• Corpus ID: 16641896

Nucleic Acid Enzymes: The Fusion of Self-assembly and Conformational Computing

@article{Ramlan2009NucleicAE,
  title={Nucleic Acid Enzymes: The Fusion of Self-assembly and Conformational Computing},
  author={Effirul Ikhwan Ramlan and Klaus-Peter Zauner},
  journal={Int. J. Unconv. Comput.},
  year={2009},
  volume={5},
  pages={165-189}
}
Macromolecules are the predominant physical substrate sup-porting information processing in organisms. Two key characteristics—conformational dynamics and self-assembly properties—render macro-molecules unique in this context. Both characteristics have been investigated for technical applications. In nature’s information processors self-assembly and conformational switching commonly appear in combination and are typically realised with proteins. At the current state of biotechnology the best… 
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Citation Type

Functional nucleic acids as substrate for information processing
TLDR
This thesis investigated, to what extent the construction of molecular building blocks for a particular purpose is possible with the support of a software environment, and developed a computational protocol that functions on a multi-molecular level, which enable it to directly incorporate the dynamic characteristics of nucleic acids molecules.
In-silico design of computational nucleic acids for molecular information processing
TLDR
This study demonstrates the simplicity with which one can construct a set of nucleic acid computing units using a new computational protocol that would enable the construction of a network of interconnecting nucleic acids (as a circuit) for molecular information processing.
Design of interacting multi-stable nucleic acids for molecular information processing
TLDR
An algorithm capable of designing groups self-assembling of nucleic acid molecules with multiple conformational states is introduced, and the thermodynamic properties of the generated candidates are within the same approximation as the customised trans-acting switching molecules reported in the laboratory.
AN EXTENDED DOT-BRACKET-NOTATION FOR FUNCTIONAL NUCLEIC ACIDS
Functional nucleic acids are an attractive substrate for molecular computing. A nucleic acid molecule is a linear chain of covalently bound building blocks assembled in arbitrary order from a set of…

References

SHOWING 1-10 OF 93 REFERENCES
In vitro Selection of Specific Ligand-Binding Nucleic Acids
In vitro selection is a method that allows the simultaneous screening of very large numbers of nucleic acid molecules for a wide range of properties from binding characteristics to catalytic…
Molecular computing: the lock-key paradigm
TLDR
Basic principles of molecular computing are introduced and some ways that they might combine to yield new approaches to information technology are considered, and signal-integrating, optomolecular and neuromolecules computer architectures are described.
Molecular Information Technology
Abstract Molecular materials are endowed with unique properties of unrivaled potential for high density integration of computing systems. Present applications of molecules range from organic…
The thermodynamics of DNA structural motifs.
TLDR
This review presents the current parameter set available for making accurate DNA structure predictions and also points to future directions for improvement.
Rational design of allosteric ribozymes.
TLDR
By joining an ATP-binding RNA to a self-cleaving ribozyme, this work has created the first example of an allosteric ribo enzyme that has a catalytic rate that can be controlled by ATP.
Deoxyribozymes: new activities and new applications
TLDR
The results indicate that the true catalytic power of DNA is limited by discovery and not by chemistry.
Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes
TLDR
A computational approach for designing allosteric ribozymes triggered by binding oligonucleotides was described, and four universal types of RNA switches possessing AND, OR, YES and NOT Boolean logic functions were created in modular form, which allows ligand specificity to be changed without altering the catalytic core of the ribozyme.
Conformational flexibility of four-way junctions in RNA.
TLDR
Single-molecule fluorescence spectroscopy is used to study the dynamic properties of the perfect (4H) four-way helical junction derived from the hairpin ribozyme and suggests that interconversion proceeds via an open intermediate with reduced cation binding in which coaxial stacking between helices is disrupted.
Directed evolution of nucleic acid enzymes.
  • G. F. Joyce
  • Biology, Medicine
    Annual review of biochemistry
  • 2004
TLDR
This review focuses on the development of nucleic acid enzymes starting from a population of random-sequence RNA or DNA molecules, and two especially well-studied categories of catalytic nucleic acids are considered: RNA enzymes that catalyze the template-directed ligation of RNA and DNA enzymes that Catalyst the cleavage of RNA.
Enzymatic Computing
TLDR
This work constructed a tabletop prototype to implement enzymatic signal processing in a device context and employed it in conjunction with malate dehydrogenase to perform the linearly inseparable exclusive‐or operation, showing that proteins can execute signal processing operations that are more complex than those performed by individual threshold elements.
...
1
2
3
4
5
...