A structural basis for S1 nuclease sensitivity of double-stranded DNA

doi:10.1016/S0092-8674(85)80122-7

Cell

Volume 42, Issue 1, August 1985, Pages 271-280

https://doi.org/10.1016/S0092-8674(85)80122-7 Get rights and content

Summary

A protonated form of a cloned simple repeating DNA sequence d(TC)n·d(GA) is detectable in equilibrium with the usual Watson-Crick base-paired form at pHs up to 7. This form is anomalously sensitive to a variety of single-strand-specific endonucleases. The observed pH dependent protection of N-7 of dG residues within the insert suggests that these residues are either Hoogsteen or reverse Hoogsteen base-paired to protonated dC residues of the polypyrimidine strand. A structure in which dA:dT Watson-Crick base pairs alternate with Hoogsteen ^syndG:dCH⁺ pairs appears to be the most stereochemically acceptable structure consistent with the chemical properties of this protonated DNA. Protonated d(TC)n·d(GA)n interacts with an anti-Z DNA antibody raised against brominated d(GC)n·d(GC)n.

References (64)

BuggC.E. et al.
Base stacking in nucleic acid components: the crystal structures of guanine, guanosine and inosine
Biochim. Biophys. Res. Commun.
(1968)
CrabtreeG.R. et al.
Organization of the rat γ-fibrinogen gene: alternative mRNA splice patterns produce the γA and γB(γ′) chains of fibrinogen
Cell
(1982)
GendelS. et al.
A novel shuttle cloning vector for the cyanobacterium Anacystis nidulans
FEMS Microbiol. Lett.
(1983)
KlugA. et al.
A hypothesis on a specific sequence dependent conformation of DNA and its relation to the binding of the lac-repressor
J. Mol. Biol.
(1979)
LarsenA. et al.
An altered DNA conformation detected by S1 nuclease occurs at specific regions in active chicken globin chromatin
Cell
(1982)
MorganA.R. et al.
Specificity of the three stranded complex formation between double-stranded DNA and singlestranded RNA containing repeating nucleotide sequences
J. Mol. Biol.
(1968)
NickolJ.M. et al.
DNA conformation at the 5′ end of the chicken adult β-globin gene
Cell
(1983)
NordheimA. et al.
Negatively supercoiled plasmids contain left-handed Z-DNA segments as detected by specific antibody binding
Cell
(1982)
SchonE. et al.
Conformation of promotor DNA: fine structure mapping of S1-hypersensitive sites
Cell
(1983)
SingerB.
The chemical effects of nucleic acid alkylation and their relation to mutagenesis and carcinogenesis
Prog. Nucl. Acids Res. and Mol. Biol.
(1975)

SobellH.M.

The crystal structure of a purine-pyrimidine hydrogen bonded complex: 9-ethyl-2-aminopurine and 1-methyl-5-fluoro-uracil

J. Mol. Biol.

(1966)

SuresI. et al.

The DNA sequence of sea urchin (S. purpuratus) H2A, H2B and H3 histone coding and spacer regions

Cell

(1978)

VieiraJ. et al.

The pUC plasmids, an M13mp7 derivative for insertion mutagenesis and sequencing with synthetic universal primers

Gene

(1982)

WeintraubH.

A dominant role for DNA secondary structure in forming hypersensitive structures in chromatin

Cell

(1983)

Arndt-JovinD.J. et al.

Dependence of Z-DNA binding antibody binding to polytene chromosomes

AzorinF. et al.

Formation of Z-DNA in negatively supercoiled plasmids is sensitive to small changes in salt concentration within the physiological range

EMBO J.

(1983)

BenhamC.J.

Theoretical analysis of transitions between B- and Z-conformations in torsionally stressed DNA

Nature

(1980)

BrownD.M. et al.

Photochemical demonstration of stacked C·C⁺ base pairs in a novel DNA secondary structure

Biochemistry

(1985)

CantorC.R. et al.

Possible structure of homopurine homopyrimidine S1-hypersensitive sites

Nucl. Acids Res.

(1984)

ChengH.L. et al.

Structure of the genes for membrane and secreted murine IgD heavy chains

Nature

(1982)

CourtoisY. et al.

