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PDBsum entry 1fc8
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RNA/DNA chimera PDB id
1fc8

 

 

 

 

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Contents
DNA/RNA
PDB id:
1fc8
Name: RNA/DNA chimera
Title: Nmr solution structure of a chimeric oligonucleotide hairpin r(ggac) d(ttcg)2'f-a(gtcc)
Structure: 5'-r( Gp Gp Ap Cp)d( Tp Tp Cp Gp (Gfl)p (Taf)p (Cfl) p (Cfl))-3'. Chain: a. Synonym: RNA/2'f-ana hairpin. Engineered: yes
Source: Synthetic: yes. Other_details: solid phase synthesis. Phosphoramidite chemistry
NMR struc: 5 models
Authors: J.-F.Trempe,K.Gehring
Key ref: J.F.Trempe et al. (2001). NMR solution structure of an oligonucleotide hairpin with a 2'F-ANA/RNA stem: implications for RNase H specificity toward DNA/RNA hybrid duplexes. J Am Chem Soc, 123, 4896-4903. PubMed id: 11457316 DOI: 10.1021/ja003859p
Date:
18-Jul-00     Release date:   30-May-01    
 Headers
 References

DNA/RNA chain
  G-G-A-C-T-T-C-G-GFL-TAF-CFL-CFL 12 bases

 

 
DOI no: 10.1021/ja003859p J Am Chem Soc 123:4896-4903 (2001)
PubMed id: 11457316  
 
 
NMR solution structure of an oligonucleotide hairpin with a 2'F-ANA/RNA stem: implications for RNase H specificity toward DNA/RNA hybrid duplexes.
J.F.Trempe, C.J.Wilds, A.Y.Denisov, R.T.Pon, M.J.Damha, K.Gehring.
 
