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DNA-Templated Synthesis

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

Deadline for manuscript submissions: closed (30 November 2011) | Viewed by 41077

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Guest Editor
Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
Interests: bioorganic chemistry; nucleic acid chemistry; organic synthesis; medicinal chemistry

Special Issue Information

Dear Colleagues,

In a living cell, many kinds of bioactive compounds are selectively and effectively synthesized, although there are thousands of reactants/products in the cell, namely, a reaction vessel. It is amazing but not magic. Nature controls the reactivity of these compounds by using macromolecules as a template of the reaction where only the necessary reactants come close each other to afford the desired products selectively. One important example of the “nature’s effective-molarity-based approach” is the nucleic acid-templated reaction. In the transcription of DNA, ribonucleotides are coupled on the templated DNA to form messenger RNA, while amino acids connected to the ribosomal RNA are coupled on the templated RNA to give proteins. Thus, nucleic acids work as a good template for the synthesis of bioactive compounds in a living cell. DNA-templated synthesis using the “nature’s effective-molarity-based approach” has attracted considerable attention in many fields of chemistry, such as organic chemistry, nucleic acids chemistry, bioorganic chemistry, analytical chemistry and medicinal chemistry. In fact, some pioneering works on the DNA-templated synthesis have been carried out so far. Among them, 1) DNA-templated synthesis for oligonucleotide linkage, and 2) DNA-templated organic synthesis are well known. The former includes the application to novel DNA analysis methods, and the latter includes the development of novel organic reactions or bioactive compounds. In addition, the design and synthesis of well-defined nanoscale architecture via DNA-templated self-assembly is also of great interest to nano science and nano technology. This Special Issue of Molecules will consider any submissions associated with DNA-Templated Synthesis in any form. I strongly encourage authors to submit manuscripts for this Special Issue.

Prof. Dr. Satoshi Obika
Guest Editor

Keywords

  • template synthesis
  • nucleic acid analogues
  • sequence analysis
  • single nucleotide polymorphism
  • chemical ligation
  • chemical library synthesis
  • DNA-encoded chemical library
  • small molecules
  • combinatorial chemistry
  • molecular evolution
  • bioactive compounds
  • DNA-templated self assembly
  • nano technology

 

Published Papers (6 papers)

