Literature
Aptamer-Related Research Papers
1. Codrea, V, Hayner, M, Hall, B, Jhaveri, S, Ellington, A: In vitro selection of RNA aptamers to a small molecule target. Current Protocols in Nucleic Acid Chemistry 2010, 9.5.1–9.5.23. doi: 10.1002/0471142700.nc0905s40.
2. Ellington, AD, Szostak, JW: In vitro selection of RNA molecules that bind specific ligands. Nature 1990, 346(6287):818-22. doi: 10.1038/346818a0.
3. Famulok, M, and Mayer, G: Aptamers and SELEX in Chemistry & Biology. Chemistry & Biology 2014, 21(9):1055-1058. REVIEW. doi: 10.1016/j.chembiol.2014.08.003.
4. Hall, B, Arshad, S, Seo, K, Bowman, C, Coreley, M, Jhaveri, SD, Ellington, AD: In vitro selection of RNA aptamers to protein target by filter immobilization. Current Protocols in Nucleic Acid Chemistry 2010, 9.3.1–9.3.27. doi: 10.1002/0471142700.nc0903s40.
5. Hall, B, Micheletti, JM, Satya, P, Ogle, K, Pollard, J, Ellington, AD: Design, synthesis, and amplification of DNA pools for in vitro selection. Current Protocols in Nucleic Acid Chemistry 2009, 9.2.1–9.2.28. doi: 10.1002/0471142700.nc0902s39.
6. Stoltenburg, R, Reinemann, C, Strehlitz, B: SELEX--a (r)evolutionary method to generate high-affinity nucleic acid ligands. Biomol Eng 2007, 24(4):381-403. REVIEW.
7. Stovall, GM, Bedenbaugh, R, Singh, S, Meyer, AJ, Hatala, PJ, Ellington, AD, Hall, B: In vitro selection using modified or unnatural nucleotides. Current Protocols in Nucleic Acid Chemistry 2014, 9.6.1–9.6.33. doi: 10.1002/0471142700.nc0906s56.
Outreach Project: Continuous Ribozyme Evolution
1. Ledbetter, MP, Hwang, TW, Stovall, GM, Ellington, AD: Continuous in vitro evolution of a ribozyme ligase: a model experiment for the evolution of a biomolecule. Biochemistry and Molecular Biology Education 2013. 41(6):433-42. doi: 10.1002/bmb.20742.
Publications & Products, Aptamer Stream Authors
FRI students (underline), TAs (bold), REs (italics), and PIs* (asterisk)
2007
1. Sokolov K, Nida D, Descour M, Lacy A, Levy M, Hall B, Dharmawardhane S, Ellington AD*, Korgel B, and Richards-Kortum R. (2007). Molecular optical imaging of the therapeutic targets of cancer. Adv Cancer Res 96:299-344. PMID: 17161684.
2. Hall B, Hesselberth JR, and Ellington AD*. (2007 May 15). Computational selection ofnucleic acid biosensors via a slip structure model. Biosens Bioelectron 22(9-10):1939-47. PMID: 16996258. doi: 10.1016/j.bios.2006.08.019
2008
3. Gnanam AJ, Hall B, Shen X, Piasecki S, Vernados A, Galyov EE, Smither SJ, Kitto GB, Titball RW, Ellington AD*, and Brown KA. (2008 Dec). Development of aptamers specific for potential diagnostictargets in Burkholderia pseudomallei. Trans R Soc Hyg Trop Med 102(Suppl 1):S55-7. PMID: 19121689. PMCID: PMC3636715. doi: 10.1016/S0035-9203(08)70015-4
4. Li N, Wang Y, Pothukuchy A, Syrett A, Husain N, Gopalakrisha S, Kosaraju P, and Ellington AD*. (2008 Dec). Aptamers that recognize drug resistant HIV-1 reverse transcriptase. Nucleic Acids Res36(21):6739-51. PMID: 18948292. PMCID: PMC2588506. doi: 10.1093/nar/gkn775
2009
5. Piasecki SK, Hall B, and Ellington AD*. (2009). Nucleic acid pool preparation and characterization. Methods Mol Biol 535:3-18. PMID: 19377997. doi: 10.1007/978-1-59745-557-2_1
