Hairpin Formation during DNA Synthesis Primer Realignmentin Vitro in Triplet Repeat Sequences from Human Hereditary Disease Genes*

@article{Ohshima1997HairpinFD,
  title={Hairpin Formation during DNA Synthesis Primer Realignmentin Vitro in Triplet Repeat Sequences from Human Hereditary Disease Genes*},
  author={Keiichi Ohshima and R. D. Wells},
  journal={The Journal of Biological Chemistry},
  year={1997},
  volume={272},
  pages={16798 - 16806}
}
Genetic expansion of DNA triplet repeat sequences (TRS) found in neurogenetic disorders may be due to abnormal DNA replication. We have previously observed strong DNA synthesis pausings at specific loci within the long tracts (>∼70 repeats) of CTG·CAG and CGG·CCG as well as GTC·GAC by primer extensions in vitro using DNA polymerases (the Klenow fragment ofEscherichia coli DNA polymerase I, the modified T7 DNA polymerase (Sequenase), and human DNA polymerase β). Herein, we have isolated and… 

Figures and Tables from this paper

Abasic Sites Induce Triplet-repeat Expansion during DNA Replication in Vitro *

TLDR
It is shown that a single abasic site analog, synthesized in the triplet-repeat tract at the 5′ end of the template strand, induced dramatic TRE during DNA synthesis, implying that DNA damage can play a significant role in generating TRE in vivo.

DNA Polymerase III Proofreading Mutants Enhance the Expansion and Deletion of Triplet Repeat Sequences in Escherichia coli *

TLDR
It is concluded that the expansion and deletion of triplet repeats are enhanced by mutations that reduce the fidelity of replication.

Expansion and Deletion of Triplet Repeat Sequences inEscherichia coli Occur on the Leading Strand of DNA Replication*

TLDR
Rolling circle replication has been established in vitro as a model for leading strand synthesis, and it is concluded that triplet repeat instability can also occur on the leading strand of DNA replication.

Effects of temperature, Mg2+ concentration and mismatches on triplet-repeat expansion during DNA replication in vitro.

TLDR
The results imply that cellular environment and whether the growing strand contains a nick or gap are important factors for the expansion process in vivo.

Efficient isothermal expansion of human telomeric and minisatellite repeats by Thermococcus litoralis DNA polymerase

TLDR
This work describes the efficient and convenient expansion of repetitive telomeric and minisatellite DNA sequences starting from small synthetic templates to final product lengths of several hundreds to thousands of nucleotides by the thermostable DNA polymerase from Thermococcus litoralis (VentDNA polymerase).

DNA Ligase I Competes with FEN1 to Expand Repetitive DNA Sequences in Vitro *

TLDR
Examination of expansion in vitro enables dissection of substrate and replication enzyme dynamics on repeat sequences, and increased MgCl2 disfavored ligation of substrate intermediates that result in expansion products.

Weak Strand Displacement Activity Enables Human DNA Polymerase β to Expand CAG/CTG Triplet Repeats at Strand Breaks*

TLDR
It is found that human DNA polymerase β effectively catalyzes CAG/CTG triplet repeat expansions by slippage initiated at nicks or 1-base gaps within short (14 triplet) repeat tracts in DNA duplexes under physiological conditions.

Analysis of Strand Slippage in DNA Polymerase Expansions of CAG/CTG Triplet Repeats Associated with Neurodegenerative Disease*

TLDR
Using a synthetic self-priming DNA, containing CAG and CTG repeats implicated in Huntington’s disease and several other neurological disorders, the equilibrium distribution of hairpin folding is measured and triplet repeat expansions by polymerase-catalyzed extensions of the hairpin folds are generated.

Genetic Instabilities in (CTG·CAG) Repeats Occur by Recombination*

TLDR
The relationships between CTG·CAG sequences, multiple fold expansions, genetic recombination, formation of new recombinant DNA products, and the presence of both drug resistance genes are established.

Double-strand breaks in the myotonic dystrophy type 1 and the fragile X syndrome triplet repeat sequences induce different types of mutations in DNA flanking sequences in Escherichia coli

TLDR
Non-B DNA structures (slipped structures with loops, cruciforms, triplexes and tetraplexes) as well as microhomologies are postulated to participate in the recombination and/or repair processes.
...

References

SHOWING 1-10 OF 58 REFERENCES

Pausing of DNA Synthesis in Vitro at Specific Loci in CTG and CGG Triplet Repeats from Human Hereditary Disease Genes (*)

TLDR
Results indicate that appropriate lengths of the triplets adopt a non-B conformation(s) that blocks DNA polymerase progression; the resultant idling polymerase may catalyze slippages to give expanded sequences and hence provide the molecular basis for this non-Mendelian genetic process.

Sequence-specific pausing during in vitro DNA replication on double-stranded DNA templates.

TLDR
A clustering of sites is observed, suggesting that the polymerase holoenzyme may become destabilized when moving along selected regions of the DNA and then pause at one or more of several closely spaced positions.

Gene Targeting in Rat Embryo Fibroblasts Promoted by the Polyomavirus Large T Antigen Associated With Neurological Diseases

TLDR
Surprisingly, the folds formed by 30 repeats of CTG or CAG have no higher melting temperature and are only 40% more stable in free energy than those formed by 10 repeats, suggesting that triplet expansions with higher repeat number may result from the formation of more folded structures with similar stability rather than fewer but longer folds of greater stability.

Hairpin properties of single-stranded DNA containing a GC-rich triplet repeat: (CTG)15.

TLDR
Potential functions of hairpins containing Class I triplet repeats are discussed with respect to protein translation and mRNA splicing and potential roles of hairpin structures in triplet repeat expansion events are discussed.

In vivo duplication of genetic elements by the formation of stem-loop DNA without an RNA intermediate.

TLDR
The experiments in this study suggest that during DNA replication, template switching at the stem-loop structure formed by the IR structure gives rise to slDNA utilizing the nascent DNA strand or the parental strand as a template.

Formation of DNA triplexes accounts for arrests of DNA synthesis at d(TC)n and d(GA)n tracts.

  • N. BaranA. LapidotH. Manor
  • Chemistry, Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1991
TLDR
To study the mechanism of arrest of DNA synthesis at d(TC)n and d(GA)n sequences, single-stranded DNA molecules used as templates for in vitro assays of complementary DNA synthesis performed by extension of a primer with the Klenow polymerase or the Taq polymerase (Thermus aquaticus DNA polymerase).

Cloning, Characterization, and Properties of Seven Triplet Repeat DNA Sequences*

TLDR
Novel cloning strategies with chemically synthesized oligonucleotides to clone seven of the triplet repeat sequences and a model to explain the reduction in mRNA abundance in Friedreich's ataxia based on intermolecular triplex formation is proposed.

Preferential DNA secondary structure mutagenesis in the lagging strand of replication in E. coli

TLDR
The results suggest that replication-dependent deletion between direct repeats may occur preferentially in the lagging strand, and this design of a palindromic fragment to create an 'asymmetric palINDromic insert' in the chloram-phenicol acetyltransferase gene of plasmid pBR325 is reported.
...