Between Objectivity and Whim: Nucleic Acid Structural Biology

2005 ◽  
pp. 77-88 ◽  
Author(s):  
Loren Dean Williams
Keyword(s):  
Nucleic Acid ◽  
Structural Biology

Role of Nucleic Acid and Protein Manipulation Technologies in High‐throughput Structural Biology Efforts

2003 ◽  
Author(s):  
David J. Aceti ◽  
Paul G. Blommel ◽  
Yaeta Endo ◽  
Brian G. Fox ◽  
Ronnie O. Frederick ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Structural Biology ◽  
High Throughput

Synthetic bPNAs as Allosteric Triggers of Hammerhead Ribozyme Catalysis

2019 ◽  
Author(s):  
Dennis Bong ◽  
Yufeng Liang ◽  
Jie Mao
Keyword(s):  
Nucleic Acid ◽  
Secondary Structure ◽  
Structure Function ◽  
Structural Biology ◽  
Peptide Nucleic Acid ◽  
Hammerhead Ribozyme ◽  
Structural Elements ◽  
Sugar Phosphate ◽  
Turn On ◽  
Bond Scission

The biochemistry and structural biology of the hammerhead ribozyme (HHR) has been well-elucidated. The secondary and tertiary structural elements that enable sugar-phosphate bond scission to be be catalyzed by this RNA are clearly understood. We have taken advantage of this knowledge base to test the extent to which synthetic molecules, may be used to trigger structure in secondary structure and tertiary interactions and thereby control HHR catalysis. These molecules belong to a family of molecules we call generally call “bPNAs” based on our work on bifacial peptide nucleic acid (bPNA). This family of molecules display the “bifacial” heterocycle melamine, which acts as a base-triple upon capturing two equivalents of thymine or uracil. Loosely structured internal oligouridylate bulges of 4-20 nucleotides can be restructured as triplex hybrid stems upon binding bPNAs. As such, a duplex stem element can be replaced with a bPNA triplex hybrid stem; similarly, a tertiary loop-stem interaction can be replaced with a loop-bPNA-stem complex. In this chapter, we discuss how bPNAs are prepared and applied to study structure-function turn-on in the hammerhead ribozyme system.

Synthetic bPNAs as Allosteric Triggers of Hammerhead Ribozyme Catalysis

2019 ◽  
Author(s):  
Dennis Bong ◽  
Yufeng Liang ◽  
Jie Mao
Keyword(s):  
Nucleic Acid ◽  
Secondary Structure ◽  
Structure Function ◽  
Structural Biology ◽  
Peptide Nucleic Acid ◽  
Hammerhead Ribozyme ◽  
Structural Elements ◽  
Sugar Phosphate ◽  
Turn On ◽  
Bond Scission

The biochemistry and structural biology of the hammerhead ribozyme (HHR) has been well-elucidated. The secondary and tertiary structural elements that enable sugar-phosphate bond scission to be be catalyzed by this RNA are clearly understood. We have taken advantage of this knowledge base to test the extent to which synthetic molecules, may be used to trigger structure in secondary structure and tertiary interactions and thereby control HHR catalysis. These molecules belong to a family of molecules we call generally call “bPNAs” based on our work on bifacial peptide nucleic acid (bPNA). This family of molecules display the “bifacial” heterocycle melamine, which acts as a base-triple upon capturing two equivalents of thymine or uracil. Loosely structured internal oligouridylate bulges of 4-20 nucleotides can be restructured as triplex hybrid stems upon binding bPNAs. As such, a duplex stem element can be replaced with a bPNA triplex hybrid stem; similarly, a tertiary loop-stem interaction can be replaced with a loop-bPNA-stem complex. In this chapter, we discuss how bPNAs are prepared and applied to study structure-function turn-on in the hammerhead ribozyme system.

The emerging role of MS in structure elucidation of protein–nucleic acid complexes

2008 ◽  
Vol 36 (4) ◽  
pp. 723-731 ◽  
Author(s):  
Yuliya Gordiyenko ◽  
Carol V. Robinson
Keyword(s):  
Nucleic Acid ◽  
High Resolution ◽  
Structural Biology ◽  
Structure Elucidation ◽  
Protein Complexes ◽  
Subunit Interactions ◽  
Protein Nucleic Acid ◽  
Architectural Organization ◽  
Rna Protein Complexes

Developments in MS enable us to apply this technique to non-covalent complexes, defining their stoichiometry, subunit interactions and architectural organization. We illustrate the application of this non-covalent MS approach to uncovering the overall topological arrangements of subunits and interactions within RNA–protein complexes studied in our laboratory over the last 5 years. These studies exemplify the emerging role and potential of MS as a complementary structural biology methodology and demonstrate its unique niche in investigations of dynamic or heterogeneous protein–nucleic acid complexes, which are not accessible to classical high-resolution structural biology techniques.

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