spacer
spacer

PDBsum entry 176d
Go to PDB code: 
dna_rna ligands links
Peptide nucleic acid/RNA PDB id
176d

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
DNA/RNA
Ligands
GPN-APN-APN-CPN-
TPN-CPN
PDB id:
176d
Name: Peptide nucleic acid/RNA
Title: Nmr solution structure of a peptide nucleic acid complexed with RNA
Structure: DNA (5'-d( Gpn Apn Apn Cpn Tpn Cpn)-3'). Chain: a. Engineered: yes. RNA (5'-r(p Gp Ap Gp Up Up C)-3'). Chain: b. Engineered: yes
Source: Synthetic: yes. Other_details: chemically synthesized. Other_details: chemically synthesized
NMR struc: 10 models
Authors: S.C.Brown,J.M.Veal
Key ref: S.C.Brown et al. (1994). NMR solution structure of a peptide nucleic acid complexed with RNA. Science, 265, 777-780. PubMed id: 7519361 DOI: 10.1126/science.7519361
Date:
17-May-94     Release date:   01-Nov-94    
 Headers
 References

DNA/RNA chain
  G-A-G-U-U-C 6 bases

 

 
DOI no: 10.1126/science.7519361 Science 265:777-780 (1994)
PubMed id: 7519361  
 
 
NMR solution structure of a peptide nucleic acid complexed with RNA.
S.C.Brown, S.A.Thomson, J.M.Veal, D.G.Davis.
 
