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PMID: 8127706 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Most compact hairpin-turn structure exerted by a short DNA fragment, d(GCGAAGC) in solution: an extraordinarily stable structure resistant to nucleases and heat.

Nucleic acids research ·Vol. 22 ·No. 4 ·1994-02-25 ·Pages 576-82

Hirao I, Kawai G, Yoshizawa S, Nishimura Y, Ishido Y, Watanabe K, Miura K

Abstract

The three-dimensional structure of a short DNA fragment, d(GCGAAGC) exhibiting an extraordinarily stable hairpin structure was determined by nuclear magnetic resonance spectroscopy. Two possible models were obtained by molecular modelling using distance and torsion constraints. Only one of these two models is the correct structure, which can clearly explain all the 1H chemical shifts. d(GCGAAGC) is folded back on itself between A4 and A5, and all the sugars in the fragment adopt the C2'-endo conformation. This compact molecule is stabilized by regular extensive base-stacking interaction within each B-form helical strand of G1C2G3A4 and A5G6C7, and by two G-C and one G3-A5 base pairs. The molecule is hard to differentiate into stem and loop regions, so that we classify it as a turn (hairpin-turn) structure experted by a single-stranded DNA. This highly stacked structure shows high thermostability and strong resistance against nucleases contained in E. coli extracts and in human serum.

