RNA structure

Current Opinion in Structural Biology

Volumn 8, Issue 3, 1998, Pages 278-285

  Conn, Graeme L ^a   Draper, David E ^a  

^a JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

CRYSTAL STRUCTURE; INTRON; PRIORITY JOURNAL; REVIEW; RNA STRUCTURE; STRUCTURE ACTIVITY RELATION;

EID: 0032102762     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(98)80059-6     Document Type: Article

References (49)

1. Pley HW, Flaherty KM, McKay DB. Three-dimensional structure of a hammerhead ribozyme. Nature. 372:1994;68-74.
2. Scott WG, Finch JT, Klug A. Crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell. 81:1995;991-1002.
3. Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Kundrot CE, Cech TR, Doudna JA. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science. 273:1996;1678-1685.
4. Tanner MA, Cech TR. Joining the two domains of a group I ribozyme to form the catalytic core. Science. 275:1997;847-849.
5. Tanner MA, Anderson EM, Gutell RR, Cech TR. Mutagenesis and comparative sequence analysis of a base triple joining the two domains of group I ribozymes. RNA. 3:1997;1037-1051.
6. Kalurachchi K, Uma K, Zimmermann RA, Nikonowicz EP. Structural features of the binding site for ribosomal protein S8 in Escherichia coli 16S rRNA defined using NMR spectroscopy. Proc Natl Acad Sci USA. 94:1997;2139-2144.
7. Tao J, Chen L, Frankel AD. Dissection of the proposed base triple in human immunodeficiency virus TAR RNA indicates the importance of the Hoogsteen interaction. Biochemistry. 36:1997;3491-3495.
8. Jaeger L, Michel F, Westhof E. Involvement of GNRA tetraloops in long-range RNA tertiary interactions. J Mol Biol. 236:1994;1271-1276.
9. Lehnert V, Jaeger L, Michel F, Westhof E. New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme. Chem Biol. 3:1996;993-1009.
10. Jestin JL, Deme E, Jacquier A. Identification of structural elements critical for inter-domain interactions in a group II self-splicing intron. EMBO J. 16:1997;2945-2954.
11. Costa M, Deme E, Jacquier A, Michel F. Multiple tertiary interactions involving domain II of group II self-splicing introns. J Mol Biol. 267:1997;520-536.
12. Massire C, Jaeger L, Westhof E. Phylogenetic evidence for a new tertiary interaction in bacterial RNase P RNAs. RNA. 3:1997;553-556.
13. Costa M, Michel F. Rules for RNA recognition of GNRA tetraloops deduced by in vitro selection: comparison with in vivo evolution. of special interest EMBO J. 16:1997;3289-3302 Receptors to GUGA and GAAA tetraloops were identified using an in vitro selection procedure. In addition to previously observed sequences, a number of new high affinity receptors were found that suggest a role for the variable position in the specificity of recognition.
14. Abramovitz DL, Pyle AM. Remarkable morphological variability of a common RNA folding motif: the GNRA tetraloop-receptor interaction. of outstanding interest J Mol Biol. 266:1997;493-506 The conformational features of the GNRA tetraloop required for interaction with its cognate receptor are examined. Sequences with a discontinuous backbone, various insertions and/or deletions or an expanded loop are tolerated, indicating that the 'tetraloop' - receptor type interaction can be supported by a range of structures that incorporate the key nucleotides.
15. Pley HW, Flaherty KM, McKay DB. Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix. Nature. 372:1994;111-113.
16. Butcher SE, Dieckmann T, Feigon J. Solution structure of a GAAA tetraloop receptor RNA. of outstanding interest EMBO J. 16:1997;7490-7499 The structure of a 23 nucleotide stem - loop RNA containing the conserved residues of the GAAA tetraloop receptor is examined using NMR spectroscopy. The central adenosines were found to be in a base-zipper motif, quite different from the adenosine platform observed in the crystal structure of the P4-P6 domain [3]. A model for the docking of the tetraloop and the subsequent conformational rearrangement of the receptor is proposed.
17. Puglisi EV, Green R, Noller HF, Puglisi JD. Structure of a conserved RNA component of the peptidyl transferase centre. of special interest Nat Struct Biol. 4:1997;775-778 This paper presents the solution structure of a universally conserved hairpin loop (the P loop) from 23S ribosomal RNA. This loop is required for tRNA binding in the P site. The loop is closed by a noncanonical G·C pair that causes a local reversal of backbone orientation and exposes the loop guanines for RNA recognition.
18. Stallings SC, Moore PB. The structure of an essential splicing element: stem loop IIa from yeast U2 snRNA. Structure. 5:1997;1173-1185.
