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Nucleic Acid Structure01:25

Nucleic Acid Structure

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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
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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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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RNA Interference01:23

RNA Interference

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RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
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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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RNA Structure01:19

RNA Structure

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The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. 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) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
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Riboswitches01:56

Riboswitches

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Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...
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Related Experiment Video

Updated: Mar 7, 2026

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

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Cell-SELEX Identifies a "Sticky" RNA Aptamer Sequence.

Partha Ray1, Rebekah R White1

  • 1Department of Surgery, UC San Diego School of Medicine, La Jolla, CA, USA; Department of Surgery, Duke University School of Medicine, Durham, NC, USA.

Journal of Nucleic Acids
|February 15, 2017
PubMed
Summary
This summary is machine-generated.

Researchers used cell-SELEX to find aptamers that enter cells. A common RNA sequence was identified, but it binds to a general surface protein, not specific cancer targets.

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Area of Science:

  • Biotechnology
  • Molecular Biology
  • Cancer Research

Background:

  • Systematic Evolution of Ligands by Exponential Enrichment (Cell-SELEX) is a method for aptamer discovery.
  • Aptamers are short nucleic acid sequences with high specificity for their targets.
  • Cell-internalizing aptamers offer potential for targeted drug delivery and diagnostics.

Purpose of the Study:

  • To select for cell-internalizing aptamers using a modified cell-SELEX approach.
  • To identify specific aptamer sequences that internalize into pancreatic cancer cells.
  • To investigate the target binding characteristics of selected aptamers.

Main Methods:

  • Cell-SELEX was performed on pancreatic cancer cell lines.
  • RNAse treatment was introduced as an additional selection pressure to eliminate surface-binding aptamers.
  • Independent selection rounds were conducted to identify common aptamer sequences.

Main Results:

  • A common RNA sequence was consistently identified across independent cell-SELEX experiments.
  • This identified aptamer sequence demonstrated non-specific binding to pancreatic cancer cell lines.
  • The aptamer sequence appears to bind a highly abundant or high-affinity surface protein, not a cancer-specific target.

Conclusions:

  • The identified aptamer sequence is not specific to pancreatic cancer cells.
  • A common structural motif suggests binding to a broadly expressed surface protein.
  • Removing this non-specific sequence during cell-SELEX could improve the selection of cell type-specific aptamers.