RNA Structure/Function Studies

RNA structure is thought to play a central role in many cellular processes, including transcription initiation, elongation and termination, mRNA splicing, and retroviral infection of eukaryotic cells.  Elucidating the mechanistic aspects of these intricate processes will require detailed understanding of the underlying RNA structure. RNA molecules usually possess a variety of single-stranded and double-stranded regions that give rise to complex three-dimensional structures. These structures are involved in the molecule's interactions with other nucleic acids, proteins, and small molecules.  We have developed an extensive portfolio of Ambion® products for the synthesis and modification of RNA in order to further understand the role of RNA structure.

Tools for RNA Structure/Function Research

Enzymes

 

 
  • RNA-Grade Ribonucleases: A collection of ribonucleases (RNases A, V1, and T1) that are optimized for researchers performing RNA structure, RNA sequencing, protein footprinting and boundary experiments.
  • Poly(A)Polymerase: Catalyzes the addition of adenosine to the 3' end of RNA in a sequence-independent fashion.
  • T4 Polynucleotide Kinase: Transfers the terminal phosphate of ATP to the 5´ hydroxyl terminus of DNA or RNA. Used for 5' end labeling of oligonucleotides and polynucleotides.
  • T4 RNA Ligase: Catalyzes the formation of a phosphodiester linkage between a 5´-phosphoryl-terminated ribonucleic acid and a 3´-hydroxyl-terminated ribonucleic acid.

In Vitro Transcription Kits

 

 
  • MEGAscript™ SP6, T7 and T3 Kits: Synthesize ultra-high yields of RNA, 10 to 50 times as much as produced by conventional transcription reactions.

Other

 

 
  • Cap Analog & Variants: m7G(5´)ppp(5´)G (Cap Analog) and Cap Variants. The Cap Analog is used for synthesis of 5´-capped RNA molecules.
  • Modified UTPs: Incorporate these nucleotides to confer unique characteristics and test for particular reactive groups.

Reference Information

1. Moine H, Ehresmann B, Ehresmann C, and Romby P. (1998) Probing RNA structure and function in solution. In: Simons RW and Grunberg-Manago M (editors). RNA Structure and Function, Cold Spring Harbor Laboratory Press. p. 77-115.

2. Knapp G. (1989) Enzymatic approaches to probing of RNA secondary and tertiary structure. Methods Enzymol 180:192-212. Abstract

3. Krol A and Carbon P. (1989) A guide for probing native small nuclear RNA and ribonucleoprotein structures. Methods Enzymol 180:212-227. Abstract

4. Tinoco I Jr, and Bustamante C. (1999) How RNA folds. J Mol Biol 293(2):271-281. Abstract

5. Doudna J A. (2000) Structural genomics of RNA. Nature Struct Biol 7 Suppl:954-956. Abstract

 

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