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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...
Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to  N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis pathway,...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...

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

Published on: September 21, 2017

TATA binding proteins can recognize nontraditional DNA sequences.

Sunmin Ahn1, Chia-Ling Huang, Emre Ozkumur

  • 1Department of Biomedical Engineering, Boston University, Boston, MA, USA.

Biophysical Journal
|October 16, 2012
PubMed
Summary
This summary is machine-generated.

TATA binding protein (TBP) binds strongly to single-stranded DNA, particularly polythymine (poly-T) stretches, not just TATA boxes. This discovery, using novel optical technology, reveals poly-T

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Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids
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DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling
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DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling

Published on: October 8, 2019

Area of Science:

  • Molecular Biology
  • Biophysics
  • Genomics

Background:

  • Receptor-ligand interactions are crucial in biological processes.
  • TATA binding protein (TBP) is a key transcription factor.
  • Understanding TBP's DNA binding is essential for gene regulation studies.

Purpose of the Study:

  • To develop and apply a label-free optical technology for high-throughput receptor-ligand interaction studies.
  • To investigate the binding activity of TBP with single-stranded and double-stranded DNA, including polythymine (poly-T) stretches.
  • To correlate TBP binding with DNA length and analyze its prevalence in human promoters.

Main Methods:

  • Development of a quantitative, label-free optical technology for microarray analysis.
  • Preparation of single-stranded and double-stranded DNA microarrays.
  • TBP binding assays using microarrays, gel electrophoresis, and computational genome analysis.

Main Results:

  • TBP exhibits strong binding to single-stranded DNA, especially polythymine (poly-T) sequences, in addition to TATA boxes.
  • TBP binding increases over 7-fold with increasing oligomer length from 9 to 40 nucleotides.
  • Genome-wide analysis reveals that 35.5% of human promoters contain poly-T stretches.

Conclusions:

  • TBP's interaction with poly-T stretches is significant and previously unreported.
  • The novel optical technology enables accurate, high-throughput analysis of molecular interactions.
  • The prevalence of poly-T stretches in promoters suggests a broader role for TBP in gene regulation.