scholarly journals Telomere DNA G-quadruplex folding within actively extending human telomerase

2018 ◽  
Author(s):  
Linnea I. Jansson ◽  
Joseph W. Parks ◽  
Jendrik Hentschel ◽  
Terren R. Chang ◽  
Rishika Baral ◽  
...  
Keyword(s):  
Single Molecule ◽  
Time Series Data ◽  
Series Data ◽  
Dna Repeats ◽  
Repeat Sequences ◽  
Dna Repeat ◽  
G Quadruplex ◽  
Dna Repeat Sequences ◽  
Dna Primers

ABSTRACTTelomerase maintains telomere length by reverse transcribing short G-rich DNA repeat sequences from its internal RNA template. G-rich telomere DNA repeats readily fold into G-quadruplex (GQ) structures in vitro, and the presence of GQ-prone sequences throughout the genome introduces challenges to replication in vivo. Using a combination of ensemble and single-molecule telomerase assays we discovered that GQ folding of the nascent DNA product during processive addition of multiple telomere repeats modulates the kinetics of telomerase catalysis and dissociation. Telomerase reactions performed with telomere DNA primers of varying sequence or using K+ versus Li+ salts yield changes in DNA product profiles consistent with formation of GQ structure within the telomerase-DNA complex. Single-molecule FRET experiments reveal complex DNA structural dynamics during real-time catalysis, supporting the notion of nascent product folding within the active telomerase complex. To explain the observed distributions of telomere products, we fit telomerase time series data to a global kinetic model that converges to a unique set of rate constants describing each successive telomere repeat addition cycle. Our results highlight the potential influence of the intrinsic folding properties of telomere DNA during telomerase catalysis and provide a detailed characterization of GQ modulation of polymerase function.SIGNIFICANCETelomeres protect the ends of linear chromosomes from illicit DNA processing events that can threaten genome stability. Telomere structure is built upon repetitive G-rich DNA repeat sequences that have the ability to fold into stable secondary structures called G-quadruplexes (GQs). In rapidly dividing cells, including the majority of human cancers, telomeres are maintained by the specialized telomerase enzyme. Thus, telomerase and its telomere DNA substrates represent important targets for developing novel cancer drugs. In this work, we provide evidence for GQ folding within the newly synthesized DNA product of an actively extending telomerase enzyme. Our results highlight the delicate interplay between the structural properties of telomere DNA and telomerase function.

scholarly journals Telomere DNA G-quadruplex folding within actively extending human telomerase

2019 ◽  
Vol 116 (19) ◽  
pp. 9350-9359 ◽  
Author(s):  
Linnea I. Jansson ◽  
Jendrik Hentschel ◽  
Joseph W. Parks ◽  
Terren R. Chang ◽  
Cheng Lu ◽  
...  
Keyword(s):  
Single Molecule ◽  
Time Series Data ◽  
Resonance Energy ◽  
Series Data ◽  
Dna Repeats ◽  
Telomere Repeat ◽  
G Quadruplex ◽  
Dna Primers

Telomerase reverse transcribes short guanine (G)-rich DNA repeat sequences from its internal RNA template to maintain telomere length. G-rich telomere DNA repeats readily fold into G-quadruplex (GQ) structures in vitro, and the presence of GQ-prone sequences throughout the genome introduces challenges to replication in vivo. Using a combination of ensemble and single-molecule telomerase assays, we discovered that GQ folding of the nascent DNA product during processive addition of multiple telomere repeats modulates the kinetics of telomerase catalysis and dissociation. Telomerase reactions performed with telomere DNA primers of varying sequence or using GQ-stabilizing K+ versus GQ-destabilizing Li+ salts yielded changes in DNA product profiles consistent with formation of GQ structures within the telomerase–DNA complex. Addition of the telomerase processivity factor POT1–TPP1 altered the DNA product profile, but was not sufficient to recover full activity in the presence of Li+ cations. This result suggests GQ folding synergizes with POT1–TPP1 to support telomerase function. Single-molecule Förster resonance energy transfer experiments reveal complex DNA structural dynamics during real-time catalysis in the presence of K+ but not Li+, supporting the notion of nascent product folding within the active telomerase complex. To explain the observed distributions of telomere products, we globally fit telomerase time-series data to a kinetic model that converges to a set of rate constants describing each successive telomere repeat addition cycle. Our results highlight the potential influence of the intrinsic folding properties of telomere DNA during telomerase catalysis, and provide a detailed characterization of GQ modulation of polymerase function.

scholarly journals Survey of genomic repeat sequence-PCRs that detect differences between inbred mouse strains

1995 ◽  
Vol 65 (2) ◽  
pp. 151-155 ◽  
Author(s):  
Philip A. Wood ◽  
Doug A. Hamm
Keyword(s):  
Genomic Dna ◽  
Inbred Mouse ◽  
Pcr Amplification ◽  
Repeat Sequence ◽  
Mouse Strains ◽  
Repeat Sequences ◽  
Dna Repeat ◽  
Polymerase Chain ◽  
Dna Repeat Sequences ◽  
Congenic Mouse Strains

SummaryWe have developed molecular markers that distinguish between several inbred and congenic mouse strains using polymerase chain reaction (PCR) amplification of genomic DNA repeat sequences. Mouse genomic DNA, digested with four base recognition site-restriction endonucleases, was amplified by PCR using primers for the following repeat sequences: Bl (Alu homolog), LINE, LLR3, IAP, human Alu and myoglobin. Amplification products analysed by agarose gel electrophoresis and stained with ethidium bromide produced unique DNA fragments, some of which are specific for each of 12 strains tested. This method can be used for molecular analysis of the mouse genome, including genetic monitoring.