  ABSTRACT  
 
Peptide nucleic acids (PNA) incorporating nucleic acid bases into an achiral polyamide backbone bind to DNA in a sequence-dependent manner. The structure of a PNA-ribonucleic acid (RNA) complex was determined with nuclear magnetic resonance methods. A hexameric PNA formed a 1:1 complex with a complementary RNA that is an antiparallel, right-handed double helix with Watson-Crick base pairing similar to the "A" form structure of RNA duplexes. The achiral PNA backbone assumed a distinct conformation upon binding that differed from previously proposed models and provides a basis for further structure-based design of antisense agents.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20386807 W.He, M.J.Crawford, S.Rapireddy, M.Madrid, R.R.Gil, D.H.Ly, and C.Achim (2010).
The structure of a gamma-modified peptide nucleic acid duplex.
  Mol Biosyst, 6, 1619-1629.
PDB code: 2kvj
17478520 A.Sen, and P.E.Nielsen (2007).
On the stability of peptide nucleic acid duplexes in the presence of organic solvents.
  Nucleic Acids Res, 35, 3367-3374.  
17071666 C.M.Topham, and J.C.Smith (2007).
Orientation preferences of backbone secondary amide functional groups in peptide nucleic acid complexes: quantum chemical calculations reveal an intrinsic preference of cationic D-amino acid-based chiral PNA analogues for the P-form.
  Biophys J, 92, 769-786.  
17266023 H.Xue-Wen, P.Jie, A.Xian-Yuan, and Z.Hong-Xiang (2007).
Inhibition of bacterial translation and growth by peptide nucleic acids targeted to domain II of 23S rRNA.
  J Pept Sci, 13, 220-226.  
  18026568 K.Braun, L.von Brasch, R.Pipkorn, V.Ehemann, J.Jenne, H.Spring, J.Debus, B.Didinger, W.Rittgen, and W.Waldeck (2007).
BioShuttle-mediated plasmid transfer.
  Int J Med Sci, 4, 267-277.  
17073451 G.Gavory, M.F.Symmons, Y.Krishnan Ghosh, D.Klenerman, and S.Balasubramanian (2006).
Structural analysis of the catalytic core of human telomerase RNA by FRET and molecular modeling.
  Biochemistry, 45, 13304-13311.  
16683135 S.Karkare, and D.Bhatnagar (2006).
Promising nucleic acid analogs and mimics: characteristic features and applications of PNA, LNA, and morpholino.
  Appl Microbiol Biotechnol, 71, 575-586.  
16936319 S.Modi, A.H.Wani, and Y.Krishnan (2006).
The PNA-DNA hybrid I-motif: implications for sugar-sugar contacts in i-motif tetramerization.
  Nucleic Acids Res, 34, 4354-4363.  
15791685 H.Strasdeit (2005).
New studies on the Murchison meteorite shed light on the pre-RNA world.
  Chembiochem, 6, 801-803.  
16103987 L.J.Ma, G.L.Zhang, S.Y.Chen, B.Wu, J.S.You, C.Q.Xia, and X.Q.Yu (2005).
The first synthesis of chiral PNA monomer-cyclen conjugates.
  J Pept Sci, 11, 812-817.  
16098189 T.Rathinavelan, and N.Yathindra (2005).
Molecular dynamics structures of peptide nucleic acid x DNA hybrid in the wild-type and mutated alleles of Ki-ras proto-oncogene--stereochemical rationale for the low affinity of PNA in the presence of an AC mismatch.
  FEBS J, 272, 4055-4070.  
14512516 V.Menchise, G.De Simone, T.Tedeschi, R.Corradini, S.Sforza, R.Marchelli, D.Capasso, M.Saviano, and C.Pedone (2003).
Insights into peptide nucleic acid (PNA) structural features: the crystal structure of a D-lysine-based chiral PNA-DNA duplex.
  Proc Natl Acad Sci U S A, 100, 12021-12026.
PDB code: 1nr8
11856853 V.Menchise, G.De Simone, R.Corradini, S.Sforza, N.Sorrentino, A.Romanelli, M.Saviano, and C.Pedone (2002).
Crystallization and preliminary X-ray diffraction studies of a D-lysine-based chiral PNA-DNA duplex.
  Acta Crystallogr D Biol Crystallogr, 58, 553-555.  
11139627 A.J.Tackett, L.Wei, C.E.Cameron, and K.D.Raney (2001).
Unwinding of nucleic acids by HCV NS3 helicase is sensitive to the structure of the duplex.
  Nucleic Acids Res, 29, 565-572.  
11572603 H.Kuhn, V.V.Demidov, B.D.Gildea, M.J.Fiandaca, J.C.Coull, and M.D.Frank-Kamenetskii (2001).
PNA beacons for duplex DNA.
  Antisense Nucleic Acid Drug Dev, 11, 265-270.  
  11198930 C.Malchère, J.Verheijen, S.van der Laan, L.Bastide, J.van Boom, B.Lebleu, and I.Robbins (2000).
A short phosphodiester window is sufficient to direct RNase H-dependent RNA cleavage by antisense peptide nucleic acid.
  Antisense Nucleic Acid Drug Dev, 10, 463-468.  
11118909 E.Kai, K.Ikebukuro, S.Hoshina, H.Watanabe, and I.Karube (2000).
Detection of PCR products of Escherichia coli O157:H7 in human stool samples using surface plasmon resonance (SPR).
  FEMS Immunol Med Microbiol, 29, 283-288.  
11291031 M.Oyama, T.Ikeda, T.Lim, K.Ikebukuro, Y.Masuda, and I.Karube (2000).
