl. 2016 Sep 26;55(40):12372-5. Generation of high-affinity DNA aptamers using an expanded genetic alphabet. Kimoto M, Yamashige R, Matsunaga K, Yokoyama S, Hirao I. Nat Biotechnol. 2013 May;31(5):453-7. A Versatile Approach Towards Nucleobase-Modified Aptamers. Tolle F, Brändle GM, Matzner D, Mayer G. Angew Chem Int Ed Engl. 2015 Sep 7;54(37):10971-4. Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets. Davies DR, Gelinas AD, Zhang C, Rohloff JC, Carter JD, O’Connell D, Waugh SM, Wolk SK, Mayfield WS, Burgin AB, Edwards TE, Stewart LJ, Gold L, Janjic N, Jarvis TC. Proc Natl Acad Sci U S A. 2012 Dec 4;109(49):19971-6. Crystal structure of interleukin-6 in complex with a modified nucleic acid ligand. Gelinas AD, Davies DR, Edwards TE, Rohloff JC, Carter JD, Zhang C, Gupta S, Ishikawa Y, Hirota M, Nakaishi Y, Jarvis TC, Janjic N. J Biol Chem. 2014 Mar 21;289(12):8720-34. Non-helical DNA Triplex Forms a Unique Aptamer Scaffold for High Affinity Recognition of Nerve Growth Factor. Jarvis TC, Davies DR, Hisaminato A, Resnicow DI, Gupta S, Waugh SM, Nagabukuro A, Wadatsu T, Hishigaki H, Gawande B, Zhang C, Wolk SK, Mayfield WS, Nakaishi Y, Burgin AB, Stewart LJ, Edwards TE, Gelinas AD, Schneider DJ, Janjic N. Structure. 2015 Jul 7;23(7):1293-304. Structural basis for IL-1α recognition by a modified DNA aptamer that specifically inhibits IL-1α signaling. Ren X, Gelinas AD, von Carlowitz I, Janjic N, Pyle AM. Nat Commun. 2017 Oct 9;8(1):810. A Receptor-Guided Design Strategy for Ligand Identification. Rosenthal M, Pfeiffer F, Mayer G. Angew Chem Int Ed Engl. 2019 Jul 29;58(31):10752-10755.
how can i design the Capture-SELEX Library and Primers for PCR? Can you tell me?
Please check out the papers mentioned in the webinar - you can find a list here: www.oligotherapeutics.org/advances-in-selex-technologies-for-aptamer-selection/
Thanks for your quick response
No problem - if you still have questions after reading the papers you could try asking your questions on our twitter feed @OTSociety or emailing the authors of the papers or the webinar presenters.
I can’t access the page. Please how I design the capture SELEX library ?
@@MyRandomVideos09 Was OTS cut off by the Great Wall of China? Here are all the paper references:
Selection and Biosensor Application of Aptamers for Small Molecules.
Pfeiffer F, Mayer G.
Front Chem. 2016 Jun 15;4:25.
By-product formation in repetitive PCR amplification of DNA libraries during SELEX.
Tolle F, Wilke J, Wengel J, Mayer G.
PLoS One. 2014 Dec 9;9(12):e114693.
In vitro selection of structure-switching signaling aptamers.
Nutiu R, Li Y.
Angew Chem Int Ed Engl. 2005 Feb 4;44(7):1061-5.
Capture-SELEX: Selection of DNA Aptamers for Aminoglycoside Antibiotics.
Stoltenburg R, Nikolaus N, Strehlitz B.
J Anal Methods Chem. 2012;2012:415697.
Synthetic genetic polymers capable of heredity and evolution.
Pinheiro VB, Taylor AI, Cozens C, Abramov M, Renders M, Zhang S, Chaput JC, Wengel J, Peak-Chew SY, McLaughlin SH, Herdewijn P, Holliger P.
Science. 2012 Apr 20;336(6079):341-4.
A synthetic genetic polymer with an uncharged backbone chemistry based on alkyl phosphonate nucleic acids.
Arangundy-Franklin S, Taylor AI, Porebski BT, Genna V, Peak-Chew S, Vaisman A, Woodgate R, Orozco M, Holliger P.
