The Disney Lab
Publications
79. Liu B, Wang D, Childs-Disney JL, Gallo SM, Disney MD. Analysis of Human Pre-microRNA Secondary Structural Elements. Submitted.
78. Guan L, Disney MD. Covalent small molecule-RNA complex formation in living cells enables cellular profiling of small molecule-RNA interactions. Submitted.
77. Tran T, Childs-Disney JL, Guan L, Liu B, Rzuczek S, Disney MD. Rationally Designed Small Molecules Target Structured RNAs More Effectively Than Oligonucleotides. Submitted.
76. Disney MD. Rational design of chemical genetic probes of RNA function and lead therapeutics targeting repeating transcripts. Submitted.
75. Sellier C, Freyermuth F, Tabet R, Tran T, He F, Ruffenach F, Alunni V, Moine H, Thibault C, Page A, Tassone F, Willemsen R, Disney MD, Hagerman PJ, Todd PK, Charlet-Berguerand N. Sequestration of DROSHA and DGCR8 by expanded CGG-repeats RNA alters microRNA processing in Fragile X-Associated Tremor/Ataxia Syndrome. Cell Reports, in press.
74. Disney MD. Computational methods to enable the design of bioactive small molecules targeting RNA. Submitted.
73. Velagapudi SP, Disney MD. High Affinity and Selective RNA Motifs that Bind Carbohydrate-based Molecular Transporters. Submitted.
72. Velagapudi SP, Disney MD. Defining RNA Motif-Aminoglycoside Interactions via Two-Dimensional Combinatorial Screening (2DCS) and Structure-Activity Relationships by Sequencing (StARTS). Submitted.
71. Velagapudi SP, Gallo SM, Disney MD. Design of Selective Small Molecules Targeting RNA Oncogenes from Sequence. Submitted.
70. Yildirim, I, Park H, Disney MD, Schatz GC. A Dynamic Structural Model of Expanded RNA CAG Repeats: A Refined X-ray Structure and Computational Investigations Using Molecular Dynamics and Umbrella Sampling Simulations. Journal of the American Chemical Society, in press.
69. Childs-Disney JL, Parkesh R, Nakamori M, Thornton CA, Disney MD. Rational Design of Bioactive, Modularly Assembled Aminoglycosides Targeting the RNA that Causes Myotonic Dystrophy Type 1. ACS Chemical Biology, in press.
68. Guan L, Disney MD. Small Molecule-Mediated Cleavage of RNA in Living Cells. Angewandte Chemie, in press.
67. Velegapudi SP, Pushechnikov P, Labuda LP, French JM, Disney MD. Probing a 2-Aminobenzimidazole Library for Binding to RNA Internal Loops via Two-Dimensional Combinatorial Screening. ACS Chemical Biology, in press.
66. Tran T, Disney MD. Identifying the Preferred RNA Motifs and Chemotypes that Interact by Probing Millions of Combinations. Nature Communications, (2012), 3, 1125. PMID: 23047683.
65. Disney MD, Liu B, Yang WY, Sellier C, Tran T, Charlet-Berguerand N, Childs-Disney JL. A Small Molecule That Targets r(CGG)(exp) and Improves Defects in Fragile X-Associated Tremor Ataxia Syndrome. ACS Chem Biol. (2012), PMCID: PMC3477254.
64. Guan L, Disney MD. Recent advances in developing small molecules targeting RNA. ACS Chemical Biology (2012), 7, 73-86.
63. Childs‐Disney JL, Hoskins J, Rzuczek SG, Thornton CA, Disney MD. Rationally designed small molecules targeting the RNA that causes myotonic dystrophy type 1 are potently bioactive. ACS Chem Biol. (2012), 7, 856-62. PMCID: PMC3356481.
62. Parkesh R, Childs‐Disney JL, Nakamori M, Kumar A, Wang E, Wang T, Hoskins J, Tran T, Housman D, Thornton CA, Disney MD. Design of a bioactive small molecule that targets the myotonic dystrophy type 1 RNA via an RNA motif-ligand database and chemical similarity searching. J Am Chem Soc. (2012), 134, 4731-42. PMCID: PMC3306011.
61. Kumar A, Parkesh R, Sznajder LJ, Childs‐Disney JL, Sobczak K, Disney MD. Chemical correction of pre-mRNA splicing defects associated with sequestration of muscleblind-like 1 protein by expanded r(CAG)-containing transcripts. ACS Chem Biol. (2012), 7, 496-505. PMCID: PMC3306454.
