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Special Issue "DNA-Directed Chemistry"

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A special issue of Molecules (ISSN 1420-3049).

Deadline for manuscript submissions: closed (20 September 2012)

Special Issue Editor

Guest Editor
Dr. Paul Paukstelis

Department of Chemistry and Biochemistry, University of Maryland, College Park,Maryland 20742-4454, USA
E-Mail
Interests: DNA nanotechnology; DNA self-assembly; Non-canonical DNA

Special Issue Information

Dear Colleagues,

Nearly 60 years after becoming the emblematic “molecule of life”, DNA has continued to shed its purely biological skin to become an important polymer in nearly all aspects of chemistry. The properties that make DNA a robust carrier of genetic information – simplicity, stability, and programmability – have also made it the premier biopolymer at the rapidly emerging interface of biology, chemistry, materials science, and engineering. No longer just a code to be read by the cell, DNA is now a catalyst, building material, machine, robot, and computer.

This special issue of Molecules welcomes previously unpublished manuscripts that highlight non-biological roles of DNA and its properties that enable broad functionality in chemistry and biology. Topics will include, but are not limited to: DNA nanotechnology, catalysis, self-assembly, DNA-derived polymers, sensors and beacons, DNA-directed synthesis, DNA machines, and DNA computation.

Dr. Paul Paukstelis
Guest Editor

Keywords

  • DNA catalysis
  • DNA-directed synthesis
  • DNA-directed transfer reactions
  • ligation assay
  • multiplex assay
  • native chemical ligation
  • peptide nucleic acids
  • templates
  • template
  • catalysis
  • turnover
  • DNA nanotechnology
  • DNA beacons
  • DNA sensors
  • DNA self-assembly
  • DNA origami

Published Papers (4 papers)

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Research

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Open AccessArticle Spatial Control of DNA Reaction Networks by DNA Sequence
Molecules 2012, 17(11), 13390-13402; doi:10.3390/molecules171113390
Received: 25 September 2012 / Revised: 5 November 2012 / Accepted: 5 November 2012 / Published: 9 November 2012
Cited by 6 | PDF Full-text (578 KB)
Abstract
We have developed a set of DNA circuits that execute during gel electrophoresis to yield immobile, fluorescent features in the gel. The parallel execution of orthogonal circuits led to the simultaneous production of different fluorescent lines at different positions in the gel. The
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We have developed a set of DNA circuits that execute during gel electrophoresis to yield immobile, fluorescent features in the gel. The parallel execution of orthogonal circuits led to the simultaneous production of different fluorescent lines at different positions in the gel. The positions of the lines could be rationally manipulated by changing the mobilities of the reactants. The ability to program at the nanoscale so as to produce patterns at the macroscale is a step towards programmable, synthetic chemical systems for generating defined spatiotemporal patterns. Full article
(This article belongs to the Special Issue DNA-Directed Chemistry)

Review

Jump to: Research

Open AccessReview Nucleoside Triphosphates — Building Blocks for the Modification of Nucleic Acids
Molecules 2012, 17(11), 13569-13591; doi:10.3390/molecules171113569
Received: 21 September 2012 / Revised: 7 November 2012 / Accepted: 9 November 2012 / Published: 15 November 2012
Cited by 58 | PDF Full-text (442 KB)
Abstract
Nucleoside triphosphates are moldable entities that can easily be functionalized at various locations. The enzymatic polymerization of these modified triphosphate analogues represents a versatile platform for the facile and mild generation of (highly) functionalized nucleic acids. Numerous modified triphosphates have been utilized in
[...] Read more.
Nucleoside triphosphates are moldable entities that can easily be functionalized at various locations. The enzymatic polymerization of these modified triphosphate analogues represents a versatile platform for the facile and mild generation of (highly) functionalized nucleic acids. Numerous modified triphosphates have been utilized in a broad palette of applications spanning from DNA-tagging and -labeling to the generation of catalytic nucleic acids. This review will focus on the recent progress made in the synthesis of modified nucleoside triphosphates as well as on the understanding of the mechanisms underlying their polymerase acceptance. In addition, the usefulness of chemically altered dNTPs in SELEX and related methods of in vitro selection will be highlighted, with a particular emphasis on the generation of modified DNA enzymes (DNAzymes) and DNA-based aptamers. Full article
(This article belongs to the Special Issue DNA-Directed Chemistry)
Open AccessReview DNA as a Chiral Scaffold for Asymmetric Synthesis
Molecules 2012, 17(11), 12792-12803; doi:10.3390/molecules171112792
Received: 21 September 2012 / Revised: 12 October 2012 / Accepted: 25 October 2012 / Published: 31 October 2012
Cited by 18 | PDF Full-text (347 KB) | HTML Full-text | XML Full-text
Abstract DNA as a Chiral Scaffold for Asymmetric Synthesis Full article
(This article belongs to the Special Issue DNA-Directed Chemistry)
Open AccessReview DNA-Directed Base Pair Opening
Molecules 2012, 17(10), 11947-11964; doi:10.3390/molecules171011947
Received: 16 August 2012 / Revised: 28 September 2012 / Accepted: 9 October 2012 / Published: 11 October 2012
Cited by 3 | PDF Full-text (3200 KB) | HTML Full-text | XML Full-text
Abstract
Strand separation is a fundamental molecular process essential for the reading of the genetic information during DNA replication, transcription and recombination. However, DNA melting in physiological conditions in which the double helix is expected to be stable represents a challenging problem. Current models
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Strand separation is a fundamental molecular process essential for the reading of the genetic information during DNA replication, transcription and recombination. However, DNA melting in physiological conditions in which the double helix is expected to be stable represents a challenging problem. Current models propose that negative supercoiling destabilizes the double helix and promotes the spontaneous, sequence-dependent DNA melting. The present review examines an alternative view and reveals how DNA compaction may trigger the sequence dependent opening of the base pairs. This analysis shows that in DNA crystals, tight DNA-DNA interactions destabilize the double helices at various degrees, from the alteration of the base-stacking to the opening of the base-pairs. The electrostatic repulsion generated by the DNA close approach of the negatively charged sugar phosphate backbones may therefore provide a potential source of the energy required for DNA melting. These observations suggest a new molecular mechanism for the initial steps of strand separation in which the coupling of the DNA tertiary and secondary interactions both actively triggers the base pair opening and stabilizes the intermediate states during the melting pathway. Full article
(This article belongs to the Special Issue DNA-Directed Chemistry)

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