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Related Concept Videos

DNA as a Genetic Template02:05

DNA as a Genetic Template

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...
DNA as a Genetic Template02:05

DNA as a Genetic Template

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...
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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Structure of a Gene01:30

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A gene is the fundamental unit of heredity. Every individual has two copies of each gene, one inherited from each parent. Although most people contain the same genes, there is a small fraction that is slightly different amongst people. A gene with a small difference in its sequence of DNA bases forms different alleles, contributing to different phenotypes.
However, only 1% of the DNA is composed of genes that encode proteins; the rest, 99% is non-coding DNA. This non-coding DNA performs...
Synthetic Biology02:55

Synthetic Biology

Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
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Analyzing and Building Nucleic Acid Structures with 3DNA
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Modeling structure-function relationships in synthetic DNA sequences using attribute grammars.

Yizhi Cai1, Matthew W Lux, Laura Adam

  • 1Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America.

Plos Computational Biology
|October 10, 2009
PubMed
Summary
This summary is machine-generated.

Attribute grammars formally link DNA sequences to biological functions. This computational approach enables precise modeling of genetic parts and their functions in synthetic biology.

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Area of Science:

  • Synthetic biology
  • Computational biology
  • Genetics

Background:

  • The concept of genetic parts offers finer granularity than traditional genes.
  • A formal method to relate genetic parts to biological functions is currently lacking.
  • Synthetic biology requires and can test such formalisms for DNA sequence-phenotype relationships.

Purpose of the Study:

  • To develop a formalism for relating DNA sequences (genetic parts) to biological functions.
  • To leverage attribute grammars for translating DNA sequences into molecular interaction network models.
  • To validate the proposed formalism by simulating phenotypes from designed genetic constructs.

Main Methods:

  • Attribute grammars were employed to associate attributes with genetic parts.
  • Rules describing DNA sequence structure were used to modify attribute values.
  • A multi-pass compilation process translated DNA sequences into network models.
  • Phenotypes were systematically generated, translated, and simulated for validation.

Main Results:

  • Attribute grammars successfully translated DNA sequences into molecular interaction network models.
  • Example grammars demonstrated the dependency of gene expression rates on genetic parts.
  • Simulation of all sequences in a design space validated the translation process.
  • The framework effectively connected genetic parts with models of biological function.

Conclusions:

  • Attribute grammars provide a flexible framework for linking genetic parts to biological function models.
  • This formalism is crucial for building mathematical models of genetic constructs.
  • The approach lays a foundation for computer-assisted design in synthetic biology.