scholarly journals Tutorial: Investigating SARS-CoV-2 evolution and phylogeny using MNHN-Tree-Tools

2021 ◽  
Author(s):  
Thomas Haschka
Keyword(s):  
Global Economy ◽  
Scientific Community ◽  
High Performance ◽  
Daily Life ◽  
Repeat Sequences ◽  
Dna Repeat ◽  
Versatile Tool ◽  
Dna Repeat Sequences

The Covid-19 pandemic has caused at more than 3 million deaths by Mai this year. It had a significant impact on the daily life and the global economy. The virus has since its first recorded outbreak in China mutated into new strains. The Nextstrain project has so far been monitoring the evolution of the virus. At the same time we were developing in our lab the MNHN-Tree-Tools toolkit, primarily for the investigation of DNA repeat sequences. We have further extended MNHN-Tree-Tools to guide phylogenetics. As such the toolkit has evolved into a high performance code, allowing for a fast investigation of millions of sequences. Given the context of the pandemic it became evident that we will use our versatile tool to investigate the evolution of SARS-CoV-2 sequences. Our efforts have cumulated in this tutorial that we share with the scientific community.

scholarly journals MICROSATELLITE INSTABILITY TESTING'S BENEFITS IN A VARIETY OF CANCERS

2021 ◽  
Vol 8 (8) ◽  
pp. 1-5
Keyword(s):  
Microsatellite Instability ◽  
Cancer Diagnosis ◽  
Detection Method ◽  
Treatment Options ◽  
Genetic Change ◽  
Repeat Sequences ◽  
Dna Repeat ◽  
Dna Repeat Sequences

The accumulation of mutations across the genome, notably in microsatellite (MS) DNA repeat sequences, is a hallmark of MSI/dMMR tumors. Microsatellite instability (MSI) is a genetic change in which microsatellites, which typically have one to six nucleotide repetitions, acquire mutations corresponding to small nucleotide deletions or insertions. Immunohistochemistry or a PCR-based test directed against a set of five MS areas were used to create an MSI detection method. MSI is a significant biomarker for cancer diagnosis, prognosis, and treatment options.

scholarly journals Characterization of Flowering Genes of Arabidopsis thaliana for Mirror Repeats

2021 ◽  
Vol 12 (3) ◽  
pp. 2852-2861
Keyword(s):  
Arabidopsis Thaliana ◽  
Genetic Diseases ◽  
Dna Repeats ◽  
Quick Method ◽  
Flowering Genes ◽  
Repeat Sequences ◽  
Mutational Hotspots ◽  
And Function

A variety of simple DNA repeats are enriched in the eukaryotic genomes. Recent studies have proven their importance in understanding genome organization and function, especially how genomes evolve using them as mutational hotspots during DNA replication. Mirror repeat sequences, the most underrated subset of this class of repeats, are now gaining importance because of their probable involvement in developing several genetic diseases in humans. These repeats typically adopt H-DNA conformations in both in-vitro and in-vivo conditions. On the other end, plants were still not analyzed for their presence or distribution and whether they are responsible for causing diseases in them or not. The present study aims to extract mirror repeats in the flowering genes of Arabidopsis thaliana. To this end, we have deployed FPCB (FASTA-PARALLEL COMPLEMENT-BLAST), an efficacious and quick method to extract perfect and degenerate mirror repeat sequences through pattern matching of alignments with user-defined algorithmic parameters. All the analyzed genes were reported to have quite high densities of mirror sequences. A total of 93 unique mirror repeats of significant lengths were extracted in the analyzed genes.

scholarly journals Role of Hfq in Genome Evolution: Instability of G-Quadruplex Sequences in E. coli

2019 ◽  
Vol 8 (1) ◽  
pp. 28 ◽  
Author(s):  
Virali J. Parekh ◽  
Brittany A. Niccum ◽  
Rachna Shah ◽  
Marisa A. Rivera ◽  
Mark J. Novak ◽  
...  
Keyword(s):  
Genomic Instability ◽  
Dna Repeats ◽  
Loop Formation ◽  
Bacterial Gene ◽  
Quadruplex Dna ◽  
E Coli ◽  
Alternative Structures ◽  
Bacterial Gene Expression ◽  
G Quadruplex

Certain G-rich DNA repeats can form quadruplex in bacterial chromatin that can present blocks to DNA replication and, if not properly resolved, may lead to mutations. To understand the participation of quadruplex DNA in genomic instability in Escherichia coli (E. coli), mutation rates were measured for quadruplex-forming DNA repeats, including (G3T)4, (G3T)8, and a RET oncogene sequence, cloned as the template or nontemplate strand. We evidence that these alternative structures strongly influence mutagenesis rates. Precisely, our results suggest that G-quadruplexes form in E. coli cells, especially during transcription when the G-rich strand can be displaced by R-loop formation. Structure formation may then facilitate replication misalignment, presumably associated with replication fork blockage, promoting genomic instability. Furthermore, our results also evidence that the nucleoid-associated protein Hfq is involved in the genetic instability associated with these sequences. Hfq binds and stabilizes G-quadruplex structure in vitro and likely in cells. Collectively, our results thus implicate quadruplexes structures and Hfq nucleoid protein in the potential for genetic change that may drive evolution or alterations of bacterial gene expression.

DNA repeat sequences: diversity and versatility of functions

2016 ◽  
Vol 63 (3) ◽  
pp. 411-416 ◽  
Author(s):  
Zhong Qian ◽  
Sankar Adhya
Keyword(s):  
Repeat Sequences ◽  
Dna Repeat ◽  
Dna Repeat Sequences
Sign in / Sign up

Export Citation Format

Share Document