PDBsum entry 247d

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Title: Crystal structures of an a-form duplex with single- adenosine bulges and a conformational basis for site specific RNA self-cleavage
Structure: DNA/RNA (5'-r( Gp Cp Gp )-D( Ap Tp Ap Tp Ap )- R( Cp Gp C)-3'). Chain: a. Engineered: yes
Source: Synthetic: yes
Biol. unit: Dimer (from PQS)
2.80Å     R-factor:   0.187    
Authors: S.Portmann,S.Grimm,C.Workman,N.Usman,M.Egli
Key ref: S.Portmann et al. (1996). Crystal structures of an A-form duplex with single-adenosine bulges and a conformational basis for site-specific RNA self-cleavage. Chem Biol, 3, 173-184. PubMed id: 8807843
02-Feb-96     Release date:   08-Mar-96    


Chem Biol 3:173-184 (1996)
PubMed id: 8807843  
Crystal structures of an A-form duplex with single-adenosine bulges and a conformational basis for site-specific RNA self-cleavage.
S.Portmann, S.Grimm, C.Workman, N.Usman, M.Egli.
BACKGROUND: Bulged nucleotides are common secondary structural motifs in RNA molecules and are often involved in RNA-RNA and RNA-protein interactions. RNA is selectively cleaved at bulge sites (when compared to other sites within stems) in the presence of divalent metal cations. The effects of bulge nucleotides on duplex stability and topology have been extensively investigated, but no detailed X-ray structures of bulge-containing RNA fragments have been available. RESULTS: We have crystallized a self-complementary RNA-DNA chimeric 11-nucleotide sequence containing single-adenosine bulges under two different conditions, giving two distinct crystal forms. In both lattices the adenosines are looped out, leaving the stacking interactions in the duplex virtually unaffected. The bulges cause the duplex to kink in both cases. In one of the structures, the conformation of the bulged nucleotide places its modeled 2'-oxygen in line with the adjacent phosphate on the 3' side, where it is poised for nucleophilic attack. CONCLUSIONS: Single adenosine bulges cause a marked opening of the normally narrow RNA major groove in both crystal structures, rendering the bases more accessible to interacting molecules compared with an intact stem. The geometries around the looped-out adenosines are different in the two crystal forms, indicating that bulges can confer considerable local plasticity on the usually rigid RNA double helix. The results provide a conformational basis for the preferential, metal-assisted self-cleavage of RNA at bulged sites.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19946018 C.A.Minetti, D.P.Remeta, R.Dickstein, and K.J.Breslauer (2010).
Energetic signatures of single base bulges: thermodynamic consequences and biological implications.
  Nucleic Acids Res, 38, 97.  
19225675 H.S.Jeong, S.Kang, J.Y.Lee, and B.H.Kim (2009).
Probing specific RNA bulge conformations by modified fluorescent nucleosides.
  Org Biomol Chem, 7, 921-925.  
16399833 A.Barthel, and M.Zacharias (2006).
Conformational transitions in RNA single uridine and adenosine bulge structures: a molecular dynamics free energy simulation study.
  Biophys J, 90, 2450-2462.  
16492787 B.Pan, K.Shi, and M.Sundaralingam (2006).
Base-tetrad swapping results in dimerization of RNA quadruplexes: implications for formation of the i-motif RNA octaplex.
  Proc Natl Acad Sci U S A, 103, 3130-3134.
PDB code: 2awe
15731340 I.L.Kuznetsova, M.A.Zenkova, H.J.Gross, and V.V.Vlassov (2005).
Enhanced RNA cleavage within bulge-loops by an artificial ribonuclease.
  Nucleic Acids Res, 33, 1201-1212.  
15756640 J.Sandbrink, D.Ossipov, H.Aström, and R.Strömberg (2005).
Investigation of potential RNA bulge stabilizing elements.
  J Mol Recognit, 18, 318-326.  
14613111 A.Madder, R.Ehrl, and R.Strömberg (2003).
Stabilisation of RNA bulges by oligonucleotide complements containing an adenosine analogue.
  Chembiochem, 4, 1194-1200.  
12426583 M.I.Newby, and N.L.Greenbaum (2002).
Sculpting of the spliceosomal branch site recognition motif by a conserved pseudouridine.
  Nat Struct Biol, 9, 958-965.
PDB codes: 1lmv 1lpw
11350032 J.A.Berglund, M.Rosbash, and S.C.Schultz (2001).
Crystal structure of a model branchpoint-U2 snRNA duplex containing bulged adenosines.
  RNA, 7, 682-691.
PDB code: 1i9x
11828431 K.Michaelis, and M.Kalesse (2001).
Selective cleavage of unpaired uridines with a tyrosine-cyclen conjugate.
  Chembiochem, 2, 79-83.  
11423420 M.Feig, M.Zacharias, and B.M.Pettitt (2001).
Conformations of an adenine bulge in a DNA octamer and its influence on DNA structure from molecular dynamics simulations.