19. Kolk MH, Heus HA, Hilbers CW. The structure of the isolated, central hairpin of the HDV antigenomic ribozyme: novel structural features and similarity of the loop in the ribozyme and free in solution. of special interest EMBO J. 16:1997;3685-3692 The NMR structure of a hairpin loop from the hepatitis delta virus antigenomic ribozyme contains a 'reversed U-turn' motif and a new non-Watson - Crick U·C base pair. The novel twist on the U-turn motif exposes bases on the 5′ side of the loop that are thought to be important in the tertiary structure of the larger RNA.
20. Klinck R, Sprules T, Gehring K. Structural characterization of three RNA hexanucleotide loops from the internal ribosome entry site of polioviruses. Nucleic Acids Res. 25:1997;2129-2137.
21. Quigley GJ, Rich A. Structural domains of transfer RNA molecules. Science. 194:1976;796-806.
22. Biswas R, Wahl MC, Ban C, Sundaralingam M. Crystal structure of an alternating octamer r(GUAUGUA)dC with adjacent G.U wobble pairs. J Mol Biol. 267:1997;1149-1156.
23. 2 hindered crystallization) but the ion was not ordered in either structure, in contrast to an ion in a similar site in the P4-P6 structure [3].
24. Gautheret D, Konings D, Gutell RR. G.U base pairing motifs in ribosomal RNA. RNA. 1:1995;807-814.
25. Heus HA, Wijmenga SS, Hoppe H, Hilbers CW. The detailed structure of tandem G.A mismatched base-pair motifs in RNA duplexes is context dependent. of special interest J Mol Biol. 271:1997;147-158 The newest installments in the continuing saga of the tandem G·A mismatch [25,26]. With flanking U·A base pairs, the guanines adopt an S conformation, causing a local distortion in the backbone and an alteration in the hydrogen bonding within the mismatch.
26. 2 by two-dimensional NMR and the iterative relaxation matrix approach. Biochemistry. 36:1997;4449-4460.
27. 2 in solution from NMR and restrained molecular dynamics. Biochemistry. 32:1993;12612-12623.
28. Correll CC, Freeborn B, Moore PB, Steitz TA. Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain. of outstanding interest Cell. 91:1997;705-712 The novel structural features of a dodecamer model of the loop E region of 5S rRNA that may determine recognition and interaction with ribosomal protein L25 are presented. These include cross-strand stacking motifs that dramatically alter groove widths and new noncanonical base pairs. The structure of a 62 nucleotide fragment (fragment I), the second largest solved to date, is also presented but at much lower resolution.
29. of outstanding interest Dallas A, Moore PB. The loop E-loop D region of Escherichia coli 5S rRNA: the solution structure reveals an unusual loop that may be important for binding ribosomal proteins. of special interest Structure. 5:1997;1639-1653 The solution structure of a 42 nucleotide fragment of 5S RNA is described. The structural motifs and major groove narrowing of the loop E crystal structure [28] are also observed in solution (the loop E heavy atoms superimpose with a rmsd of 1.3 Å).
30. Chang KY, Tinoco I Jr. The structure of an RNA 'kissing' hairpin complex of the HIV TAR hairpin loop and its complement. of special interest J Mol Biol. 269:1997;52-66 Two hairpin loops are shown to interact through base pairing of six nucleotides in each loop in order to form a structure with three co-axially stacked helices. The central helix of the loop nucleotides has a very different conformation from A-form helical RNA and is likely to be critical for RNA - protein recognition.
31. Allain FHT, Howe PWA, Neuhaus D, Varani G. Structural basis of the RNA-binding specificity of human U1A protein. of special interest EMBO J. 16:1997;5764-5772 This paper addresses the question of binding specificity by comparing the structure of the U1A protein complexed with two different RNAs, the polyadenylation inhibition element and stem - loop II of U1 snRNA.
32. Brodsky AS, Williamson JR. Solution structure of the HIV-2 TAR-argininamide complex. J Mol Biol. 267:1997;624-639.
33. Valegård K, Murray JB, Stonehouse NJ, Worm S, Stockley PG, Liljas L. The three-dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence-specific protein-RNA interactions. J Mol Biol. 270:1997;724-738.
34. Dieckmann T, Butcher SE, Sassanfar M, Szostak JW, Feigon J. Mutant ATP-binding RNA aptamers reveal the structural basis for ligand binding. J Mol Biol. 273:1997;467-478.
35. Patel DJ, Suri AK, Jiang F, Jiang L, Fan P, Kumar RA, Nonin S. Structure, recognition and adaptive binding in RNA aptamer complexes. of special interest J Mol Biol. 272:1997;645-664 A thorough review of RNA aptamer structure up to mid 1997, including a useful discussion of the general themes observed in a variety of RNA - ligand complexes.
