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Related Concept Videos

Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...
Translesion DNA Polymerases02:10

Translesion DNA Polymerases

Translesion (TLS) polymerases rescue stalled DNA polymerases at sites of damaged bases by replacing the replicative polymerase and installing a nucleotide across the damaged site. Doing so, TLS allows additional time for the cell to repair the damage before resuming regular DNA replication.
TLS polymerases are found in all three domains of life - archaea, bacteria, and eukaryotes. Of the different classes of TLS polymerases, members of the Y family are fitted with specialized structures that...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Telomeres and Telomerase02:41

Telomeres and Telomerase

In eukaryotic DNA replication, a single-stranded DNA fragment remains at the end of a chromosome after the removal of the final primer. This section of DNA cannot be replicated in the same manner as the rest of the strand because there is no 3’ end to which the newly synthesized DNA can attach. This non-replicated fragment results in gradual loss of the chromosomal DNA during each cell duplication. Additionally, it can induce a DNA damage response by enzymes that recognize single-stranded DNA.
The DNA Replication Fork01:02

The DNA Replication Fork

An organism’s genome needs to be duplicated in an efficient and error-free manner for its growth and survival. The replication fork is a Y-shaped active region where two strands of DNA are separated and replicated continuously. The coupling of DNA unzipping and complementary strand synthesis is a characteristic feature of a replication fork.   Organisms with small circular DNA, such as E. coli, often have a single origin of replication; therefore, they have only two replication forks, one in...

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Related Experiment Video

Updated: May 26, 2026

DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling
08:04

DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling

Published on: October 8, 2019

Structural basis for sequence-specific recognition of DNA by TAL effectors.

Dong Deng1, Chuangye Yan, Xiaojing Pan

  • 1State Key Laboratory of Bio-Membrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China.

Science (New York, N.Y.)
|January 7, 2012
PubMed
Summary

Transcription activator-like (TAL) effectors bind DNA using repeat domains. Crystal structures reveal how TAL effectors recognize specific DNA sequences via their repeat variable diresidues (RVDs), aiding protein design.

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Determination of the Optimal Chromosomal Location(s) for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach
11:12

Determination of the Optimal Chromosomal Location(s) for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach

Published on: September 11, 2017

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Last Updated: May 26, 2026

DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling
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Published on: October 8, 2019

Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids
09:04

Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids

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Determination of the Optimal Chromosomal Location(s) for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach
11:12

Determination of the Optimal Chromosomal Location(s) for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach

Published on: September 11, 2017

Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biochemistry

Background:

  • Transcription activator-like (TAL) effectors are proteins secreted by phytopathogenic bacteria.
  • These effectors recognize specific host DNA sequences to modulate gene expression.
  • TAL effectors possess a central domain composed of tandem repeats, each targeting a DNA base pair via hypervariable residues (RVDs).

Purpose of the Study:

  • To elucidate the structural basis of DNA recognition by TAL effectors.
  • To determine the crystal structures of a TAL effector in both DNA-free and DNA-bound states.
  • To understand the role of RVDs in sequence-specific DNA binding.

Main Methods:

  • X-ray crystallography was employed to obtain high-resolution structures.
  • An 11.5-repeat TAL effector was studied in its apo (DNA-free) and holo (DNA-bound) forms.
  • Structural analysis focused on the repeat architecture and RVD interactions within the DNA major groove.

Main Results:

  • The crystal structures revealed that each TAL repeat consists of two helices and an RVD-containing loop.
  • An 11.5-repeat TAL effector forms a right-handed superhelical structure that binds along the DNA sense strand.
  • Repeat variable diresidues (RVDs) are positioned in the DNA major groove, with the 13th residue mediating base-specific contacts.

Conclusions:

  • The study provides detailed structural insights into the DNA recognition mechanism of TAL effectors.
  • Understanding TAL effector-DNA interactions is crucial for deciphering bacterial pathogenesis.
  • These findings may enable the rational design of novel DNA-binding proteins for biotechnological applications.