Nat Chem. 2019 Jun;11(6):533-542.
In vivo selection of tumor-targeting RNA motifs.
Mi J, Liu Y, Rabbani ZN, Yang Z, Urban JH, Sullenger BA, Clary BM.
Nat Chem Biol. 2010 Jan;6(1):22-4.
Targeting hormone refractory prostate cancer by in vivo selected DNA libraries in an orthotopic xenograft mouse model.
Civit L, Theodorou I, Frey F, Weber H, Lingnau A, Gröber C, Blank M, Dambrune C, Stunden J, Beyer M, Schultze J, Latz E, Ducongé F, Kubbutat MHG, Mayer G.
Sci Rep. 2019 Mar 21;9(1):4976.
Poly-ligand profiling differentiates trastuzumab-treated breast cancer patients according to their outcomes.
Domenyuk V, Gatalica Z, Santhanam R, Wei X, Stark A, Kennedy P, Toussaint B, Levenberg S, Wang J, Xiao N, Greil R, Rinnerthaler G, Gampenrieder SP, Heimberger AB, Berry DA, Barker A, Quackenbush J, Marshall JL, Poste G, Vacirca JL, Vidal GA, Schwartzberg LS, Halbert DD, Voss A, Magee D, Miglarese MR, Famulok M, Mayer G, Spetzler D.
Nat Commun. 2018 Mar 23;9(1):1219.
Fluorescence-activated cell sorting for aptamer SELEX with cell mixtures.
Mayer G, Ahmed MS, Dolf A, Endl E, Knolle PA, Famulok M.
Nat Protoc. 2010 Dec;5(12):1993-2004.
Robotic assisted generation of 2′-deoxy-2′-fluoro-modifed RNA aptamers - High performance enabling strategies in aptamer selection.
Breuers S, Bryant LL, Legen T, Mayer G.
Methods. 2019 May 15;161:3-9.
Aptamer-based multiplexed proteomic technology for biomarker discovery.
Gold L, Ayers D, Bertino J, Bock C, Bock A, Brody EN, Carter J, Dalby AB, Eaton BE, Fitzwater T, Flather D, Forbes A, Foreman T, Fowler C, Gawande B, Goss M, Gunn M, Gupta S, Halladay D, Heil J, Heilig J, Hicke B, Husar G, Janjic N, Jarvis T, Jennings S, Katilius E, Keeney TR, Kim N, Koch TH, Kraemer S, Kroiss L, Le N, Levine D, Lindsey W, Lollo B, Mayfield W, Mehan M, Mehler R, Nelson SK, Nelson M, Nieuwlandt D, Nikrad M, Ochsner U, Ostroff RM, Otis M, Parker T, Pietrasiewicz S, Resnicow DI, Rohloff J, Sanders G, Sattin S, Schneider D, Singer B, Stanton M, Sterkel A, Stewart A, Stratford S, Vaught JD, Vrkljan M, Walker JJ, Watrobka M, Waugh S, Weiss A, Wilcox SK, Wolfson A, Wolk SK, Zhang C, Zichi D.
PLoS One. 2010 Dec 7;5(12):e15004.
Aptamer-based multiplexed proteomic technology for biomarker discovery.
Gold L, Ayers D, Bertino J, Bock C, Bock A, Brody EN, Carter J, Dalby AB, Eaton BE, Fitzwater T, Flather D, Forbes A, Foreman T, Fowler C, Gawande B, Goss M, Gunn M, Gupta S, Halladay D, Heil J, Heilig J, Hicke B, Husar G, Janjic N, Jarvis T, Jennings S, Katilius E, Keeney TR, Kim N, Koch TH, Kraemer S, Kroiss L, Le N, Levine D, Lindsey W, Lollo B, Mayfield W, Mehan M, Mehler R, Nelson SK, Nelson M, Nieuwlandt D, Nikrad M, Ochsner U, Ostroff RM, Otis M, Parker T, Pietrasiewicz S, Resnicow DI, Rohloff J, Sanders G, Sattin S, Schneider D, Singer B, Stanton M, Sterkel A, Stewart A, Stratford S, Vaught JD, Vrkljan M, Walker JJ, Watrobka M, Waugh S, Weiss A, Wilcox SK, Wolfson A, Wolk SK, Zhang C, Zichi D.
