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Related Concept Videos

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...
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.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Southern Blot02:57

Southern Blot

Agarose gel electrophoresis is very useful in separating DNA fragments by size. Running a DNA ladder containing fragments of the known length alongside the sample helps determine the approximate length of the sample DNA fragments. However, additional steps are needed to verify the sequence identity of the sample DNA fragments.
Denatured DNA fragments must be transferred onto a carrier membrane from the gel to make it accessible to a probe - a small ssDNA fragment complementary to the target DNA...
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...
Aliasing01:18

Aliasing

Accurate signal sampling and reconstruction are crucial in various signal-processing applications. A time-domain signal's spectrum can be revealed using its Fourier transform. When this signal is sampled at a specific frequency, it results in multiple scaled replicas of the original spectrum in the frequency domain. The spacing of these replicas is determined by the sampling frequency.
If the sampling frequency is below the Nyquist rate, these replicas overlap, preventing the original signal...
¹H NMR: Interpreting Distorted and Overlapping Signals01:02

¹H NMR: Interpreting Distorted and Overlapping Signals

Spin systems where the difference in chemical shifts of the coupled nuclei is greater than ten times J are called first-order spin systems. These nuclei are weakly coupled, and their chemical shifts and coupling constant can generally be estimated from the well-separated signals in the spectrum.
As Δν decreases and the signals move closer, the doublets appear increasingly distorted. The intensities of the inner lines increase at the cost of those of the outer lines as the signals are slanted or...

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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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Sequencing-by-hybridization revisited: the analog-spectrum proposal.

Franco P Preparata1

  • 1Computer Science Department, Brown University, 115 Waterman Street, Providence, RI 02912-1910, USA. franco@cs.brown.edu

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|October 20, 2006
PubMed
Summary

This study introduces an analog-spectrum model for DNA sequencing by hybridization (SBH), moving beyond unrealistic digital models. This new approach enhances sequence reconstruction accuracy by better reflecting biochemical hybridization realities.

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Area of Science:

  • Biotechnology
  • Bioinformatics
  • Genomics

Background:

  • Current DNA sequencing by hybridization (SBH) relies on a digital-spectrum model for sequence reconstruction.
  • This digital model is biochemically unrealistic and limits the performance of SBH, especially with gapped probing patterns.
  • Existing methods face algorithmic failure due to fooling probes and densely populated spectra, limiting reconstructible sequence length.

Purpose of the Study:

  • To propose a novel analog-spectrum model for DNA sequencing by hybridization (SBH) that more accurately reflects biochemical processes.
  • To reestablish probe length as the primary performance-governing factor in SBH.
  • To introduce semidegenerate bases as improved emulators for universal bases in SBH.

Main Methods:

  • Developed a theoretical analog-spectrum model to simulate biochemical hybridization more realistically.
  • Introduced semidegenerate bases to enhance probe capabilities.
  • Analyzed the performance implications of the analog-spectrum model compared to the conventional digital-spectrum model.

Main Results:

  • The analog-spectrum model provides a more biochemically accurate representation of hybridization.
  • Probe length is reconfirmed as a critical factor for performance in the proposed model.
  • Semidegenerate bases offer a potential improvement over current universal bases for SBH.

Conclusions:

  • The proposed analog-spectrum model offers a more realistic framework for DNA sequencing by hybridization.
  • Accurate biochemical measurements are crucial for the success of SBH.
  • This theoretical work provides a foundation for future biotechnological advancements in SBH.