PDBsum entry 2dqp

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DNA-RNA hybrid PDB id
CMY ×2
Waters ×46
PDB id:
Name: DNA-RNA hybrid
Title: Structural analyses of dna:dna and rna:dna duplexes containing 5-(n-aminohexyl)carbamoyl modified uridines
Structure: DNA (5'-d( Dcp (Omu)p Dcp Dtp (Omu) p Dcp Dtp Dtp Dc)-3'). Chain: a. Engineered: yes. RNA (5'-r( Gp Ap Ap Gp Ap Ap Gp Ap G)-3'). Chain: b. Engineered: yes
Source: Synthetic: yes. Other_details: synthetic constructs. Other_details: synthetic constructs
2.10Å     R-factor:   0.222     R-free:   0.251
Authors: E.C.M.Juan,J.Kondo,T.Ito,Y.Ueno,A.Matsuda,A.Takenaka
Key ref: E.C.Juan et al. (2007). Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules. Nucleic Acids Res, 35, 1969-1977. PubMed id: 17341465
29-May-06     Release date:   17-Apr-07    


Nucleic Acids Res 35:1969-1977 (2007)
PubMed id: 17341465  
Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules.
E.C.Juan, J.Kondo, T.Kurihara, T.Ito, Y.Ueno, A.Matsuda, A.Takénaka.
Oligonucleotides containing 5-(N-aminohexyl)carbamoyl-modified uracils have promising features for applications as antigene and antisense therapies. Relative to unmodified DNA, oligonucleotides containing 5-(N-aminohexyl)carbamoyl-2'-deoxyuridine ((N)U) or 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine ((N)U(m)), respectively exhibit increased binding affinity for DNA and RNA, and enhanced nuclease resistance. To understand the structural implications of (N)U and (N)U(m) substitutions, we have determined the X-ray crystal structures of DNA:DNA duplexes containing either (N)U or (N)U(m) and of DNA:RNA hybrid duplexes containing (N)U(m). The aminohexyl chains are fixed in the major groove through hydrogen bonds between the carbamoyl amino groups and the uracil O4 atoms. The terminal ammonium cations on these chains could interact with the phosphate oxygen anions of the residues in the target strands. These interactions partly account for the increased target binding affinity and nuclease resistance. In contrast to (N)U, (N)U(m) decreases DNA binding affinity. This could be explained by the drastic changes in sugar puckering and in the minor groove widths and hydration structures seen in the (N)U(m) containing DNA:DNA duplex structure. The conformation of (N)U(m), however, is compatible with the preferred conformation in DNA:RNA hybrid duplexes. Furthermore, the ability of (N)U(m) to render the duplexes with altered minor grooves may increase nuclease resistance and elicit RNase H activity.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21297374 A.Matsuda (2011).
Development of Highly Nuclease-resistant Chemically-modified Oligonucleotides.
  Yakugaku Zasshi, 131, 285-298.  
18197661 U.D.Priyakumar, and A.D.Mackerell (2008).
Atomic detail investigation of the structure and dynamics of DNA.RNA hybrids: a molecular dynamics study.
  J Phys Chem B, 112, 1515-1524.  
18802967 Y.Sato, H.Hayashi, M.Okazaki, M.Aso, S.Karasawa, S.Ueki, H.Suemune, and N.Koga (2008).
Water-proton relaxivities of DNA oligomers carrying TEMPO radicals.
  Magn Reson Chem, 46, 1055-1058.  
17288535 M.Egli, and P.S.Pallan (2007).
Insights from crystallographic studies into the structural and pairing properties of nucleic acid analogs and chemically modified DNA and RNA oligonucleotides.
  Annu Rev Biophys Biomol Struct, 36, 281-305.  
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