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Related Concept Videos

RNA Structure01:23

RNA Structure

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Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
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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...
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Sequences01:29

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Sequences are fundamental mathematical objects consisting of ordered lists of numbers that follow a specific rule or pattern. Sequences are critical in various mathematical concepts, including calculus, series, and number theory. They can model real-world phenomena such as population growth, financial investments, and physical processes like the diminishing height of a bouncing ball.Each number in a sequence is referred to as a term. Typically, the terms are denoted as a1, a2, a3,…, where...
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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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Arithmetic Sequences01:30

Arithmetic Sequences

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An arithmetic sequence is a structured arrangement of numbers where each term is derived by adding a constant value, known as the common difference, to the previous term. This consistent pattern allows for the efficient computation of any term within the sequence as well as the cumulative sum of multiple terms. The formula for finding the nth term of an arithmetic sequence is:Here, aₙ represents the nth term of the sequence, a is the first term, d is the common difference, and n is the...
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Isolation of Adult Spinal Cord Nuclei for Massively Parallel Single-nucleus RNA Sequencing
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Isolation of Adult Spinal Cord Nuclei for Massively Parallel Single-nucleus RNA Sequencing

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Linking RNA Sequence, Structure, and Function on Massively Parallel High-Throughput Sequencers.

Sarah K Denny1, William J Greenleaf1,2,3

  • 1Stanford University Department of Genetics, Stanford, California 94305.

Cold Spring Harbor Perspectives in Biology
|October 17, 2018
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Summary
This summary is machine-generated.

New sequencing methods quantify RNA folding and interactions at scale. This approach measures RNA thermodynamics and kinetics, advancing our understanding of RNA sequence, structure, and function relationships.

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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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Area of Science:

  • Molecular Biology
  • Biophysics
  • Genomics

Background:

  • High-throughput sequencing has advanced RNA and RNA-protein interaction cataloging.
  • The complex interplay between RNA sequence, structure, and function necessitates quantitative measurement methods.
  • Current methods struggle to match the scale of RNA sequence diversity for thermodynamic and kinetic analysis.

Purpose of the Study:

  • To present a class of methods extending DNA sequencer functionality for high-throughput RNA analysis.
  • To enable quantitative thermodynamic and kinetic measurements of RNA folding and interactions.
  • To explore applications in RNA-binding proteins, riboswitches, and RNA tertiary structure.

Main Methods:

  • Leveraging core DNA sequencing technology for RNA analysis.
  • Developing high-throughput assays for RNA folding.
  • Implementing methods for measuring RNA-protein interactions at scale.

Main Results:

  • Demonstrated extension of DNA sequencer capabilities to RNA.
  • Enabled high-throughput measurement of RNA folding and RNA-protein interactions.
  • Provided insights into RNA tertiary structure energetics and riboswitch engineering.

Conclusions:

  • This method provides a scalable approach to study RNA thermodynamics and kinetics.
  • It facilitates a deeper understanding of RNA sequence-structure-function relationships.
  • The technology has broad applications in molecular biology and biotechnology.