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PDBsum entry 1ekd
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RNA PDB id
1ekd

 

 

 

 

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Contents
DNA/RNA
PDB id:
1ekd
Name: RNA
Title: Nmr and molecular modeling reveal that different hydrogen bonding patterns are possible for gu pairs: one hydrogen bond for each gu pair in r(ggcgugcc)2 and two for each gu pair in r(gagugcuc)2
Structure: RNA (5'-r( Gp Gp Cp Gp Up Gp Cp C)-3'). Chain: a, b. Engineered: yes
Source: Synthetic: yes
NMR struc: 1 models
Authors: X.Chen,J.A.Mcdowell,R.Kierzek,T.R.Krugh,D.H.Turner
Key ref:
X.Chen et al. (2000). Nuclear magnetic resonance spectroscopy and molecular modeling reveal that different hydrogen bonding patterns are possible for G.U pairs: one hydrogen bond for each G.U pair in r(GGCGUGCC)(2) and two for each G.U pair in r(GAGUGCUC)(2). Biochemistry, 39, 8970-8982. PubMed id: 10913310 DOI: 10.1021/bi992938e
Date:
07-Mar-00     Release date:   13-Nov-00    
 Headers
 References

DNA/RNA chains
  G-G-C-G-U-G-C-C 8 bases
  G-G-C-G-U-G-C-C 8 bases

 

 
DOI no: 10.1021/bi992938e Biochemistry 39:8970-8982 (2000)
PubMed id: 10913310  
 
 
Nuclear magnetic resonance spectroscopy and molecular modeling reveal that different hydrogen bonding patterns are possible for G.U pairs: one hydrogen bond for each G.U pair in r(GGCGUGCC)(2) and two for each G.U pair in r(GAGUGCUC)(2).
X.Chen, J.A.McDowell, R.Kierzek, T.R.Krugh, D.H.Turner.
 