  Biophys J, 81, 352-370.  
11424937 M.I.Newby, and N.L.Greenbaum (2001).
A conserved pseudouridine modification in eukaryotic U2 snRNA induces a change in branch-site architecture.
  RNA, 7, 833-845.  
11333021 V.Tereshko, S.T.Wallace, N.Usman, F.E.Wincott, and M.Egli (2001).
X-ray crystallographic observation of "in-line" and "adjacent" conformations in a bulged self-cleaving RNA/DNA hybrid.
  RNA, 7, 405-420.
PDB codes: 1i2x 1i2y
10968986 J.Sarzynska, T.Kulinski, and L.Nilsson (2000).
Conformational dynamics of a 5S rRNA hairpin domain containing loop D and a single nucleotide bulge.
  Biophys J, 79, 1213-1227.  
10777750 M.Zacharias, and H.Sklenar (2000).
Conformational deformability of RNA: a harmonic mode analysis.
  Biophys J, 78, 2528-2542.  
10999608 Y.Xiong, and M.Sundaralingam (2000).
Two crystal forms of helix II of Xenopus laevis 5S rRNA with a cytosine bulge.
  RNA, 6, 1316-1324.
PDB codes: 1dqf 1dqh
9649624 I.Zagórowska, S.Kuusela, and H.Lönnberg (1998).
Metal ion-dependent hydrolysis of RNA phosphodiester bonds within hairpin loops. A comparative kinetic study on chimeric ribo/2'-O-methylribo oligonucleotides.
  Nucleic Acids Res, 26, 3392-3396.  
9493396 S.Neidle, and C.M.Nunn (1998).
Crystal structures of nucleic acids and their drug complexes.
  Nat Prod Rep, 15, 1.  
9724510 U.Mueller, G.Maier, A.Mochi Onori, L.Cellai, H.Heumann, and U.Heinemann (1998).
Crystal structure of an eight-base pair duplex containing the 3'-DNA-RNA-5' junction formed during initiation of minus-strand synthesis of HIV replication.
  Biochemistry, 37, 12005-12011.
PDB code: 398d
9769094 V.T.Chu, Q.Liu, M.Podar, P.S.Perlman, and A.M.Pyle (1998).
More than one way to splice an RNA: branching without a bulge and splicing without branching in group II introns.
  RNA, 4, 1186-1202.  
9692952 V.Tereshko, S.Portmann, E.C.Tay, P.Martin, F.Natt, K.H.Altmann, and M.Egli (1998).
Correlating structure and stability of DNA duplexes with incorporated 2'-O-modified RNA analogues.
  Biochemistry, 37, 10626-10634.
PDB codes: 410d 411d 412d
9622486 X.Shui, L.McFail-Isom, G.G.Hu, and L.D.Williams (1998).
The B-DNA dodecamer at high resolution reveals a spine of water on sodium.
  Biochemistry, 37, 8341-8355.
PDB code: 355d
  9111366 C.C.Query, P.S.McCaw, and P.A.Sharp (1997).
A minimal spliceosomal complex A recognizes the branch site and polypyrimidine tract.
  Mol Cell Biol, 17, 2944-2953.  
9204271 J.A.Doudna, and J.H.Cate (1997).
RNA structure: crystal clear?
  Curr Opin Struct Biol, 7, 310-316.  
9204273 L.Jaeger (1997).
The New World of ribozymes.
  Curr Opin Struct Biol, 7, 324-335.  
8995285 M.A.O'Connell, A.Gerber, and W.Keller (1997).
Purification of human double-stranded RNA-specific editase 1 (hRED1) involved in editing of brain glutamate receptor B pre-mRNA.
  J Biol Chem, 272, 473-478.  
9414214 M.Zacharias, and H.Sklenar (1997).
Analysis of the stability of looped-out and stacked-in conformations of an adenine bulge in DNA using a continuum model for solvent and ions.
  Biophys J, 73, 2990-3003.  
8987994 D.Hüsken, G.Goodall, M.J.Blommers, W.Jahnke, J.Hall, R.Häner, and H.E.Moser (1996).
Creating RNA bulges: cleavage of RNA in RNA/DNA duplexes by metal ion catalysis.
  Biochemistry, 35, 16591-16600.  
8901542 I.Berger, M.Egli, and A.Rich (1996).
Inter-strand C-H...O hydrogen bonds stabilizing four-stranded intercalated molecules: stereoelectronic effects of O4' in cytosine-rich DNA.
  Proc Natl Acad Sci U S A, 93, 12116-12121.  
8948630 J.B.Thomson, S.T.Sigurdsson, A.Zeuch, and F.Eckstein (1996).
In vitro selection of hammerhead ribozymes containing a bulged nucleotide in stem II.
  Nucleic Acids Res, 24, 4401-4406.  
8679609 M.Egli, S.Portmann, and N.Usman (1996).
RNA hydration: a detailed look.
  Biochemistry, 35, 8489-8494.
PDB code: 259d
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