Protonated polynucleotide structures. 3. An optical rotatory dispersion study of the protonation of DNA

Eur. J. Biochem.

(1968)

CruzeW.B.T. et al.

Self base pairing in a complementary deoxynucleoside monophosphate duplex: crystal and molecular structure of deoxycytidylyl-(3′-5′-deoxyguanosine

Biochemistry

(1983)

DixonM. et al.

Enzymes

FriedmanT. et al.

Base specific reactions useful for DNA sequencing: methylene blue sensitized photooxidation of guanine and osmium tetraoxide modification of thymine

Nucl. Acids Res.

(1978)

GuschlbauerW.

Why is guanosine different?

HaleP. et al.

E. coli RNA polymerase promotors on superhelical SV40 DNA are highly selective targets for chemical modification

Nature

(1980)

HaleP. et al.

Carbodiimide inactivation of E. coli RNA polymerase promotors on supercoiled simian virus 40 and CoIE1 DNAs occurs by a one hit process at salt concentrations in the physiological range

J. Biol. Chem.

(1982)

HamadaH. et al.

Potential Z-DNA forming sequences are highly dispersed in the human genome

Nature

(1982)

HanifordD.B. et al.

Facile transition of poly [d(TG)n·d(CA)n] into a left-handed helix in physiological conditions

Nature

(1983)

HanifordD.B. et al.

The in-vivo occurrence of Z-DNA

J. Biomol. Struc. Dynam.

(1983)

HanifordD.B. et al.

Transition of a cloned d(AT)n·d(AT)n tract to a cruciform in vivo

Nucl. Acids Res.

(1985)

HaschemeyerA.E.V. et al.

The crystal structure of a hydrogen bonded complex of adenosine and 5 bromouridine

Acta Cryst.

(1965)

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Cell

ArticleA structural basis for S1 nuclease sensitivity of double-stranded DNA

Summary

Biochim. Biophys. Res. Commun.

Cell

FEMS Microbiol. Lett.

J. Mol. Biol.

Cell

J. Mol. Biol.

Cell

Cell

Cell

Prog. Nucl. Acids Res. and Mol. Biol.

J. Mol. Biol.

Cell

Gene

Cell

Dependence of Z-DNA binding antibody binding to polytene chromosomes

Formation of Z-DNA in negatively supercoiled plasmids is sensitive to small changes in salt concentration within the physiological range

EMBO J.

Theoretical analysis of transitions between B- and Z-conformations in torsionally stressed DNA

Nature

Photochemical demonstration of stacked C·C+ base pairs in a novel DNA secondary structure

Biochemistry

Possible structure of homopurine homopyrimidine S1-hypersensitive sites

Nucl. Acids Res.

Structure of the genes for membrane and secreted murine IgD heavy chains

Nature

Protonated polynucleotide structures. 3. An optical rotatory dispersion study of the protonation of DNA

Eur. J. Biochem.

Self base pairing in a complementary deoxynucleoside monophosphate duplex: crystal and molecular structure of deoxycytidylyl-(3′-5′-deoxyguanosine

Biochemistry

Enzymes

Base specific reactions useful for DNA sequencing: methylene blue sensitized photooxidation of guanine and osmium tetraoxide modification of thymine

Nucl. Acids Res.

Why is guanosine different?

E. coli RNA polymerase promotors on superhelical SV40 DNA are highly selective targets for chemical modification

Nature

Carbodiimide inactivation of E. coli RNA polymerase promotors on supercoiled simian virus 40 and CoIE1 DNAs occurs by a one hit process at salt concentrations in the physiological range

J. Biol. Chem.

Potential Z-DNA forming sequences are highly dispersed in the human genome

Nature

Facile transition of poly [d(TG)n·d(CA)n] into a left-handed helix in physiological conditions

Nature

The in-vivo occurrence of Z-DNA

J. Biomol. Struc. Dynam.

Transition of a cloned d(AT)n·d(AT)n tract to a cruciform in vivo

Nucl. Acids Res.

The crystal structure of a hydrogen bonded complex of adenosine and 5 bromouridine

Acta Cryst.

Article
A structural basis for S1 nuclease sensitivity of double-stranded DNA

Photochemical demonstration of stacked C·C⁺ base pairs in a novel DNA secondary structure