6. Li N, Ebright JN, Stovall GM, Chen X, Nguyen HH, Singh A, Syrett A, and Ellington AD*. (2009 May). Technical and biological issues relevant to cell typing with aptamers. J Proteome Res 8(5):2438-48. PMID: 19271740. doi: 10.1021/pr801048z
7. Narayanaswamy R, Levy M, Tsechansky M, Stovall GM, O'Connell JD, Mirrielees J, Ellington AD*, and Marcotte EM. (2009 Jun 23). Widespread reorganization ofmetabolic enzymes into reversible assemblies upon nutrient starvation. Proc Natl Acad Sci U S A 106(25):10147-52. PMID: 19502427. PMCID: PMC2691686. doi: 10.1073/pnas.0812771106
8. Hall B, Cater S, Levy M, and Ellington AD*. (2009 Aug 15). Kinetic optimization of aprotein-responsive aptamer beacon. Biotechnol Bioeng 103(6):1049-59. PMID: 19431189. doi: 10.1002/bit.22355
9. Hall B, Arshad S, Seo K, Bowman C, Corley M, Jhaveri SD, and Ellington AD*. (2009 Oct). In vitro selection of RNA aptamers to a protein target by filter immobilization. Curr Protoc Mol Biol Ch24:Unit 24.3. PMID: 19816933. doi: 10.1002/0471142727.mb2403s88
10. Hall B, Micheletti JM, Satya P, Ogle K, Pollard J, and Ellington AD*. (2009 Oct). Design, synthesis, and amplification of DNA pools for in vitro selection. Curr Protoc Mol Biol Ch24:Unit 24.2. PMID: 19816932. doi: 10.1002/0471142727.mb2402s88
11. Hall B, Micheletti JM, Satya P, Ogle K, Pollard J, and Ellington AD*. (2009 Dec). Design, synthesis, and amplification of DNA pools for in vitro selection. Curr Protoc Nucleic Acid Chem Ch9:Unit 9.2. PMID: 20013786. doi: 10.1002/0471142700.nc0902s39
2010
12. Codrea V, Hayner M, Hall B, Jhaveri S, and Ellington AD*. (2010 Mar). In vitro selection of RNA aptamers to a small molecule target. Curr Protoc Nucleic Acid Chem Ch9:Unit 9.5.1-23. PMID: 20201029. doi: 10.1002/0471142700.nc0905s40
13. Hall B, Arshad S, Seo K, Bowman C, Corley M, Jhaveri SD, and Ellington AD*. (2010 Mar). In vitro selection of RNA aptamers to a protein target by filter immobilization. Curr Protoc Nucleic Acid ChemCh9:Unit 9.3.1-27. PMID: 20201028. doi: 10.1002/0471142700.nc0903s40
14. Wang Y, Khaing ZZ, Li N, Hall B, Schmidt CE, and Ellington AD*. (2010 Mar 16). Aptamer antagonists of myelin-derived inhibitors promote axongrowth. PLoS One 5(3): e9726. PMID: 20300533. PMCID: PMC2838799. doi: 10.1371/journal.pone.0009726
15. Eckhoff G, Codrea V, Ellington AD*, and Chen X. (2010 Oct). Beyond allostry Catalytic regulation of a deoxyribozymethrough an entropy-driven DNA amplifier. Journal of Systems Chemistry 1:13. doi: 10.1186/1759-2208-1-13
2011
16. Stovall GM. (April 2011). Evaluation of Protein Aggregation and Organismal Fitness. PhD Dissertation, University of Texas at Austin.
2012
17. Hoyer D, Stovall GM, Ellington AD*. (April 2012) Poster: Aptamer Selection. UT Undergraduate Research Forum (Austin, TX).
18. Abdul S, Ahmad U, Lee O, Wu R, Miklos A, Stovall GM, Ellington AD*. (April 2012) Poster: Nucleic aptamer selection against closed form of maltose binding protein. UT Undergraduate Research Forum (Austin, TX).
19. Ledbetter M, Hwang TW, Stovall GM, Ellington AD*. (April 2012) Poster: Continuous in vitro evolution of a ribozyme ligase: A model kit for the evolution of a biomolecule. UT Undergraduate Research Forum (Austin, TX).
20. Mota E, Ellington AD*, Hall B. (April 2012) Poster: Chemically programmable immunity to treat cancer. UT Undergraduate Research Forum (Austin, TX).