  ABSTRACT  
 
G.U pairs occur frequently and have many important biological functions. The stability of symmetric tandem G.U motifs depends both on the adjacent Watson-Crick base pairs, e.g., 5'G > 5'C, and the sequence of the G.U pairs, i.e., 5'-UG-3' > 5'-GU-3', where an underline represents a nucleotide in a G.U pair [Wu, M., McDowell, J. A., and Turner, D. H. (1995) Biochemistry 34, 3204-3211]. In particular, at 37 degrees C, the motif 5'-CGUG-3' is less stable by approximately 3 kcal/mol compared with other symmetric tandem G.U motifs with G-C as adjacent pairs: 5'-GGUC-3', 5'-GUGC-3', and 5'-CUGG-3'. The solution structures of r(GAGUGCUC)(2) and r(GGCGUGCC)(2) duplexes have been determined by NMR and restrained simulated annealing. The global geometry of both duplexes is close to A-form, with some distortions localized in the tandem G.U pair region. The striking discovery is that in r(GGCGUGCC)(2) each G.U pair apparently has only one hydrogen bond instead of the two expected for a canonical wobble pair. In the one-hydrogen-bond model, the distance between GO6 and UH3 is too far to form a hydrogen bond. In addition, the temperature dependence of the imino proton resonances is also consistent with the different number of hydrogen bonds in the G.U pair. To test the NMR models, U or G in various G.U pairs were individually replaced by N3-methyluridine or isoguanosine, respectively, thus eliminating the possibility of hydrogen bonding between GO6 and UH3. The results of thermal melting studies on duplexes with these substitutions support the NMR models.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20026131 U.D.Priyakumar, and A.D.MacKerell (2010).
Role of the adenine ligand on the stabilization of the secondary and tertiary interactions in the adenine riboswitch.
  J Mol Biol, 396, 1422-1438.  
19485416 G.Chen, S.D.Kennedy, and D.H.Turner (2009).
A CA(+) pair adjacent to a sheared GA or AA pair stabilizes size-symmetric RNA internal loops.
  Biochemistry, 48, 5738-5752.  
18299285 X.Abad, M.Vera, S.P.Jung, E.Oswald, I.Romero, V.Amin, P.Fortes, and S.I.Gunderson (2008).
Requirements for gene silencing mediated by U1 snRNA binding to a target sequence.
  Nucleic Acids Res, 36, 2338-2352.  
18461991 Y.Pan, and R.Nussinov (2008).
p53-Induced DNA bending: the interplay between p53-DNA and p53-p53 interactions.
  J Phys Chem B, 112, 6716-6724.  
17526525 D.Xu, T.Landon, N.L.Greenbaum, and M.O.Fenley (2007).
The electrostatic characteristics of G.U wobble base pairs.
  Nucleic Acids Res, 35, 3836-3847.  
17430967 F.Yuan, L.Griffin, L.Phelps, V.Buschmann, K.Weston, and N.L.Greenbaum (2007).
Use of a novel Förster resonance energy transfer method to identify locations of site-bound metal ions in the U2-U6 snRNA complex.
  Nucleic Acids Res, 35, 2833-2845.  
17497831 Y.Wu, D.Bhattacharyya, C.L.King, I.Baskerville-Abraham, S.H.Huh, G.Boysen, J.A.Swenberg, B.Temple, S.L.Campbell, and S.G.Chaney (2007).
Solution structures of a DNA dodecamer duplex with and without a cisplatin 1,2-d(GG) intrastrand cross-link: comparison with the same DNA duplex containing an oxaliplatin 1,2-d(GG) intrastrand cross-link.
  Biochemistry, 46, 6477-6487.
PDB codes: 2npw 2nq0 2nq1 2nq4
16633566 D.E.Volk, V.Thiviyanathan, A.Somasunderam, and D.G.Gorenstein (2006).
Ab initio base-pairing energies of uracil and 5-hydroxyuracil with standard DNA bases at the BSSE-free DFT and MP2 theory levels.
  Org Biomol Chem, 4, 1741-1745.  
16510427 J.M.Carothers, J.H.Davis, J.J.Chou, and J.W.Szostak (2006).
Solution structure of an informationally complex high-affinity RNA aptamer to GTP.
  RNA, 12, 567-579.
PDB code: 2au4
16581850 S.B.Jang, L.W.Hung, M.S.Jeong, E.L.Holbrook, X.Chen, D.H.Turner, and S.R.Holbrook (2006).
The crystal structure at 1.5 angstroms resolution of an RNA octamer duplex containing tandem G.U basepairs.
  Biophys J, 90, 4530-4537.
PDB code: 2g3s
16307143 E.Rozners, R.Smicius, and C.Uchiyama (2005).
Expanding functionality of RNA: synthesis and properties of RNA containing imidazole modified tandem G-U wobble base pairs.
  Chem Commun (Camb), (), 5778-5780.  
15840817 X.Roca, R.Sachidanandam, and A.R.Krainer (2005).
Determinants of the inherent strength of human 5' splice sites.
  RNA, 11, 683-698.  
15558052 F.V.Murphy, V.Ramakrishnan, A.Malkiewicz, and P.F.Agris (2004).
The role of modifications in codon discrimination by tRNA(Lys)UUU.
  Nat Struct Mol Biol, 11, 1186-1191.
PDB codes: 1xmo 1xmq
15100438 I.Carmel, S.Tal, I.Vig, and G.Ast (2004).
Comparative analysis detects dependencies among the 5' splice-site positions.
  RNA, 10, 828-840.  
15007109 N.Carrasco, Y.Buzin, E.Tyson, E.Halpert, and Z.Huang (2004).
Selenium derivatization and crystallization of DNA and RNA oligonucleotides for X-ray crystallography using multiple anomalous dispersion.
  Nucleic Acids Res, 32, 1638-1646.  
12869711 J.M.Lanchy, J.D.Ivanovitch, and J.S.Lodmell (2003).
A structural linkage between the dimerization and encapsidation signals in HIV-2 leader RNA.
  RNA, 9, 1007-1018.  
14627829 M.Freund, C.Asang, S.Kammler, C.Konermann, J.Krummheuer, M.Hipp, I.Meyer, W.Gierling, S.Theiss, T.Preuss, D.Schindler, J.Kjems, and H.Schaal (2003).
A novel approach to describe a U1 snRNA binding site.
  Nucleic Acids Res, 31, 6963-6975.  
14654688 Y.Pan, and A.D.MacKerell (2003).
Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening.
  Nucleic Acids Res, 31, 7131-7140.  
12022892 D.M.John, and K.M.Weeks (2002).
Chemical interrogation of mismatches in DNA-DNA and DNA-RNA duplexes under nonstringent conditions by selective 2'-amine acylation.
  Biochemistry, 41, 6866-6874.  
12166647 S.Lima, J.Hildenbrand, A.Korostelev, S.Hattman, and H.Li (2002).
Crystal structure of an RNA helix recognized by a zinc-finger protein: an 18-bp duplex at 1.6 A resolution.
  RNA, 8, 924-932.
PDB code: 1kfo
11504865 J.Kawakami, H.Kamiya, K.Yasuda, H.Fujiki, H.Kasai, and N.Sugimoto (2001).
Thermodynamic stability of base pairs between 2-hydroxyadenine and incoming nucleotides as a determinant of nucleotide incorporation specificity during replication.
  Nucleic Acids Res, 29, 3289-3296.  
11371214 M.D.Disney, C.G.Haidaris, and D.H.Turner (2001).
Recognition elements for 5' exon substrate binding to the Candida albicans group I intron.
  Biochemistry, 40, 6507-6519.  
11170418 T.Lan, and L.W.McLaughlin (2001).
Minor groove functional groups are critical for the B-form conformation of duplex DNA.
  Biochemistry, 40, 968-976.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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