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Related Concept Videos

RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

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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...
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Sanger Sequencing01:57

Sanger Sequencing

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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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Conserved Binding Sites01:49

Conserved Binding Sites

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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.
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Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

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In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
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DNA as a Genetic Template02:05

DNA as a Genetic Template

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Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
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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

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Spec-seq: determining protein-DNA-binding specificity by sequencing.

Gary D Stormo, Zheng Zuo, Yiming Kenny Chang

    Briefings in Functional Genomics
    |November 2, 2014
    PubMed
    Summary
    This summary is machine-generated.

    This study introduces a straightforward sequencing method to precisely measure protein-DNA interactions. This technique accurately determines binding specificities, enhancing our understanding of gene regulation and protein recognition.

    Keywords:
    protein–DNA interactionspecificitytranscription factors

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    Area of Science:

    • Molecular Biology
    • Genomics
    • Biochemistry

    Background:

    • Understanding protein-DNA interactions is crucial for deciphering gene regulation.
    • Current methods for assessing binding specificity can be complex and costly.

    Purpose of the Study:

    • To develop and validate a direct, accurate, and cost-effective method for determining protein-DNA binding specificity.
    • To enable the assessment and development of predictive models for DNA-binding sites.

    Main Methods:

    • Assaying bound and unbound DNA fractions using high-throughput sequencing in a standard binding reaction.
    • Analyzing sequence data to quantify binding affinities and specificities.
    • Applying the method to study individual factor binding and cooperative binding of multiple factors.

    Main Results:

    • The sequencing-based method provides high accuracy for thousands of sequences in parallel.
    • The approach allows for the evaluation of existing models (e.g., position weight matrices) and the development of more complex predictive models.
    • New insights into the binding of the lac repressor were obtained.

    Conclusions:

    • This method offers a powerful tool for characterizing protein-DNA interactions and their specificity.
    • It facilitates a deeper understanding of molecular recognition mechanisms in DNA binding.
    • The technique is versatile and applicable to studying complex regulatory networks involving multiple DNA-binding proteins.