21. Ilyas A, Asghar W, Allen PB, Duhon H, Ellington AD*, and Iqbal SM. (2012 Jul 11). Electrical detection of cancerbiomarker using aptamers with nanogap break-junctions. Nanotechnology 23(27):275502. PMID: 22706642. PMCID: PMC3404891. doi: 10.1088/0957-4484/23/27/275502
22. Ledbetter MP, Hwang TW, Stovall GM, Ellington AD*. (July 2012) Presentation, Conference Proceeding Publication, and Poster: Continuous in vitro Evolution of a Ribozyme Ligase: A Model Kit for The Evolution of a Biomolecule. Artificial Life (A-Life) Conference (East Lansing, MI).
23. Allen PB, Arshad SA, Li B, Chen X, and Ellington AD*. (2012 Aug 21). DNA circuits as amplifiers for the detection ofnucleic acids on a paperfluidic platform. Lab Chip 12(16):2951-8. PMID: 22729075. PMCID: PMC3454488. doi: 10.1039/c2lc40373k
24. Brahmaroutu A, Ellington AD*, Stovall GM. (October 2012) Poster: Aptamer Research. Rice Regional Undergraduate Symposium (Houston, TX).
25. McDonald H, Ellington AD*, Stovall GM. (October 2012) Poster: Aptamer Research. Rice Regional Undergraduate Symposium (Houston, TX).
26. Nam G, Ellington AD*, Stovall GM. (October 2012) Poster: Aptamer Research. Rice Regional Undergraduate Symposium
(Houston, TX).
2013
27. Oladoyin V, Ellington AD*, Stovall GM. (March 2013) Poster: Aptamer Research. American Medical Student Association (AMSA) 2013 Convention (Washington DC).
28. Booker C, Hall B. (April 2013) Poster: Altermune Aptamer Research. UT Undergraduate Research Forum (Austin, TX).
29. Hughes T, Bedenbaugh RS, Stovall GM, Ellington AD*. (April 2013) Poster: FGF8b aptamer selection. UT Undergraduate Research Forum (Austin, TX).
30. Huynh V, Ellington AD*, Stovall GM. (April 2013) Poster: Is It a Ligand Switch or a Dipstick Diagnostic Tool? Yes! RNA Aptamer against Calf Intestinal Alkaline Phosphatase. UT Undergraduate Research Forum (Austin, TX).
31. Manjunath S, Ellington AD*, Stovall GM. (April 2013) Poster: Aptamer Research. UT Undergraduate Research Forum (Austin, TX).
32. McDonald H, Hall B. (April 2013) Poster: Altermune Aptamer Research. UT Undergraduate Research Forum (Austin, TX).
33. Nguyen JM, Ellington AD*, Stovall GM. (April 2013) Poster: FGF-2 Aptamer Selection: A Validation of Published Results. UT Undergraduate Research Forum (Austin, TX).
34. Singh S, Kar R, Ellington AD*, Stovall GM. (April 2013) Poster: RNA Aptamer Selection Against Transferrin: "Escort Aptamers" for Targeted Drug Delivery. UT Undergraduate Research Forum (Austin, TX).
35. Ledbetter M, Hwang T, Stovall GM, Ellington AD*. (April 2013) Poster: Continuous in vitro Evolution of a Ribozyme Ligase: A Model Experiment for The Evolution of a Biomolecule. UT Undergraduate Research Forum (Austin, TX).
36. Ledbetter M, Hwang T, Stovall GM, Ellington AD*. (2013) Poster: Continuous in vitro Evolution of a Ribozyme Ligase: A Model Experiment for The Evolution of a Biomolecule. 2013 Synthetic Biology Conference (Imperial College, London, England).
37. Gaddikoppula M, Ellington AD*, Stovall GM. (October 2013) Presentation: Next Generation of Beta-Glucuronidase (GUS) Reporter Assay Using an Aptamer Inhibitor. Rice Undergraduate Symposium (Houston, TX).
38. Huynh V, Ellington AD*, Stovall GM. (October 2013) Presentation: Is It a Ligand Switch or a Dipstick Diagnostic Tool? Yes! RNA Aptamer against Calf Intestinal Alkaline Phosphatase. Rice Undergraduate Symposium (Houston, TX).
39. Jamali T, Ellington AD*, Stovall GM. (October 2013) Presentation: Anti-FGF8b aptamers for utilization in cancer diagnostics. Rice Undergraduate Symposium (Houston, TX).
40. Klein K, Ellington AD*, Stovall GM. (October 2013) Presentation: Nucleic acid aptamer selection against fibroblast growth factor 8b for development of diagnostics and therapeutics for cancer. Rice Undergraduate Symposium (Houston, TX).