60. Childs-Disney JL, Tsitovich PB, Disney MD. Using Modularly Assembled Ligands To Bind RNA Internal Loops Separated by Different Distances. ChemBioChem, (2011), 12, 2143-2146. PMCID: PMC3378996
59. Lee MM, Disney MD. Influencing Uptake and Localization of Aminoglycoside-Functionalized Peptoids. Molecular Biosystems, (2011), 7, 2441-51. PMCID: PMC3135690
58. Kumar A, Fang P, Park H, Guo M, Nettles K, Disney MD. Crystal Structure of the Repeating CGG Motif Found in the RNA that Causes Fragile X Syndrome. ChemBioChem (2011), 12, 2140-2142.
57. Kumar A, Park H, Fang P, Parkesh R, Guo M, Nettles K, Disney MD. Crystal Structure of the Triplet Repeat in Myotonic Dystrophy Reveals Heterogeneous 1x1 Nucleotide UU Internal Loop Conformations. Biochemistry (2011), 50, 9928-9935.
56. Velagapudi SP, Seedhouse S, French J, Disney MD. Defining the RNA Internal Loops Preferred by Drug-Like Ligands via Two-Dimensional Combinatorial Screening. Journal of the American Chemical Society, (2011), 133, 10111-8.
55. Parkesh R, Fountain M, Disney MD. NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1. Biochemistry, (2011), 50, 599-601.
54. Tran T, Disney MD. Molecular Recognition of 6’-N-5-Hexynoate Kanamycin A and RNA 1x1 Internal Loops Containing CA Mismatches. Biochemistry, (2010), 49, 1833-42.
53. Velagapudi SP, Disney MD. Identifying And Characterizing RNA-Ligand Interactions Using 2-Dimensional Combinatorial Screening and Structure-Activity Relationships Through Sequencing. In Methods for Studying Nucleic Acid/drug Interactions, Edited by Wanunu, M. and Tor, Y.
52. Disney MD. Studying modification of aminoglycoside antibiotics by resistance-causing enzymes via microarray. Methods In Molecular Biology (2012), 808, 303-20.
51. Aminova O, Disney MD. A microarray-based method to perform nucleic acid selections. Methods in Molecular Biology, (2010), 669, 209-224.
50. Disney MD. RNA targeting compounds and methods for making and using same. US Patent Application No. 20080227213 (9/18/2008).
49. Tsitovich PB, Pushechnikov A, French JM, Disney MD. A chemoenzymatic route to diversify aminoglycosides enables a microarray-based method to probe acetyltransferase activity. ChemBioChem (2010), 11, 1656-1660. Inside cover article.
48. Velagapudi SP, Seedhouse SJ, Disney MD. Structure-activity relationships through sequencing (StARTS) defines optimal and suboptimal RNA motif targets for small molecules. Angewandte Chemie International Edition, English (2010), 49, 3816-3818.
47. Tran T, Disney MD. Two-dimensional combinatorial screening of a bacterial rRNA A-site-like motif library: defining privileged asymmetric internal loops that bind aminoglycosides. Biochemistry (2010), 49, 1833-1842
46. Seedhouse SJ, Labuda LP, Disney MD. The Privileged Chemical Space Predictor (PCSP): a computer program that identifies privileged chemical space from screens of modularly assembled chemical libraries. Bioorganic Medicinal Chemistry Letters (2010), 20, 1338-1343.
45. Disney MD, Lee MM, Pushechnikov A, Childs-Disney JL. The role of flexibility in the rational design of modularly assembled ligands targeting the RNAs that cause the myotonic dystrophies. ChemBioChem (2010), 11, 375-382.
44. Lee MM, Childs-Disney JL, Pushechnikov A, French JM, Sobczak K, Thornton CA, Disney MD. Controlling the specificity of modularly assembled small molecules for RNA via ligand module spacing: targeting the RNAs that cause myotonic muscular dystrophy. Journal of the American Chemical Society (2009), 131, 17464-17472.
43. Paul DJ, Seedhouse SJ, Disney MD. Two-dimensional combinatorial screening and the RNA Privileged Space Predictor (RNA-PSP) efficiently identify aminoglycoside-RNA hairpin loop interactions. Nucleic Acids Research, (2009), 37, 5894-5907.
42. Pushechnikov A, Lee MM, Childs-Disney JL, Sobczak K, French, JM, Thornton CA, Disney MD. Rational design of ligands targeting triplet repeating transcripts that cause RNA dominant disease: Application to myotonic muscular dystrophy type 1 and spinocerebellar ataxia type 3. Journal of the American Chemical Society, (2009), 131, 9767-9779. Highlighted by Faculty of 1000.
