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Literature DB >> 19678613

Small molecule ligands for bulged RNA secondary structures.

Abstract

A class of wedge-shaped small molecules has been designed, synthesized, and shown to bind bulged RNA secondary structures. These minimally cationic ligands exhibit good affinity and selectivity for certain RNA bulges as demonstrated in a fluorescent intercalator displacement assay.

Entities: Chemical Disease Gene

Mesh：

Substances：
Intercalating Agents
RNA

Year: 2009 PMID： 19678613 PMCID： PMC4975938 DOI： 10.1021/ol901478x

Source DB: PubMed Journal: Org Lett ISSN： 1523-7052 Impact factor: 6.005

21 in total

1. A Structural Basis for RNAminus signLigand Interactions.

Authors: Christine S. Chow; Felicia M. Bogdan
Journal: Chem Rev Date: 1997-08-05 Impact factor: 60.622

2. Targeting DNA bulged microenvironments with synthetic agents: lessons from a natural product.

Authors: Zhen Xi; Geum-Sook Hwang; Irving H Goldberg; Jeffrey L Harris; William T Pennington; Farid S Fouad; Ghassan Qabaja; Justin M Wright; Graham B Jones
Journal: Chem Biol Date: 2002-08

3. Size-specific ligands for RNA hairpin loops.

Authors: Jason R Thomas; Xianjun Liu; Paul J Hergenrother
Journal: J Am Chem Soc Date: 2005-09-14 Impact factor: 15.419

4. Probing DNA bulges with designed helical spirocyclic molecules.

Authors: Lizzy S Kappen; Yiqing Lin; Graham B Jones; Irving H Goldberg
Journal: Biochemistry Date: 2007-01-16 Impact factor: 3.162

5. HIO3 and I2O5: mild and selective alternative reagents to IBX for the dehydrogenation of aldehydes and ketones.

Authors: K C Nicolaou; Tamsyn Montagnon; Phil S Baran
Journal: Angew Chem Int Ed Engl Date: 2002-04-15 Impact factor: 15.336

6. Solution structure of a two-base DNA bulge complexed with an enediyne cleaving analog.

Authors: A Stassinopoulos; J Ji; X Gao; I H Goldberg
Journal: Science Date: 1996-06-28 Impact factor: 47.728

7. Biochemical and thermodynamic characterization of compounds that bind to RNA hairpin loops: toward an understanding of selectivity.

Authors: Jason R Thomas; Xianjun Liu; Paul J Hergenrother
Journal: Biochemistry Date: 2006-09-12 Impact factor: 3.162

8. RNA-ligand interactions: affinity and specificity of aminoglycoside dimers and acridine conjugates to the HIV-1 Rev response element.

Authors: Nathan W Luedtke; Qi Liu; Yitzhak Tor
Journal: Biochemistry Date: 2003-10-07 Impact factor: 3.162

9. Deoxystreptamine dimers bind to RNA hairpin loops.

Authors: Xianjun Liu; Jason R Thomas; Paul J Hergenrother
Journal: J Am Chem Soc Date: 2004-08-04 Impact factor: 15.419

10. Structure-activity relationships of novel vasopressin antagonists containing C-terminal diaminoalkanes and (aminoalkyl)guanidines.

Authors: J F Callahan; D Ashton-Shue; H G Bryan; W M Bryan; G D Heckman; L B Kinter; J E McDonald; M L Moore; D B Schmidt; J S Silvestri
Journal: J Med Chem Date: 1989-02 Impact factor: 7.446

8 in total

Small molecule ligands for bulged RNA secondary structures.

1. A Structural Basis for RNAminus signLigand Interactions.

2. Targeting DNA bulged microenvironments with synthetic agents: lessons from a natural product.

3. Size-specific ligands for RNA hairpin loops.

4. Probing DNA bulges with designed helical spirocyclic molecules.

5. HIO3 and I2O5: mild and selective alternative reagents to IBX for the dehydrogenation of aldehydes and ketones.

6. Solution structure of a two-base DNA bulge complexed with an enediyne cleaving analog.

7. Biochemical and thermodynamic characterization of compounds that bind to RNA hairpin loops: toward an understanding of selectivity.

8. RNA-ligand interactions: affinity and specificity of aminoglycoside dimers and acridine conjugates to the HIV-1 Rev response element.

9. Deoxystreptamine dimers bind to RNA hairpin loops.

10. Structure-activity relationships of novel vasopressin antagonists containing C-terminal diaminoalkanes and (aminoalkyl)guanidines.

1. A modified fluorescent intercalator displacement assay for RNA ligand discovery.

2. Structure-activity studies of RNA-binding oxazolidinone derivatives.

3. Synthetic RNA recognition motifs that selectively recognize HIV-1 trans-activation response element hairpin RNA.

4. Shortening the HIV-1 TAR RNA Bulge by a Single Nucleotide Preserves Motional Modes over a Broad Range of Time Scales.

Review 5. Fluorescent indicator displacement assays to identify and characterize small molecule interactions with RNA.

6. An Evolved RNA Recognition Motif That Suppresses HIV-1 Tat/TAR-Dependent Transcription.

7. Structural characterization of naturally occurring RNA single mismatches.

Review 8. Frameworks for targeting RNA with small molecules.