41. Nourani A, Ellington AD*, Stovall GM. (October 2013) Presentation: Aptamer selection against Hcp-6 for diagnosis and detection of Burkholderia pseudomallei. Rice Undergraduate Symposium (Houston, TX).
42. Sheth J, Stovall GM, Ellington AD*. (October 2013) Presentation: An Aptamer against Progesterone for Breast Cancer Drug Delivery. Rice Undergraduate Symposium (Houston, TX).
43. Singh S, Ledbetter M, Ellington AD*, Stovall GM. (October 2013) Presentation: Development of a classroom evolution demonstration. Rice Undergraduate Symposium (Houston, TX).
44. Wei E, Huynh VD, Ellington AD*, Stovall GM. (October 2013) Presentation: Novel Molecular Reporter System using an Anti-Calf Intestinal Alkaline Phosphatase Aptamer. Rice Undergraduate Symposium (Houston, TX).
45. McDonald H, Ellington AD*, Hall B, Meyer A. (October 2013) Poster: Utilization of novel T7 RNA polymerases for the incorporation of modified nucleotides during aptamer selection. Aptamers in Medicine (Naples, Italy).
46. Ledbetter MP, Hwang TW, Stovall GM, and Ellington AD*. (2013 Nov 09). Continuous in vitro evolution of a ribozyme ligase: a model experiment for the evolution of a biomolecule. Biochem Mol Biol Educ41(6):433-42. PMID: 24214216. doi: 10.1002/bmb.20742
47. Huynh V, Ellington AD*, Stovall GM. (December 2013) Poster: Is It a Ligand Switch or a Dipstick Diagnostic Tool? Yes! RNA Aptamer against Calf Intestinal Alkaline Phosphatase. ABCRMS Conference (Nashville, Tennessee).
2014
48. Nguyen JM, Weitekamp CA, Hofmann HA. (January 2014) Poster: Dopaminergic Regulation of Social Competence in a Cichlid Fish. Society of Integrative and Comparative Biology (Austin, TX).
49. Stovall GM, Bedenbaugh RS, Singh S, Meyer AJ, Hatala PJ, Ellington AD*, and Hall B. (January 2014). In Vitro Selection Using Modified or Unnatural Nucleotides. Curr Protoc Nucleic Acid Chem Ch9:Unit 9.6.1-9.6.33. doi: 10.1002/0471142700.nc0906s56
50. Xu J, Tack D, Hughes RA, Ellington AD*, and Gray JJ. (Feb 2014). Structure-based non-canonical amino acid design to covalently crosslink an antibody-antigen complex. J Struct Biol 185(2):215-22. PMID: 23680795. doi: 10.1016/j.jsb.2013.05.003
51. Bedenbaugh R, Ellington AD*, Stovall GM. (March 2014) Poster: Aptamers in the Study of Fibroblast Growth Factor 8b. Aptamer 2014 Conference (Oxford, England).
52. McDonald H, Ellington AD*, Hall B. (March 2014) Poster: Selection against Igf-1R. Aptamers 2014 Conference (Oxford, England).
53. Huynh V, Ellington AD*, Stovall GM. (March 2014) Poster: Is It a Ligand Switch or a Dipstick Diagnostic Tool? Yes! RNA Aptamer against Calf Intestinal Alkaline Phosphatase. ACS Conference (Dallas, TX).
54. Wei E, Huynh VD, Ellington AD*, Stovall GM. (March 2014) Poster: Novel Molecular Reporter System using an Anti-Calf Intestinal Alkaline Phosphatase Aptamer. ACS Conference (Dallas, TX).
55. Airhart E, Ellington AD*, Stovall GM. (April 2014) Poster: Nucleic acid aptamer selection against beta-glucuronidase. UT Undergraduate Research Forum (Austin, TX).
56. Bedenbaugh R, Ellington AD*, Stovall GM. (April 2014) Poster: Aptamers in the Study of Fibroblast Growth Factor 8b. UT Undergraduate Research Forum (Austin, TX).
57. DeSai C, Pierce-Shimomura J, Ellington AD*, Stovall GM. (April 2014) Poster: Inhibiting amyloid precursor protein to prevent neurodegeneration in Down Syndrome and Alzheimer’s Disease. UT Undergraduate Research Forum (Austin, TX).