  ABSTRACT  
 
The first structure of a 2'-deoxy-2'-fluoro-D-arabinose nucleic acid (2'F-ANA)/RNA duplex is presented. We report the structural characterization by NMR spectroscopy of a small hybrid hairpin, r(GGAC)d(TTCG)2'F-a(GTCC), containing a 2'F-ANA/RNA stem and a four-residue DNA loop. Complete (1)H, (13)C, (19)F, and (31)P resonance assignments, scalar coupling constants, and NOE constraints were obtained from homonuclear and heteronuclear 2D spectra. In the chimeric duplex, the RNA strand adopts a classic A-form structure having C3' endo sugar puckers. The 2'F-ANA strand is neither A-form nor B-form and contains O4' endo sugar puckers. This contrasts strongly with the dynamic sugar conformations previously observed in the DNA strands of DNA/RNA hybrid duplexes. Structural parameters for the duplex, such as minor groove width, x-displacement, and inclination, were intermediate between those of A-form and B-form duplexes and similar to those of DNA/RNA duplexes. These results rationalize the enhanced stability of 2'F-ANA/RNA duplexes and their ability to elicit RNase H activity. The results are relevant for the design of new antisense drugs based on sugar-modified nucleic acids.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20413581 G.F.Deleavey, J.K.Watts, T.Alain, F.Robert, A.Kalota, V.Aishwarya, J.Pelletier, A.M.Gewirtz, N.Sonenberg, and M.J.Damha (2010).
Synergistic effects between analogs of DNA and RNA improve the potency of siRNA-mediated gene silencing.
  Nucleic Acids Res, 38, 4547-4557.  
20071751 J.K.Watts, N.Martín-Pintado, I.Gómez-Pinto, J.Schwartzentruber, G.Portella, M.Orozco, C.González, and M.J.Damha (2010).
Differential stability of 2'F-ANA*RNA and ANA*RNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility.
  Nucleic Acids Res, 38, 2498-2511.
PDB codes: 2kp3 2kp4
19899814 A.A.Williams, A.Darwanto, J.A.Theruvathu, A.Burdzy, J.W.Neidigh, and L.C.Sowers (2009).
Impact of sugar pucker on base pair and mispair stability.
  Biochemistry, 48, 11994-12004.  
19333476 P.S.Pallan, T.P.Prakash, F.Li, R.L.Eoff, M.Manoharan, and M.Egli (2009).
A conformational transition in the structure of a 2'-thiomethyl-modified DNA visualized at high resolution.
  Chem Commun (Camb), (), 2017-2019.
PDB codes: 3ey1 3ey2 3ey3
17636049 C.G.Peng, and M.J.Damha (2007).
G-quadruplex induced stabilization by 2'-deoxy-2'-fluoro-D-arabinonucleic acids (2'F-ANA).
  Nucleic Acids Res, 35, 4977-4988.  
17284457 J.K.Watts, N.Choubdar, K.Sadalapure, F.Robert, A.S.Wahba, J.Pelletier, B.M.Pinto, and M.J.Damha (2007).
2'-fluoro-4'-thioarabino-modified oligonucleotides: conformational switches linked to siRNA activity.
  Nucleic Acids Res, 35, 1441-1451.  
16421272 A.Kalota, L.Karabon, C.R.Swider, E.Viazovkina, M.Elzagheid, M.J.Damha, and A.M.Gewirtz (2006).
2'-deoxy-2'-fluoro-beta-D-arabinonucleic acid (2'F-ANA) modified oligonucleotides (ON) effect highly efficient, and persistent, gene silencing.
  Nucleic Acids Res, 34, 451-461.  
16622887 C.Kreutz, H.Kählig, R.Konrat, and R.Micura (2006).
A general approach for the identification of site-specific RNA binders by 19F NMR spectroscopy: proof of concept.
  Angew Chem Int Ed Engl, 45, 3450-3453.  
16566588 F.Li, S.Sarkhel, C.J.Wilds, Z.Wawrzak, T.P.Prakash, M.Manoharan, and M.Egli (2006).
2'-Fluoroarabino- and arabinonucleic acid show different conformations, resulting in deviating RNA affinities and processing of their heteroduplexes with RNA by RNase H.
  Biochemistry, 45, 4141-4152.
PDB codes: 2fih 2fii 2fij 2fil
17145930 N.Ferrari, D.Bergeron, A.L.Tedeschi, M.M.Mangos, L.Paquet, P.M.Renzi, and M.J.Damha (2006).
Characterization of antisense oligonucleotides comprising 2'-deoxy-2'-fluoro-beta-D-arabinonucleic acid (FANA): specificity, potency, and duration of activity.
  Ann N Y Acad Sci, 1082, 91.  
16440307 W.H.Pan, and G.A.Clawson (2006).
Antisense applications for biological control.
  J Cell Biochem, 98, 14-35.  
12736318 J.I.Gyi, D.Gao, G.L.Conn, J.O.Trent, T.Brown, and A.N.Lane (2003).
The solution structure of a DNA*RNA duplex containing 5-propynyl U and C; comparison with 5-Me modifications.
  Nucleic Acids Res, 31, 2683-2693.
PDB code: 1oo7
14530434 J.T.Nielsen, P.C.Stein, and M.Petersen (2003).
NMR structure of an alpha-L-LNA:RNA hybrid: structural implications for RNase H recognition.
  Nucleic Acids Res, 31, 5858-5867.
PDB code: 1okf
11876654 C.N.Lok, E.Viazovkina, K.L.Min, E.Nagy, C.J.Wilds, M.J.Damha, and M.A.Parniak (2002).
Potent gene-specific inhibitory properties of mixed-backbone antisense oligonucleotides comprised of 2'-deoxy-2'-fluoro-D-arabinose and 2'-deoxyribose nucleotides.
  Biochemistry, 41, 3457-3467.  
11691916 A.Y.Denisov, A.M.Noronha, C.J.Wilds, J.F.Trempe, R.T.Pon, K.Gehring, and M.J.Damha (2001).
Solution structure of an arabinonucleic acid (ANA)/RNA duplex in a chimeric hairpin: comparison with 2'-fluoro-ANA/RNA and DNA/RNA hybrids.
  Nucleic Acids Res, 29, 4284-4293.
PDB codes: 1ho6 1hoq
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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