41. Lee MM, Pushechnikov A, Disney MD. Rational and modular design of potent ligands targeting the RNA that causes myotonic muscular dystrophy 2. ACS Chemical Biology, (2009), 4, 345-355.
40. Labuda LP, Pushechnikov A, Disney MD. Small molecule microarrays of RNA-focused peptoids help identify inhibitors of a pathogenic group I intron. ACS Chemical Biology, (2009), 4, 299-307.
39. Aminova O, Paul DJ, Childs-Disney JL, Disney MD. Two-dimensional combinatorial screening identifies specific 6’acylated kanamycin A- and 6’ acylated neamine-RNA hairpin interactions. Biochemistry, (2008), 47, 12670-12679.
38. Barrett OJ, Pushechnikov A, Wu M, Disney MD. Studying aminoglycoside modification by the acetyltransferase class of resistance-causing enzymes via microarray. Carbohydrate Research, (2008), 343, 2924-2931
37. Testa SM, Disney MD, Gryaznov SM, Turner DH. Methods and Compositions for Inhibition of RNA Splicing. US Patent No. 6958215 (issued on 10/25/2005).
36. Pushechnikov A, Disney MD. Dihydro-2(3H)-thiophenimine hydrochloride. Electronic Encyclopedia of Reagents for Organic Reagents (e-EROS).
35. Disney MD. Book Review: Biochips as pathways to drug discovery. ChemMedChem (2008), 3, 363.
34. Disney MD, Childs-Disney JL. “Supra”molecular recognition of Galectin-1. Chemistry & Biology (2007), 14, 1095-1097.
33. Disney MD. Short-circuiting RNA splicing, Nature Chemical Biology, (2008), 4, 723-724.
32. Disney MD, Labuda LP, Paul DJ, Poplawski SG, Pushechnikov A, Tran T, Velagapudi SP, Wu M, Childs-Disney JL. Two-dimensional combinatorial screening identifies specific aminoglycoside-RNA internal loop partners. Journal of the American Chemical Society, (2008), 130, 11185‐11194.
31. Childs-Disney JL, Disney MD. A simple ligation-based method to increase the information density in sequencing experiments used to deconvolute nucleic acid selections. RNA, (2008), 14, 390‐394.
30. Disney MD, Barrett OJ. An aminoglycoside microarray platform for directly monitoring and studying resistance. Biochemistry (2007), 46, 11223-11230.
29. Childs-Disney JL, Wu M, Pushechnikov A, Aminova O, Disney MD. A small molecule microarray platform to select RNA internal loop-ligand interactions. ACS Chemical Biology (2007), 2, 745-754. Highlighted by Faculty of 1000.
28. Disney MD, Childs-Disney JL. Using selection to identify and chemical microarray to study the RNA internal loops recognized by 6’-N-acylated kanamycin A. ChemBioChem, (2007), 8, 649-656.
27. Barrett OJ, Childs JL, Disney MD. Chemical microarrays to identify ligands that bind pathogenic cells. ChemBioChem, (2006), 7, 1882-1885.
26. Kehr JC, Zilliges Y, Springer A, Disney MD, Ratner DD, Bouchier C, Seeberger PH, de Marsac NT, Dittmann E. A mannan binding lectin is involved in cell-cell attachment in a toxic strain of Microcystis aeruginosa. Molecular Microbiology, (2006), 59, 893-906.
25. Brun MA, Disney MD, Seeberger PH. Miniaturization of microwave-assisted carbohydrate functionalization to create oligosaccharide microarrays. ChemBioChem, (2006), 7, 421-424.
24. Disney MD, Hook D, Namoto K, Seeberger PH, Seebach D. N-linked glycosylated beta-peptides are resistant to degradation by glycoamidase A. Chemistry and Biodiversity, (2005), 2, 1624-1634.
23. Disney MD, Stephenson R, Wright TW, Haidaris CG, Turner DH, Gigliotti F. Activity of Hoechst 33258 against Pneumocystis carinii, f. sp. muris, Candida albicans, and Candida dubliniensis. Antimicrobial Agents Chemotherapy, (2005), 49, 1326-1330.
22. Disney MD, Seeberger PH. The use of carbohydrate microarrays to study carbohydrate-cell interactions and to detect pathogens. Chemistry and Biology, (2004), 11, 1701-1707. Highlighted by Faculty of 1000.