58. Huynh V, Ellington AD*, Stovall GM. (April 2014) Poster: Is it a ligand switch or a dipstick diagnostic tool? Yes! RNA aptamer against calf intestinal alkaline phosphatase. UT Undergraduate Research Forum (Austin, TX).
59. Jamali T, Ellington AD*, Stovall GM. (April 2014) Poster: Anti-FGF8b aptamers for utilization in cancer diagnostics. UT Undergraduate Research Forum (Austin, TX).
60. Klein K, Ellington AD*, Stovall GM. (April 2014) Poster: Nucleic acid aptamer selection against fibroblast growth factor 8b for development of diagnostics and therapeutics for cancer. UT Undergraduate Research Forum (Austin, TX).
61. Nourani A, Ellington AD*, Stovall GM. (April 2014) Poster: Aptamer selection against Hcp-6 for diagnosis and detection of Burkholderia pseudomallei. UT Undergraduate Research Forum (Austin, TX).
62. Sheth J, Ellington AD*, Stovall GM. (April 2014) Poster: Progesterone aptamer for breast cancer drug delivery. UT Undergraduate Research Forum (Austin, TX).
63. Singh S, Ledbetter M, Ellington AD*, Stovall GM. (April 2014) Poster: Development of a classroom evolution demonstration. UT Undergraduate Research Forum (Austin, TX).
64. St. Cyr M, Brown K, Ellington AD*, Stovall GM. (April 2014) Poster: Nucleic acid aptamer selection against Burkholderia pseudomallei for the diagnosis of melioidosis. UT Undergraduate Research Forum (Austin, TX).
65. DeSai C, Stovall GM, Ellington AD*, Pierce-Shimomura J. (April 2014) Poster: Inhibiting amyloid precursor protein to prevent neurodegeneration in Down syndrome and Alzheimer's disease. UT Longhorn Research Bazaar (Austin, TX).
66. Klein K, Khoo K, Singh S, Stovall GM, Ellington AD*. (October 2014) Conference Talk: Continuous evolution in a tube: A high school evolution demonstration. Rice Gulf Coast Undergraduate Research Symposium (Houston, TX).
67. Huynh V, Wei E, Ellington AD*, Stovall GM. (October 2014) Conference Talk: Alternative ELISA using an RNA Aptamer against Calf Intestinal Alkaline Phosphatase. Rice Gulf Coast Undergraduate Research Symposium (Houston, TX).
68. Satarasinghe P, Ellington AD*, Stovall GM. (October 2014) Conference Talk: Attacking Alzheimer’s: Developing an Aptamer against Amyloid Precursor Protein (APP). Rice Gulf Coast Undergraduate Research Symposium (Houston, TX).
69. Singh S, Marco J, Gutierrez S, Jackson J. (October 2014) Conference Talk: Thymus Regeneration Project: Regeneration of the Thymic Microenvironment by in vitro Cell Seeding of a Thymus Scaffold. Rice Gulf Coast Undergraduate Research Symposium (Houston, TX).
2015
70. Meyer, AJ, Garry, DJ, Hall, B, Byrom, MM, McDonald, HG, Yang, X, Yin, YW, and Ellington, AD*. (2015). Transcription yield of fully 2’-modified RNA can be increased by the addition of thermostabilizing mutations to T7 RNA polymerase mutants. Nucleic Acids Res [Epub ahead of print] PMID: 26209133. doi:10.1093/nar/gkv734
Clark G, Russell J, Enyeart P, Graci, B, Wessel A, Jarmoskaite I, Polioudaki, D, Stuart Y, Gonzalez T, MacKrell A, Rodenbusch S, Stovall GM, Beckham J, Montgomery M, Tasneem T, Jones J, Simmons S, Roux S: Middle school science educational outreach programs: “Present your Ph.D. thesis to a 12-year-old” and “Shadow a scientist.” PLoS Biology 2015. Submitted (5/2015).
Beckham JT, Farre J, Stovall GM, Simmons SL: The Freshman Research Initiative as a model for addressing shortages and disparities in STEM engagement. Conference: New Directions for Mathematics Research Experience for Undergraduates (REUs) - Mt. Holyoke College. Submitted (8/2014).
Huynh V, Wei E, Mahadevan S, Guerrero L, Parthiban P, Reveles M, Khoo K, Ellington AD, Stovall GM: Aptamer ELISA: Alternative Reporter Conjugations. Analytical Biochemistry. In preparation (tentative submission date of 9/2015).