(Q34688459)

English

The genome-wide distribution of non-B DNA motifs is shaped by operon structure and suggests the transcriptional importance of non-B DNA structures in Escherichia coli

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scholarly article

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

The genome-wide distribution of non-B DNA motifs is shaped by operon structure and suggests the transcriptional importance of non-B DNA structures in Escherichia coli (English)

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

Escherichia coli

1 reference

based on heuristic

inferred from title

Teresa M. Przytycka

object named as

Teresa M Przytycka

6

0 references

4

object named as

David Levens

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

author name string

Xiangjun Du

1

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

Damian Wojtowicz

2

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

Albert A Bowers

3

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

Craig J Benham

5

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

language of work or name

0 references

publication date

25 April 2013

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

number of pages

13

1 reference

based on heuristic

inferred from page(s)

Nucleic Acids Research

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

41

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

12

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

5965-5977

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

Mitochondrial DNA deletions are associated with non-B DNA conformations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

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Theoretical analysis of competing conformational transitions in superhelical DNA.

1 reference

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Cruciform structures are a common DNA feature important for regulating biological processes.

1 reference

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7 July 2018

A dynamic programming algorithm for identification of triplex-forming sequences

1 reference

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7 July 2018

DNA stress and strain, in silico, in vitro and in vivo

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

G4 motifs correlate with promoter-proximal transcriptional pausing in human genes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Theoretical analysis of the stress induced B-Z transition in superhelical DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Database resources of the National Center for Biotechnology Information

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

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RNA G-Quadruplexes in the model plant species Arabidopsis thaliana: prevalence and possible functional roles

1 reference

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7 July 2018

G-Quadruplex DNA Sequences Are Evolutionarily Conserved and Associated with Distinct Genomic Features in Saccharomyces cerevisiae

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

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The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome

1 reference

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Altered gene expression in the Werner and Bloom syndromes is associated with sequences having G-quadruplex forming potential

1 reference

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The role of supercoiling in transcriptional control of MYC and its importance in molecular therapeutics

1 reference

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7 July 2018

Genome-wide colonization of gene regulatory elements by G4 DNA motifs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Genome-wide analysis of a G-quadruplex-specific single-chain antibody that regulates gene expression

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Non-B DNA structure-induced genetic instability and evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Rho directs widespread termination of intragenic and stable RNA transcription.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

G-quadruplex structures: in vivo evidence and function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

The importance of negative superhelicity in inducing the formation of G-quadruplex and i-motif structures in the c-Myc promoter: implications for drug targeting and control of gene expression

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

A Z-DNA sequence reduces slipped-strand structure formation in the myotonic dystrophy type 2 (CCTG) x (CAGG) repeat

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Evidence of genome-wide G4 DNA-mediated gene expression in human cancer cells.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Discovery of the role of non-B DNA structures in mutagenesis and human genomic disorders

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Termination factor Rho and its cofactors NusA and NusG silence foreign DNA in E. coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Structures, folding patterns, and functions of intramolecular DNA G-quadruplexes found in eukaryotic promoter regions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

DNA triple helices: biological consequences and therapeutic potential

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Superhelical destabilization in regulatory regions of stress response genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Genome-wide analysis reveals regulatory role of G4 DNA in gene transcription

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Genomic distribution and functional analyses of potential G-quadruplex-forming sequences in Saccharomyces cerevisiae.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Discovery of alternative DNA structures: a heroic decade (1979-1989).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Phylogenomic analysis of the emergence of GC-rich transcription elements

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Slipped strand DNA structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Non-B DNA conformations, mutagenesis and disease

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Z-DNA, an active element in the genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Supercoil-driven DNA structures regulate genetic transactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

G-quadruplexes in promoters throughout the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Genome-wide prediction of G4 DNA as regulatory motifs: role in Escherichia coli global regulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

SIDDBASE: a database containing the stress-induced DNA duplex destabilization (SIDD) profiles of complete microbial genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Prevalence of quadruplexes in the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Highly prevalent putative quadruplex sequence motifs in human DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

DNA supercoiling - a global transcriptional regulator for enterobacterial growth?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

The dynamic response of upstream DNA to transcription-generated torsional stress

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Inverted repeat structure of the human genome: the X-chromosome contains a preponderance of large, highly homologous inverted repeats that contain testes genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Stress-induced DNA duplex destabilization (SIDD) in the E. coli genome: SIDD sites are closely associated with promoters

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Genetical Implications of the Structure of Deoxyribonucleic Acid

2 references

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7 July 2018

https://pubmed.ncbi.nlm.nih.gov/23620297

12 December 2020

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Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Timeline: Z-DNA: the long road to biological function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Z-DNA-binding proteins can act as potent effectors of gene expression in vivo

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

DNA topology-mediated control of global gene expression in Escherichia coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Potent stimulation of transcription-coupled DNA supercoiling by sequence-specific DNA-binding proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

DNA supercoiling-dependent transcriptional coupling between the divergently transcribed promoters of the ilvYC operon of Escherichia coli is proportional to promoter strengths and transcript lengths

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Loss of FBP function arrests cellular proliferation and extinguishes c-myc expression

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Simple sequence repeats in Escherichia coli: abundance, distribution, composition, and polymorphism

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

DNA structure and transcription

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Inhibition of DNA supercoiling-dependent transcriptional activation by a distant B-DNA to Z-DNA transition

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Tandem repeats finder: a program to analyze DNA sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Multiple single-stranded cis elements are associated with activated chromatin of the human c-myc gene in vivo

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Sites of predicted stress-induced DNA duplex destabilization occur preferentially at regulatory loci

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Occurrence of potential cruciform and H-DNA forming sequences in genomic DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Transcription termination at intrinsic terminators: the role of the RNA hairpin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

A novel repeated element with Z-DNA-forming potential is widely found in evolutionarily diverse eukaryotic genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

The chemistry and biology of left-handed Z-DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Compilation and analysis ofEscherichia colipromoter DNA sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Unusual DNA structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Ribonucleoprotein and protein factors bind to an H-DNA-forming c-myc DNA element: possible regulators of the c-myc gene.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

A cis-acting transcription element of the c-myc gene can assume an H-DNA conformation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

An E. coli promoter that regulates transcription by DNA superhelix-induced cruciform extrusion

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Local supercoil-stabilized DNA structures

1 reference

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7 July 2018

Mapping Z-DNA in the human genome. Computer-aided mapping reveals a nonrandom distribution of potential Z-DNA-forming sequences in human genes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Transcription of human c-myc in permeabilized nuclei is associated with formation of Z-DNA in three discrete regions of the gene

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

7 July 2018

Genome-wide computational and expression analyses reveal G-quadruplex DNA motifs as conserved cis-regulatory elements in human and related species.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

26 October 2018

The functional response of upstream DNA to dynamic supercoiling in vivo

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

26 October 2018

A long purine-pyrimidine homopolymer acts as a transcriptional diode

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

26 October 2018

Conformation of promoter DNA: Fine mapping of S1-hypersensitive sites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695496

26 October 2018

Demonstration of ligand decoration, and ligand-induced perturbation, of G-quadruplexes in a plasmid using atomic force microscopy

1 reference

https://pubmed.ncbi.nlm.nih.gov/23620297

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Enrichment of G4 DNA motif in transcriptional regulatory region of chicken genome

1 reference

https://pubmed.ncbi.nlm.nih.gov/23620297

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1093/NAR/GKT308

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

ResearchGate publication ID

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