Extraordinary stable structure of short single-stranded DNA fragments containing a specific base sequence: d(GCGAAAGC).

Nucleic acids research ·Vol. 17 ·No. 6 ·1989-03-25 ·Pages 2223-31

Hirao I, Nishimura Y, Naraoka T, Watanabe K, Arata Y, Miura K

Abstract

Short single-stranded DNA fragments carrying a GCGAAAGC sequence were found to move unexpectedly faster than other fragments of the same length in electrophoresis on a polyacrylamide gel containing a denaturing agent. The fragments were noted to have a stable structure even in 7M urea solution, but the stability cannot be explained simply on the basis of base pair formation alone. Physical characterization of the GCGAAAGC fragment indicated that it takes a hairpin-like structure in spite of the short chain length with only two G-C base pairs, comprised of GCG and AAAGC subsegments, each possessing a helical configuration independent of the others. Some biological implications of this unusual structure are discussed.

MeSH Terms

Base Composition Base Sequence Circular Dichroism DNA, Single-Stranded Drug Stability Electrophoresis, Polyacrylamide Gel Magnetic Resonance Spectroscopy Nucleic Acid Conformation Oligodeoxyribonucleotides

Chemicals

DNA, Single-Stranded Oligodeoxyribonucleotides

Authors & Affiliations

6 authors, click to expand affiliations / ORCID

Hirao I

Department of Industrial Chemistry, Faculty of Engineering, University of Tokyo, Japan.

Nishimura Y

Naraoka T

Watanabe K

Arata Y

Miura K

References (25)

25 references, click to expand

Use of T4 DNA polymerase replacement synthesis for specific labeling of plasmid-cloned inserts.
Anal Biochem. 1983 Dec;135(2):456-65 PMID: 6318604
Hairpin and duplex formation in DNA fragments CCAATTTTGG, CCAATTTTTTGG, and CCATTTTTGG: a proton NMR study.
Biochemistry. 1988 Apr 19;27(8):3024-31 PMID: 3401464
Multidimensional spectroscopic data correlation in the conformation transition of biological macromolecules.
J Biochem Biophys Methods. 1980 May;2(5):257-69 PMID: 7052943
Cloning DNA restriction endonuclease fragments with protruding single-stranded ends.
Gene. 1980 May;9(3-4):307-19 PMID: 6248431
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
Static bend of DNA helix at the activator recognition site of the ompF promoter in Escherichia coli.
Gene. 1987;54(1):57-64 PMID: 3301541
Calibration of DNA curvature and a unified description of sequence-directed bending.
Proc Natl Acad Sci U S A. 1988 Mar;85(6):1763-7 PMID: 3162306
Hairpin and duplex formation of the DNA octamer d(m5C-G-m5C-G-T-G-m5C-G) in solution. An NMR study.
Nucleic Acids Res. 1986 May 27;14(10):4187-96 PMID: 3714474
On the sequence determinants and flexibility of the kinetoplast DNA fragment with abnormal gel electrophoretic mobilities.
J Mol Biol. 1985 Nov 5;186(1):1-11 PMID: 3001314
DNA chain length markers and the influence of base composition on electrophoretic mobility of oligodeoxyribonucleotides in polyacrylamide-gels.
Nucleic Acids Res. 1979;6(6):2069-87 PMID: 461182
The intrinsic curvature of DNA in solution.
J Mol Biol. 1988 May 5;201(1):127-37 PMID: 3418695
Bent helical structure in kinetoplast DNA.
Proc Natl Acad Sci U S A. 1982 Dec;79(24):7664-8 PMID: 16593261
The RNA primer synthesized by primase to initiate phage G4 DNA replication.
J Biol Chem. 1978 Feb 10;253(3):765-9 PMID: 340458
Oligonucleotide interactions. 3. Circular dichroism studies of the conformation of deoxyoligonucleotides.
Biopolymers. 1970;9(9):1059-77 PMID: 5449435
Nucleotide sequence of bacteriophage G4 DNA.
Nature. 1978 Nov 16;276(5685):236-47 PMID: 714153
DNA bending at adenine . thymine tracts.
Nature. 1986 Apr 10-16;320(6062):501-6 PMID: 3960133
Synthetic oligodeoxyribonucleotides showing abnormal mobilities on polyacrylamide gel electrophoresis.
Biochem Int. 1988 Jan;16(1):157-62 PMID: 3355571
Three-dimensional structure of a DNA hairpin in solution: two-dimensional NMR studies and distance geometry calculations on d(CGCGTTTTCGCG).
Biochemistry. 1986 Sep 9;25(18):5341-50 PMID: 3768352
DNA hairpin structures in solution: 500-MHz two-dimensional 1H NMR studies on d(CGCCGCAGC) and d(CGCCGTAGC).
Biochemistry. 1987 Dec 1;26(24):7715-23 PMID: 3427100
The integration host factor of Escherichia coli binds to bent DNA at the origin of replication of the plasmid pSC101.
Cell. 1987 Jun 5;49(5):709-17 PMID: 3555843
Direct evidence for DNA bending at the lambda replication origin.
Science. 1987 Apr 24;236(4800):416-22 PMID: 2951850
The locus of sequence-directed and protein-induced DNA bending.
Nature. 1984 Apr 5-11;308(5959):509-13 PMID: 6323997
Terminal labeling and addition of homopolymer tracts to duplex DNA fragments by terminal deoxynucleotidyl transferase.
Nucleic Acids Res. 1976 Apr;3(4):863-77 PMID: 775445
Influence of loop residues on the relative stabilities of DNA hairpin structures.
Proc Natl Acad Sci U S A. 1988 Sep;85(17):6242-6 PMID: 3413094
Sequence-directed curvature of DNA.
Nature. 1986 May 22-28;321(6068):449-50 PMID: 3713816

Article Info

Journal

Nucleic acids research

Abbr.

Nucleic Acids Res

ISSN

0305-1048

DOI

10.1093/nar/17.6.2223

Published

1989-03-25

Pages

2223-31

Language

English

Region

England

NLM ID

0411011

PMCID

PMC317592

Subset

External Links

PubMed source DOI: 10.1093/nar/17.6.2223 PMC Full Text View journal details

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Extraordinary stable structure of short single-stranded DNA fragments containing a specific base sequence: d(GCGAAAGC).

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