PLoS One. 2010 Dec 7;5(12):e15004.
Nucleic Acid Ligands With Protein-like Side Chains: Modified Aptamers and Their Use as Diagnostic and Therapeutic Agents.
Rohloff JC, Gelinas AD, Jarvis TC, Ochsner UA, Schneider DJ, Gold L, Janjic N.
Mol Ther Nucleic Acids. 2014 Oct 7;3:e201.
Customised nucleic acid libraries for enhanced aptamer selection and performance.
Pfeiffer F, Rosenthal M, Siegl J, Ewers J, Mayer G.
Curr Opin Biotechnol. 2017 Dec;48:111-118.
In vitro selection with artificial expanded genetic information systems.
Sefah K, Yang Z, Bradley KM, Hoshika S, Jiménez E, Zhang L, Zhu G, Shanker S, Yu F, Turek D, Tan W, Benner SA.
Proc Natl Acad Sci U S A. 2014 Jan 28;111(4):1449-54.
Identification and characterization of nucleobase-modified aptamers by click-SELEX.
Pfeiffer F, Tolle F, Rosenthal M, Brändle GM, Ewers J, Mayer G.
Nat Protoc. 2018 May;13(5):1153-1180.
Aptamers against Cells Overexpressing Glypican 3 from Expanded Genetic Systems Combined with Cell Engineering and Laboratory Evolution.
Zhang L, Yang Z, Le Trinh T, Teng IT, Wang S, Bradley KM, Hoshika S, Wu Q, Cansiz S, Rowold DJ, McLendon C, Kim MS, Wu Y, Cui C, Liu Y, Hou W, Stewart K, Wan S, Liu C, Benner SA, Tan W.
Angew Chem Int Ed Engl. 2016 Sep 26;55(40):12372-5.
Generation of high-affinity DNA aptamers using an expanded genetic alphabet.
Kimoto M, Yamashige R, Matsunaga K, Yokoyama S, Hirao I.
Nat Biotechnol. 2013 May;31(5):453-7.
A Versatile Approach Towards Nucleobase-Modified Aptamers.
Tolle F, Brändle GM, Matzner D, Mayer G.
Angew Chem Int Ed Engl. 2015 Sep 7;54(37):10971-4.
Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets.
Davies DR, Gelinas AD, Zhang C, Rohloff JC, Carter JD, O’Connell D, Waugh SM, Wolk SK, Mayfield WS, Burgin AB, Edwards TE, Stewart LJ, Gold L, Janjic N, Jarvis TC.
Proc Natl Acad Sci U S A. 2012 Dec 4;109(49):19971-6.
Crystal structure of interleukin-6 in complex with a modified nucleic acid ligand.
Gelinas AD, Davies DR, Edwards TE, Rohloff JC, Carter JD, Zhang C, Gupta S, Ishikawa Y, Hirota M, Nakaishi Y, Jarvis TC, Janjic N.
J Biol Chem. 2014 Mar 21;289(12):8720-34.
Non-helical DNA Triplex Forms a Unique Aptamer Scaffold for High Affinity Recognition of Nerve Growth Factor.
Jarvis TC, Davies DR, Hisaminato A, Resnicow DI, Gupta S, Waugh SM, Nagabukuro A, Wadatsu T, Hishigaki H, Gawande B, Zhang C, Wolk SK, Mayfield WS, Nakaishi Y, Burgin AB, Stewart LJ, Edwards TE, Gelinas AD, Schneider DJ, Janjic N.
Structure. 2015 Jul 7;23(7):1293-304.
Structural basis for IL-1α recognition by a modified DNA aptamer that specifically inhibits IL-1α signaling.
Ren X, Gelinas AD, von Carlowitz I, Janjic N, Pyle AM.
Nat Commun. 2017 Oct 9;8(1):810.
A Receptor-Guided Design Strategy for Ligand Identification.
Rosenthal M, Pfeiffer F, Mayer G.
Angew Chem Int Ed Engl. 2019 Jul 29;58(31):10752-10755.
Very informative