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Related Concept Videos

Labeling DNA Probes03:31

Labeling DNA Probes

DNA probes are fragments of DNA labeled with a reporter tag to enable their detection or purification. The resulting labeled DNA probes can then hybridize to target nucleic acid sequences through complementary base-pairing, and may be used to recover or identify these regions.
Radioisotopes, fluorophores, or small molecule binding partners like biotin or digoxigenin, are the most widely used reporter tags for labeling DNA probes. These labels can be attached to the probe DNA molecule via...
Nucleic Acid Structure01:25

Nucleic Acid Structure

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.
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Sanger Sequencing01:57

Sanger Sequencing

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...
Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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Although all next-generation methods use different technologies, they all share a set of standard features.
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

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
The...
RNA-seq03:21

RNA-seq

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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Split Hybridization Probe Utilizing a DNA Fluorescent Light-up Aptamer as a Signal Reporter for Sequence-Specific Nucleic Acid Analysis
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Nucleic acid structure and sequence probing using fluorescent base analogue tC(O).

Karl Börjesson1, Peter Sandin, L Marcus Wilhelmsson

  • 1Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.

Biophysical Chemistry
|October 31, 2008
PubMed
Summary

The fluorescent probe tC(O) offers a novel method for analyzing nucleic acid structures. It accurately detects individual melting processes and structural features like bulges and loops.

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Kinetic Screening of Nuclease Activity using Nucleic Acid Probes
06:52

Kinetic Screening of Nuclease Activity using Nucleic Acid Probes

Published on: November 1, 2019

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Biophysical Chemistry

Background:

  • Nucleic acid structures exhibit complex secondary motifs crucial for function.
  • Conventional methods like UV-melting lack the resolution to analyze individual transitions in complex systems.
  • Fluorescent probes offer potential for high-resolution analysis of nucleic acid structures.

Purpose of the Study:

  • To present the fluorescent cytosine analog tC(O) as a superior local probe for nucleic acid systems.
  • To demonstrate the utility of tC(O) in detecting individual melting processes of complex nucleic acid structures.
  • To showcase tC(O)'s capability in identifying structural anomalies such as bulges and loops and distinguishing base-pair mismatches.

Main Methods:

  • Synthesis and characterization of the fluorescent cytosine analog tC(O).
  • Application of tC(O) as a fluorescent probe in various nucleic acid systems.
  • Comparative analysis with conventional UV-melting techniques.

Main Results:

  • tC(O) is identified as the brightest fluorescent probe of its kind, with minimal impact on DNA secondary structure.
  • tC(O) successfully detects individual melting processes in complex nucleic acid structures, overcoming limitations of global UV-melting analysis.
  • The probe effectively identifies bulges and loops in nucleic acids.
  • tC(O) can differentiate between matched and mismatched base pairs.

Conclusions:

  • tC(O) provides a new, high-resolution method for characterizing complex nucleic acid structures.
  • Its sensitivity to individual melting transitions and structural features makes it invaluable for nucleic acid research.
  • tC(O) advances the study of nucleic acid dynamics and fidelity.