36. Zimmermann GR, Jenison RD, Wick CL, Simorre JP, Pardi A. Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA. of outstanding interest Nat Struct Biol. 4:1997;644-649 This paper describes the structure of a selective, high affinity theophylline-binding RNA complexed with theophylline. The theophylline-binding pocket is formed by several different overlapping motifs including a base-triple sandwich, a base zipper, an adenosine platform and a novel 1-3-2 stack. The structure, which involves extensive stabilizing stacking interactions, is absolutely dependent on the bound theophylline.
37. Jenison RD, Gill SC, Pardi A, Polisky B. High-resolution molecular discrimination by RNA. Science. 263:1994;1425-1429.
38. Pan J, Thirumalai D, Woodson SA. Folding of RNA involves parallel pathways. of outstanding interest J Mol Biol. 273:1997;7-13 A small fraction of the Tetrahymena self-splicing RNA folds very rapidly. This result is interpreted in terms of a kinetic partitioning mechanism whereby some molecules fold to the native state by direct paths while the remainder are trapped as misfolded structures. As also seen by Pan and Sosnick [39], urea increases the rate of folding.
39. Pan T, Sosnick TR. Intermediates and kinetic traps in the folding of a large ribozyme revealed by circular dichroism and UV absorbance spectroscopies and catalytic activity. of outstanding interest Nat Struct Biol. 4:1997;931-938 This is a thorough study of the folding energetics of the B. subtilis RNase P ribozyme, in which circular dichroism detected a conformational transition that is silent in UV absorbance measurements. Folding can be accelerated up to 30-fold by the addition of urea, indicating that the disruption of misfolded structures, rather than the formation of tertiary structure, is rate limiting.
40. + on an equilibrium between alternative conformations of an RNA pseudoknot. of special interest J Mol Biol. 270:1997;451-463 The rate-limiting step in the conversion of one folded form of a nested pseudo-knot to another is initiated by the binding of a single magnesium ion, although several ions are involved in the overall reaction.
41. 2+ ions in the tertiary structure. Biochemistry. 36:1997;4718-4730.
42. Sclavi B, Woodson S, Sullivan M, Chance MR, Brenowitz M. Time-resolved resolved synchrotron X-ray 'footprinting', a new approach to the study of nucleic acid structure and function: application to protein-DNA interactions and RNA folding. of special interest J Mol Biol. 266:1997;144-159 A new method for following the kinetics of tertiary structure formation at the nucleotide level is described, and promises to resolve kinetic steps on a 10 ms time scale.
43. Downs WD, Cech TR. Kinetic pathway for folding of the Tetrahymena ribozyme revealed by three UV-inducible crosslinks. RNA. 2:1996;718-732.
44. Zarrinkar PP, Williamson JR. Kinetic intermediates in RNA folding. Science. 265:1994;918-924.
45. Cate JH, Hanna RL, Doudna JA. A magnesium ion core at the heart of a ribozyme domain. of outstanding interest Nat Struct Biol. 4:1997;553-558 This crystallographic study of magnesium and manganese ion coordination in the P4-P6 domain reveals an intriguing cluster of five ions associated with a region containing unusual backbone conformations. Ions that are directly coordinated to as many as three phosphates are observed.
46. Kieft JS, Tinoco I Jr. Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt (III) hexamine. Structure. 5:1997;713-721.
47. Bukhman YV, Draper DE. Affinities and selectivities of divalent cation binding sites within an RNA tertiary structure. of outstanding interest J Mol Biol. 274:1997;1020-1031 This study uses melting curves to measure the stoichiometry and affinity of divalent ions for an RNA tertiary structure. The survey of alkaline earth ions provides a novel probe of the ion environment. Two sites are observed; affinity at one site is inversely proportional to ion radius, whereas the other discriminates against intermediate size ions (calcium and strontium).
48. Gluick TC, Wills NM, Gesteland RF, Draper DE. Folding of an mRNA pseudoknot required for stop codon readthrough: effects of mono- and divalent ions on stability. of special interest Biochemistry. 36:1997;16173-16186 The authors argue that magnesium ions stabilize an mRNA pseudo-knot because of enhanced non-specific interactions in a region of high charge density, rather than site-specific binding to the pseudo-knot.
49. Anderson CF, Record MT Jr. Salt-nucleic acid interactions. Annu Rev Phys Chem. 46:1995;657-700.