Detection of toxic chemicals with high sensitivity by measuring the quantity of induced P450 mRNAs based on surface plasmon resonance.
  Biotechnol Bioeng, 71, 217-222.  
11086725 T.Vilaivan, C.Khongdeesameor, P.Harnyuttanakorn, M.S.Westwell, and G.Lowe (2000).
Synthesis and properties of chiral peptide nucleic acids with a N-aminoethyl-D-proline backbone.
  Bioorg Med Chem Lett, 10, 2541-2545.  
10807005 H.J.Larsen, T.Bentin, and P.E.Nielsen (1999).
Antisense properties of peptide nucleic acid.
  Biochim Biophys Acta, 1489, 159-166.  
10387088 K.M.Lee, S.Sif, R.E.Kingston, and J.J.Hayes (1999).
hSWI/SNF disrupts interactions between the H2A N-terminal tail and nucleosomal DNA.
  Biochemistry, 38, 8423-8429.  
10361091 P.E.Nielsen (1999).
Peptide nucleic acids as therapeutic agents.
  Curr Opin Struct Biol, 9, 353-357.  
10422241 S.Sawata, E.Kai, K.Ikebukuro, T.Iida, T.Honda, and I.Karube (1999).
Application of peptide nucleic acid to the direct detection of deoxyribonucleic acid amplified by polymerase chain reaction.
  Biosens Bioelectron, 14, 397-404.  
9649324 B.Armitage, D.Ly, T.Koch, H.Frydenlund, H.Orum, and G.B.Schuster (1998).
Hairpin-forming peptide nucleic acid oligomers.
  Biochemistry, 37, 9417-9425.  
9204276 A.Lebrun, and R.Lavery (1997).
Unusual DNA conformations.
  Curr Opin Struct Biol, 7, 348-354.  
9100003 C.W.Cross, J.S.Rice, and X.Gao (1997).
Solution structure of an RNA x DNA hybrid duplex containing a 3'-thioformacetal linker and an RNA A-tract.
  Biochemistry, 36, 4096-4107.
PDB code: 1ac3
9183865 D.R.Corey (1997).
Peptide nucleic acids: expanding the scope of nucleic acid recognition.
  Trends Biotechnol, 15, 224-229.  
9033585 H.Rasmussen, J.S.Kastrup, J.N.Nielsen, J.M.Nielsen, and P.E.Nielsen (1997).
Crystal structure of a peptide nucleic acid (PNA) duplex at 1.7 A resolution.
  Nat Struct Biol, 4, 98.
PDB code: 1pup
9003193 J.S.Rice, and X.Gao (1997).
Conformation of formacetal and 3'-thioformacetal nucleotide linkers and stability of their antisense RNA.DNA hybrid duplexes.
  Biochemistry, 36, 399-411.  
  9303195 L.Good, and P.E.Nielsen (1997).
Progress in developing PNA as a gene-targeted drug.
  Antisense Nucleic Acid Drug Dev, 7, 431-437.  
9305980 S.E.Hamilton, A.E.Pitts, R.R.Katipally, X.Jia, J.P.Rutter, B.A.Davies, J.W.Shay, W.E.Wright, and D.R.Corey (1997).
Identification of determinants for inhibitor binding within the RNA active site of human telomerase using PNA scanning.
  Biochemistry, 36, 11873-11880.  
9164451 S.L.Miller (1997).
Peptide nucleic acids and prebiotic chemistry.
  Nat Struct Biol, 4, 167-169.  
8689239 B.Hyrup, and P.E.Nielsen (1996).
Peptide nucleic acids (PNA): synthesis, properties and potential applications.
  Bioorg Med Chem, 4, 5.  
8577768 D.S.Thaler, S.Liu, and G.Tombline (1996).
Extending the chemistry that supports genetic information transfer in vivo: phosphorothioate DNA, phosphorothioate RNA, 2'-O-methyl RNA, and methylphosphonate DNA.
  Proc Natl Acad Sci U S A, 93, 1352-1356.  
8602363 H.Knudsen, and P.E.Nielsen (1996).
Antisense properties of duplex- and triplex-forming PNAs.
  Nucleic Acids Res, 24, 494-500.  
8612069 M.Eriksson, and P.E.Nielsen (1996).
Solution structure of a peptide nucleic acid-DNA duplex.
  Nat Struct Biol, 3, 410-413.
PDB code: 1pdt
9080548 M.Eriksson, and P.E.Nielsen (1996).
PNA-nucleic acid complexes. Structure, stability and dynamics.
  Q Rev Biophys, 29, 369-394.  
8548453 M.M.Basti, J.W.Stuart, A.T.Lam, R.Guenther, and P.F.Agris (1996).
Design, biological activity and NMR-solution structure of a DNA analogue of yeast tRNA(Phe) anticodon domain.
  Nat Struct Biol, 3, 38-44.
PDB code: 229d
8570609 R.A.Torres, and T.C.Bruce (1996).
Interresidue hydrogen bonding in a peptide nucleic acid.RNA heteroduplex.
  Proc Natl Acad Sci U S A, 93, 649-653.  
7583633 A.De Mesmaeker, K.H.Altmann, A.Waldner, and S.Wendeborn (1995).
Backbone modifications in oligonucleotides and peptide nucleic acid systems.
  Curr Opin Struct Biol, 5, 343-355.  
7537874 M.A.Bonham, S.Brown, A.L.Boyd, P.H.Brown, D.A.Bruckenstein, J.C.Hanvey, S.A.Thomson, A.Pipe, F.Hassman, and J.E.Bisi (1995).
An assessment of the antisense properties of RNase H-competent and steric-blocking oligomers.
  Nucleic Acids Res, 23, 1197-1203.  
8527834 R.C.Jackson (1995).
Update on computer-aided drug design.
  Curr Opin Biotechnol, 6, 646-651.  
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 code is shown on the right.

 

spacer
spacer