Selected References on RNA Structure/Function Analysis

RNA Structure Analysis Reviews

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.

A great repository of information on various techniques used for RNA analysis, including enzymatic and chemical interference protocols. Recommended reading for beginners to RNA structure analysis.

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

Detailed protocols for using RNAses in secondary structure analysis. Includes useful information on RNA sequencing and making RNA ladders.

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

Detailed protocols for probing snRNA and snRNP structures. Provides a good description of the mechanisms by which commonly used chemicals (e.g., DMS, ENU, DEPC, and CMCT) modify RNA.

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
   
   Provides a good perspective on the emerging field of "ribonomics" — structural genomics of RNA.
   
   

Commonly Occuring RNA Structures and How They Are Detected

1. Pleij CWA and Bosch L (1989) RNA pseudoknots: structure, detection, and prediction. Methods Enzymol 180:289-303. Abstract

Discusses the principles behind the formation of a higher order pseudoknot structure and provides excellent examples of RNAs exhibiting this structure.

2. Klein DJ, Schmeing TM, Moore PB, and Steitz TA. (2001) The kink-turn: a new RNA secondary structure motif. EMBO J 20(15): 4214-4221. Abstract

Description of a new helix-internal loop-helix motif, called the kink-turn (K-turn), found in H. marismortui.

3. Keniry MA. (2000-2001) Quadruplex structures in nucleic acids. Biopolymers 56(3): 123-126. Abstract

This review discusses the techniques used to probe the structures of G-quadruplexes.

4. Shafer RH, and Smirnov I. (2000-2001) Biological aspects of DNA/RNA quadruplexes. Biopolymers 56(3): 209-227. Abstract
   
   Evidence for the presence of quadruplexes and the roles and applications of such structures in gene regulation and therapeutics.
   
   
5. Gorodkin J, Stricklin SL, Stormo GD. (2001) Discovering common stem-loop motifs in unaligned RNA sequences. Nucleic Acids Res 29(10):2135-2144. Abstract
   
   Information on two RNA structure prediction programs in identifying stem-loop RNA motifs.
   
   
6. Wyatt JR, Puglisi JD, Tinoco I Jr. (1989) RNA folding: pseudoknots, loops and bulges. Bioessays 11(4): 100-106. Abstract
   
   
7. Van Batenburg FH, Gultyaev AP, and Pleij CW. (2001) PseudoBase: structural information on RNA pseudoknots. Nucleic Acids Res 29(1): 194-195. Abstract
   
   
8. Doherty EA, Doudna JA. (2001) Ribozyme structures and mechanisms. Annu Rev Biophys Biomol Struct 30:457-475. Abstract
   
   

Techniques to Analyze Protein-RNA Interactions

1. Culver GM and Noller HF. (2000) Directed hydroxyl radical probing of RNA from iron(II) tethered to proteins in ribonucleoprotein complexes. Methods Enzymol 318:461-475.

Strategies for Introducing Modified Nucleotides into RNA Molecules

1. Conrad F, Hanne A, Gaur RK, Krupp G. (1995) Enzymatic synthesis of
   2'-modified nucleic acids: identification of important phosphate and ribose
   moieties in RNase P substrates. Nucleic Acids Res. 23(11):1845-1853.
   
   
2. Yu YT, and Steitz JA. (1997) A new strategy for introducing photoactivatable 4-thiouridine ((4S)U) into specific positions in a long RNA molecule. RNA 3(7):807-810.

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