Structure-activity relationships through sequencing (StARTS) defines optimal and suboptimal RNA motif targets for small molecules

Angewandte Chemie - International Edition

Volumn 49, Issue 22, 2010, Pages 3816-3818

  Velagapudi, Sai Pradeep ^a   Seedhouse, Steven J ^a   Disney, Matthew D ^a  

^a UNIVERSITY AT BUFFALO   (United States)

Author keywords

Aminoglycosides; Drug design; Nucleic acids; RNA; Structure activity relationships

Indexed keywords

AMINOGLYCOSIDES; COMBINATORIAL SCREENINGS; DRUG DESIGN; EXPERIMENTAL APPROACHES; RNA MOTIFS; RNA STRUCTURES; SMALL MOLECULES; STRUCTURE ACTIVITY RELATIONSHIPS;

NUCLEIC ACIDS; OPTIMIZATION; TARGETS;

RNA;

AMINOGLYCOSIDE; LIGAND; RNA;

ARTICLE; CHEMISTRY; CONFORMATION; MICROARRAY ANALYSIS; NUCLEIC ACID HYBRIDIZATION; NUCLEOTIDE SEQUENCE; STRUCTURE ACTIVITY RELATION;

AMINOGLYCOSIDES; BASE SEQUENCE; LIGANDS; MICROARRAY ANALYSIS; NUCLEIC ACID CONFORMATION; NUCLEIC ACID HYBRIDIZATION; RNA; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 77952658021     PISSN: 14337851     EISSN: 15213773     Source Type: Journal    
DOI: 10.1002/anie.200907257     Document Type: Article

References (12)

1. J. L. Childs-Disney, M. Wu, A. Pushechnikov, O. Aminova, M. D. Disney, ACS Chem. Biol. 2007, 2, 745-754;
2. M. D. Disney, L. P. Labuda, D. J. Paul, S. G. Poplawski, A. Pushechnikov, T. Tran, S. P. Velagapudi, M. Wu, J. L. Childs-Disney, J. Am. Chem. Soc. 2008, 130, 11185-11194.
3. D. J. Paul, S. J. Seedhouse, M. D. Disney, Nucleic Acids Res. 2009, 57, 5895-5907.
4. J. R. Thomas, P. J. Hergenrother, Chem. Rev. 2008, 108, 1171-1224.
5. K. F. Blount, R. R. Breaker, Nat Biotechnol. 2006, 24, 1558-1564;
6. K. Jeyaseelan, W. B. Herath, A. Armugam, Expert Opin. Ther. Targets 2007, 11, 1119-1129;
7. T.M. Wheeler, Neurotherapeutics 2008, 5, 592-600.
8. M. M. Lee, A. Pushechnikov, M. D. Disney, ACS Chem. Biol. 2009, 4, 345-355;
9. A. Pushechnikov, M. M. Lee, J. L. Childs-Disney, K. Sobczak, J. M. French, C. A. Thornton, M. D. Disney, J. Am Chem. Soc. 2009, 131, 9767-9779.
10. J. L. Childs-Disney, M. D. Disney, RNA 2008, 14, 390-394. Each sequencing reaction contained multiple selected RNAs (∼3).
11. Analysis of the highest Z-score features did not correlate with measured affinity. Details are given in the Supporting Information.
12. Details of the RNA-PSP v. 2.0 program are given in the Supporting Information. The program will be available upon publication for free download at http://www.nsm.buffalo.edu/ Research/ma/.