Nucleic Acids Research, 1994, Vol. 22, No. 4 576-582
© 1994
STRUCTURAL BIOLOGY |
Most compact hairpin-turn structure exerted by a short DNA fragment, d(GCGAAGC) in solution: an extraordinarily stable structure resistant to nucleases and heat
Laboratory of Pharmaceutical Chemistry, Tokyo College of Pharmacy 1432-1 Horinouchi, Hachioji, Tokyo 192-03 1Department of Industrial Chemistry, Faculty of Engineering The University of Tokyo, 7-3-1 Hongo, Tokyo 113 2Graduate School of Integrated Science Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236 3Institute for Biomolecular Science Gakushuin University, Mejiro, Tokyo 171, Japan
Received November 22, 1993. Accepted December 24, 1993.
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 As, 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 AgGeCy, 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 (halrpln-tum) structure exerted by a single-stranded DNA. This highly stacked structure shows high thermostabillty and strong resistance against nucleases contained in E.coli extracts and in human serum.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  Z. Chen, K. A. Lewis, R. K. Shultzaberger, I. G. Lyakhov, M. Zheng, B. Doan, G. Storz, and T. D. Schneider Discovery of Fur binding site clusters in Escherichia coli by information theory models Nucleic Acids Res., November 7, 2007; 35(20): 6762 - 6777. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Kannan and M. Zacharias Folding of a DNA Hairpin Loop Structure in Explicit Solvent Using Replica-Exchange Molecular Dynamics Simulations Biophys. J., November 1, 2007; 93(9): 3218 - 3228. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. K. Davydova, T. J. Santangelo, and L. B. Rothman-Denes Bacteriophage N4 virion RNA polymerase interaction with its promoter DNA hairpin PNAS, April 24, 2007; 104(17): 7033 - 7038. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Kaushik and S. Kukreti Structural polymorphism exhibited by a quasipalindrome present in the locus control region (LCR) of the human {beta}-globin gene cluster Nucleic Acids Res., July 19, 2006; 34(12): 3511 - 3522. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Kim, S. Doose, H. Neuweiler, and M. Sauer The initial step of DNA hairpin folding: a kinetic analysis using fluorescence correlation spectroscopy. Nucleic Acids Res., January 1, 2006; 34(9): 2516 - 2527. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Canalia and J. L. Leroy Structure, internal motions and association-dissociation kinetics of the i-motif dimer of d(5mCCTCACTCC) Nucleic Acids Res., October 4, 2005; 33(17): 5471 - 5481. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. M. MOODY, J. T. J. LECOMTE, and P. C. BEVILACQUA Linkage between proton binding and folding in RNA: A thermodynamic framework and its experimental application for investigating pKa shifting RNA, February 1, 2005; 11(2): 157 - 172. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Kaushik, R. Kukreti, D. Grover, S. K. Brahmachari, and S. Kukreti Hairpin-duplex equilibrium reflected in the A->B transition in an undecamer quasi-palindrome present in the locus control region of the human {beta}-globin gene cluster Nucleic Acids Res., December 1, 2003; 31(23): 6904 - 6915. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. W. Habig and D. D. Loeb The Conformation of the 3' End of the Minus-Strand DNA Makes Multiple Contributions to Template Switches during Plus-Strand DNA Synthesis of Duck Hepatitis B Virus J. Virol., December 1, 2003; 77(23): 12401 - 12411. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. J. Sorin, Y. M. Rhee, B. J. Nakatani, and V. S. Pande Insights into Nucleic Acid Conformational Dynamics from Massively Parallel Stochastic Simulations Biophys. J., August 1, 2003; 85(2): 790 - 803. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Matsugami, T. Okuizumi, S. Uesugi, and M. Katahira Intramolecular Higher Order Packing of Parallel Quadruplexes Comprising a G:G:G:G Tetrad and a G(:A):G(:A):G(:A):G Heptad of GGA Triplet Repeat DNA J. Biol. Chem., July 18, 2003; 278(30): 28147 - 28153. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S.-H. Chou, K.-H. Chin, and A. H.-J. Wang Unusual DNA duplex and hairpin motifs Nucleic Acids Res., May 15, 2003; 31(10): 2461 - 2474. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. P. H. Santini, C. Pakleza, and J. A. H. Cognet DNA tri- and tetra-loops and RNA tetra-loops hairpins fold as elastic biopolymer chains in agreement with PDB coordinates Nucleic Acids Res., February 1, 2003; 31(3): 1086 - 1096. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Umezawa and M. Nishio Thymine-methyl/{pi} interaction implicated in the sequence-dependent deformability of DNA Nucleic Acids Res., May 15, 2002; 30(10): 2183 - 2192. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. W. Habig and D. D. Loeb Small DNA Hairpin Negatively Regulates In Situ Priming during Duck Hepatitis B Virus Reverse Transcription J. Virol., February 1, 2002; 76(3): 980 - 989. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. G. Lyakhov, P. N. Hengen, D. Rubens, and T. D. Schneider The P1 phage replication protein RepA contacts an otherwise inaccessible thymine N3 proton by DNA distortion or base flipping Nucleic Acids Res., December 1, 2001; 29(23): 4892 - 4900. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Ansari, S. V. Kuznetsov, and Y. Shen Configurational diffusion down a folding funnel describes the dynamics of DNA hairpins PNAS, July 3, 2001; 98(14): 7771 - 7776. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X. Dai and L. B. Rothman-Denes Sequence and DNA structural determinants of N4 virion RNA polymerase-promoter recognition Genes & Dev., September 1, 1998; 12(17): 2782 - 2790. [Abstract] [Full Text]
|
|
|
|
|
|
K. P. Williams, X.-H. Liu, T. N. M. Schumacher, H. Y. Lin, D. A. Ausiello, P. S. Kim, and D. P. Bartel Bioactive and nuclease-resistant L-DNA ligand of vasopressin PNAS, October 14, 1997; 94(21): 11285 - 11290. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Dai, M. B. Greizerstein, K. Nadas-Chinni, and L. B. Rothman-Denes Supercoil-induced extrusion of a regulatory DNA hairpin PNAS, March 18, 1997; 94(6): 2174 - 2179. [Abstract] [Full Text] [PDF]
|
|