21. Disney MD, Childs JL, Turner DH. Hoechst 33258 inhibits group I intron self-splicing by affecting RNA folding. ChemBioChem, (2004), 5, 1647-1652.
20. Ratner DM, Adams EW, Disney MD, Seeberger PH. Tools for glycomics: mapping interactions of carbohydrates in biological systems. ChemBioChem, (2004), 5, 1375-1383.
19. Disney MD, Zheng J, Swager T, Seeberger PH. Detection of bacteria with carbohydrate-functionalized fluorescent polymers. Journal of the American Chemical Society, (2004), 126, 13343-13346.
18. Disney MD, Seeberger PH. Carbohydrate arrays as tools for the glycomics revolution. Drug Discovery Today: TARGETS, (2004), 3, 151-158.
17. Disney MD, Seeberger PH. Aminoglycoside microarrays to explore interactions of antibiotics with RNAs and proteins. Chemistry-A European Journal, (2004), 10, 3308-3314. Highlighted by Faculty of 1000.
16. Disney MD, Magnet S, Blanchard JS, Seeberger PH. Aminoglycoside microarrays to study antibiotic resistance. Angewandte Chemie International Edition, (2004), 43, 1591-1594. Highlighted by Faculty of 1000.
15. Disney MD, Childs-Disney JL. Methods for identifying ligands that target nucleic acid molecules and nucleic acid structural motifs. US Patent Application No. 20080188377 (08/07/2008). Patent pending.
14. Swager TM, Seeberger PH, Zheng J, Disney MD. Polymers for Analyte Detection. US Patent Application No. 60/610,743 (9/17/2004). Patent pending.
13. Disney MD, Haidaris CG, Turner DH. Uptake and Antifungal of Oligonucleotides in Candida and Saccharomyces. Docket No.: 176/61430 (1-11033-03012). Patent pending.
12. Turner DH, Childs JL, Disney MD. Oligonucleotide Directed Misfolding of RNA (ODMiR). US Patent Application No. 60/390,241; International Application No. PCT/US2003/019302.
11. Disney MD, Childs JL, Turner DH. New approaches to targeting RNA with oligonucleotides: Inhibition of group I intron self-splicing. Biopolymers, (2004), 73, 151-161.
10. Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zucker M, Turner DH. Incorporating chemical modification restraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proceedings of the National Academy of Sciences USA, (2004), 101, 7287-7292.
9. Du H, Disney MD, Miller BL, Krauss TD. Hybridization-based unquenching of DNA hairpins on Au surfaces: Prototypical “molecular beacon” biosensors. Journal of the American Chemical Society, (2003), 125, 4012-4013.
8. Disney MD, Haidaris, CG, Turner DH. Uptake and antifungal activity of oligonucleotides in Candida albicans. Proceedings of the National Academy of Sciences USA, (2003), 100, 1530-1534.
7. Childs JL, Disney MD, Turner DH. Oligonucleotide directed misfolding of RNA inhibits Candida albicans group I intron splicing. Proceedings of the National Academy of Sciences USA, (2002), 99, 11091-11096. Highlighted by Faculty of 1000.
6. Disney MD, Turner DH. Molecular recognition by the Candida albicans group I intron: tertiary interactions with an imino G●A pair facilitate binding of the 5' exon and lower the KM for guanosine. Biochemistry, (2002), 41, 8113-8119. Highlighted by Faculty of 1000.
5. Disney MD, Matray T, Gryaznov SM, Turner DH. Binding enhancement by tertiary interactions and suicide inhibition of a Candida albicans group I intron by phosphoramidate and 2' O-methyl hexanucleotides. Biochemistry, (2001), 40, 6520-6526.
4. Disney MD, Haidaris CG, Turner DH. Recognition elements for 5' exon substrate binding to the Candida albicans group I intron. Biochemistry, (2001), 40, 6507-6519.
3. Disney MD, Gryaznov SM, Turner DH. Contributions of individual nucleotides to tertiary binding of substrate by a Pneumocystis carinii group I intron. Biochemistry, (2000), 39, 14269-14278.
2. Disney MD, Testa SM, Turner DH. Targeting a Pneumocystis carinii group I intron with methylphosphonate oligonucleotides: Backbone charge is not required for binding or reactivity. Biochemistry, (2000), 39, 6991-7000.
1. Testa SM, Disney MD, Turner DH, Kierzek R. Thermodynamics of RNA-RNA duplexes with 2- or 4-thiouridines: Implications for antisense design and targeting a group I intron. Biochemistry, (1999), 38, 16655-16662.
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