MeSH Terms
Base Sequence Deoxyribonucleases/metabolism Escherichia coli Hot Temperature Humans Magnetic Resonance Spectroscopy Models, Molecular Molecular Sequence Data Nucleic Acid Conformation Oligodeoxyribonucleotides/chemistry,metabolism Protons
Chemicals
Oligodeoxyribonucleotides Protons Deoxyribonucleases
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Hirao I
Laboratory of Pharmaceutical Chemistry, Tokyo College of Pharmacy, Japan.
Kawai G
Yoshizawa S
Nishimura Y
Ishido Y
Watanabe K
Miura K
References (29)
29 references, click to expand
  1. Mechanism of dnaB protein action. V. Association of dnaB protein, protein n', and other repriming proteins in the primosome of DNA replication.
    J Biol Chem. 1981 May 25;256(10):5273-80 PMID: 6262328
  2. Secondary structure at the 3' terminal region of RNA coliphages: comparison with tRNA.
    Biochim Biophys Acta. 1990 Aug 27;1050(1-3):110-8 PMID: 2207136
  3. The role of guanosine 5'-triphosphate in the initiation of peptide synthesis. 3. Binding of formylmethionyl-tRNA to ribosomes.
    Proc Natl Acad Sci U S A. 1967 Oct;58(4):1638-44 PMID: 4867668
  4. Extraordinarily stable mini-hairpins: electrophoretical and thermal properties of the various sequence variants of d(GCGAAAGC) and their effect on DNA sequencing.
    Nucleic Acids Res. 1992 Aug 11;20(15):3891-6 PMID: 1508675
  5. The solution structure of a DNA hairpin containing a loop of three thymidines determined by nuclear magnetic resonance and molecular mechanics.
    Nucleic Acids Res. 1991 Oct 11;19(19):5159-67 PMID: 1923802
  6. Studies on the structure and stabilizing factor of the CUUCGG hairpin RNA using chemically synthesized oligonucleotides.
    Nucleic Acids Res. 1990 Jul 11;18(13):3831-9 PMID: 1695732
  7. CUUCGG hairpins: extraordinarily stable RNA secondary structures associated with various biochemical processes.
    Proc Natl Acad Sci U S A. 1988 Mar;85(5):1364-8 PMID: 2449689
  8. Purification of viral RNA by means of bentonite.
    Virology. 1961 May;14:54-8 PMID: 13701154
  9. Consensus sequence for Escherichia coli heat shock gene promoters.
    Proc Natl Acad Sci U S A. 1985 May;82(9):2679-83 PMID: 3887408
  10. Stabilization of mRNA in an Escherichia coli cell-free translation system.
    FEBS Lett. 1993 Apr 26;321(2-3):169-72 PMID: 8477846
  11. A novel method to stabilise antisense oligonucleotides against exonuclease degradation.
    Nucleic Acids Res. 1993 Jun 25;21(12):2957-8 PMID: 8392712
  12. Unique hairpin structures occurring at the replication origin of phage G4 DNA.
    Biochim Biophys Acta. 1990 Oct 23;1087(2):199-204 PMID: 2223881
  13. Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops.
    Science. 1991 Jul 12;253(5016):191-4 PMID: 1712983
  14. Nuclear magnetic resonance and circular dichroism studies of a duplex--single-stranded hairpin loop equilibrium for the oligodeoxyribonucleotide sequence d(CGCGATTCGCG).
    Nucleic Acids Res. 1985 Sep 11;13(17):6375-86 PMID: 4047943
  15. Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops.
    Nucleic Acids Res. 1992 Feb 25;20(4):819-24 PMID: 1371866
  16. Phosphorus-proton spin-spin coupling and conformation of a dinucleoside phosphate.
    Science. 1969 Dec 19;166(3912):1504-5 PMID: 17742850
  17. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis.
    J Mol Biol. 1990 Dec 5;216(3):585-610 PMID: 2258934
  18. Sequence-dependent structural variations of hammerhead RNA enzymes.
    Nucleic Acids Res. 1990 Mar 11;18(5):1103-8 PMID: 2181399
  19. Extraordinary stable structure of short single-stranded DNA fragments containing a specific base sequence: d(GCGAAAGC).
    Nucleic Acids Res. 1989 Mar 25;17(6):2223-31 PMID: 2704619
  20. Self-stabilized antisense oligodeoxynucleotide phosphorothioates: properties and anti-HIV activity.
    Nucleic Acids Res. 1993 Jun 11;21(11):2729-35 PMID: 8392706
  21. Interaction of origin binding protein with an origin of replication of herpes simplex virus 1.
    Proc Natl Acad Sci U S A. 1988 May;85(9):2959-63 PMID: 2834723
  22. Interaction of a protein from rat liver nuclei with cruciform DNA.
    EMBO J. 1988 Mar;7(3):843-9 PMID: 3396544
  23. The solution structure of a d[C(TTCG)G] DNA hairpin and comparison to the unusually stable RNA analogue.
    Nucleic Acids Res. 1993 Jul 11;21(14):3287-93 PMID: 7688117
  24. NMR studies of G:A mismatches in oligodeoxyribonucleotide duplexes modelled after ribozymes.
    Nucleic Acids Res. 1993 Nov 25;21(23):5418-24 PMID: 8265358
  25. Structure of a small RNA hairpin.
    Nucleic Acids Res. 1993 Feb 11;21(3):537-45 PMID: 7680122
  26. A thermodynamic study of unusually stable RNA and DNA hairpins.
    Nucleic Acids Res. 1991 Nov 11;19(21):5901-5 PMID: 1719483
  27. Assignment of the 31P and 1H resonances in oligonucleotides by two-dimensional NMR spectroscopy.
    FEBS Lett. 1986 Nov 10;208(1):94-8 PMID: 3770213
  28. Solution structure of an unusually stable RNA hairpin, 5'GGAC(UUCG)GUCC.
    Nature. 1990 Aug 16;346(6285):680-2 PMID: 1696688
  29. NMR and molecular modeling evidence for a G.A mismatch base pair in a purine-rich DNA duplex.
    Proc Natl Acad Sci U S A. 1991 Jan 1;88(1):26-30 PMID: 1986374
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/22.4.576
Published
1994-02-25
Pages
576-82
Language
English
Region
England
NLM ID
0411011
PMCID
PMC307846
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/22.4.576 PMC Full Text View journal details
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