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Research

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4033 KiB  
Article
Site-Specific Incorporation of Functional Components into RNA by an Unnatural Base Pair Transcription System
by Nobuyuki Morohashi, Michiko Kimoto, Akira Sato, Rie Kawai and Ichiro Hirao
Molecules 2012, 17(3), 2855-2876; https://doi.org/10.3390/molecules17032855 - 07 Mar 2012
Cited by 31 | Viewed by 6763
Abstract
Toward the expansion of the genetic alphabet, an unnatural base pair between 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and pyrrole-2-carbaldehyde (Pa) functions as a third base pair in replication and transcription, and provides a useful tool for the site-specific, enzymatic incorporation [...] Read more.
Toward the expansion of the genetic alphabet, an unnatural base pair between 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and pyrrole-2-carbaldehyde (Pa) functions as a third base pair in replication and transcription, and provides a useful tool for the site-specific, enzymatic incorporation of functional components into nucleic acids. We have synthesized several modified-Pa substrates, such as alkylamino-, biotin-, TAMRA-, FAM-, and digoxigenin-linked PaTPs, and examined their transcription by T7 RNA polymerase using Ds-containing DNA templates with various sequences. The Pa substrates modified with relatively small functional groups, such as alkylamino and biotin, were efficiently incorporated into RNA transcripts at the internal positions, except for those less than 10 bases from the 3′-terminus. We found that the efficient incorporation into a position close to the 3′-terminus of a transcript depended on the natural base contexts neighboring the unnatural base, and that pyrimidine-Ds-pyrimidine sequences in templates were generally favorable, relative to purine-Ds-purine sequences. The unnatural base pair transcription system provides a method for the site-specific functionalization of large RNA molecules. Full article
(This article belongs to the Special Issue DNA-Templated Synthesis)
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723 KiB  
Article
Enzyme Treatment-Free and Ligation-Independent Cloning Using Caged Primers in Polymerase Chain Reactions
by Akinori Kuzuya, Keita Tanaka, Hitoshi Katada and Makoto Komiyama
Molecules 2012, 17(1), 328-340; https://doi.org/10.3390/molecules17010328 - 30 Dec 2011
Cited by 7 | Viewed by 7360
Abstract
A new simple scheme for constructing recombinant vectors that does not require any restriction enzyme, ligase, or any other special enzyme treatment has been developed. By using caged primers in PCR, unnatural sticky-ends of any sequence, which are sufficiently long for ligation-independent cloning [...] Read more.
A new simple scheme for constructing recombinant vectors that does not require any restriction enzyme, ligase, or any other special enzyme treatment has been developed. By using caged primers in PCR, unnatural sticky-ends of any sequence, which are sufficiently long for ligation-independent cloning (LIC), are directly prepared on the product after a brief UVA irradiation. Target genes and vectors amplified by this light-assisted cohesive-ending (LACE) PCR join together in the desired arrangement in a simple mixture of them, tightly enough to be repaired and ligated in competent cells. Full article
(This article belongs to the Special Issue DNA-Templated Synthesis)
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887 KiB  
Article
Template Directed Reversible Photochemical Ligation of Oligodeoxynucleotides
by Shigetaka Nakamura, Shinzi Ogasawara, Shigeo Matuda, Isao Saito and Kenzo Fujimoto
Molecules 2012, 17(1), 163-178; https://doi.org/10.3390/molecules17010163 - 27 Dec 2011
Cited by 10 | Viewed by 5925
Abstract
We demonstrated that 5-vinyldeoxyuridine (VU) and 5-carboxyvinyldeoxyuridine (CVU) can be used to photoligate a longer oligonucleotide (ODN) from smaller ODNs on a template. By performing irradiation at 366 nm, these artificial nucleotides make photoligated ODNs with high efficiency without [...] Read more.
We demonstrated that 5-vinyldeoxyuridine (VU) and 5-carboxyvinyldeoxyuridine (CVU) can be used to photoligate a longer oligonucleotide (ODN) from smaller ODNs on a template. By performing irradiation at 366 nm, these artificial nucleotides make photoligated ODNs with high efficiency without any side reactions. Moreover, by performing irradiation at 312 nm, these photoligated ODNs were reversed to the original ODN. VU needs to be irradiated 366 nm for 6 h, but CVU needs to be irradiated at 366 nm for 15 min. Finally, we made a self-assembled structure with an ODN containing CVU and observed the photoligated ODN by photoirradiation. Full article
(This article belongs to the Special Issue DNA-Templated Synthesis)
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503 KiB  
Article
Cleavage of Oligonucleotides Containing a P3’→N5’ Phosphoramidate Linkage Mediated by Single-Stranded Oligonucleotide Templates
by Kosuke Ramon Ito, Tetsuya Kodama, Futaba Makimura, Noritsugu Hosoki, Tomohisa Osaki, Ayako Orita, Takeshi Imanishi and Satoshi Obika
Molecules 2011, 16(12), 10695-10708; https://doi.org/10.3390/molecules161210695 - 20 Dec 2011
Cited by 2 | Viewed by 5847
Abstract
Double-stranded DNA (dsDNA) templates can hybridize to and accelerate cleavage of oligonucleotides containing a P3’→N5’ phosphoramidate (P-N) linkage. This dsDNA-templated cleavage of P-N linkages could be due to conformational strain placed on the linkage upon triplex formation. To determine whether duplex formation also [...] Read more.
Double-stranded DNA (dsDNA) templates can hybridize to and accelerate cleavage of oligonucleotides containing a P3’→N5’ phosphoramidate (P-N) linkage. This dsDNA-templated cleavage of P-N linkages could be due to conformational strain placed on the linkage upon triplex formation. To determine whether duplex formation also induced conformational strain, we examined the reactivity of the oligonucleotides with a P-N linkage in the presence of single-stranded templates, and compared these reactions to those with dsDNA templates. P-N oligonucleotides that are cleaved upon duplex formation could be used as probes to detect single-stranded nucleic acids. Full article
(This article belongs to the Special Issue DNA-Templated Synthesis)
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937 KiB  
Article
DNA-Templated Preparation of Gold Nanoparticles
by Jeong Sun Sohn, Young Wan Kwon, Jung Il Jin and Byung Wook Jo
Molecules 2011, 16(10), 8143-8151; https://doi.org/10.3390/molecules16108143 - 27 Sep 2011
Cited by 35 | Viewed by 7226
Abstract
DNA-mediated gold nanoparticles were prepared by chemical reduction of DNA-Au(III) complex. The DNA-Au(III) was first formed by reacting DNA with HAuCl4 at a pH of 5.6. The complex in solution was reacted with hydrazine reducing Au(III) to Au. The reduced Au formed [...] Read more.
DNA-mediated gold nanoparticles were prepared by chemical reduction of DNA-Au(III) complex. The DNA-Au(III) was first formed by reacting DNA with HAuCl4 at a pH of 5.6. The complex in solution was reacted with hydrazine reducing Au(III) to Au. The reduced Au formed nanodimensional aggregates. The particle distributions were obtained by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). This method resulted in a rather uniform dispersion of Au nanoparticles of near-spherical shape and 45~80 nm in diameter. Gold nanoparticles were embedded and stabilized by DNA. Full article
(This article belongs to the Special Issue DNA-Templated Synthesis)
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Review

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479 KiB  
Review
Oligonucleotide-Templated Reactions for Sensing Nucleic Acids
by Aya Shibata, Hiroshi Abe and Yoshihiro Ito
Molecules 2012, 17(3), 2446-2463; https://doi.org/10.3390/molecules17032446 - 29 Feb 2012
Cited by 53 | Viewed by 6832
Abstract
Oligonucleotide-templated reactions are useful for applying nucleic acid sensing. Various chemistries for oligonucleotide-templated reaction have been reported so far. Major scientific interests are focused on the development of signal amplification systems and signal generation systems. We introduce the recent advances of oligonucleotide-templated reaction [...] Read more.
Oligonucleotide-templated reactions are useful for applying nucleic acid sensing. Various chemistries for oligonucleotide-templated reaction have been reported so far. Major scientific interests are focused on the development of signal amplification systems and signal generation systems. We introduce the recent advances of oligonucleotide-templated reaction in consideration of the above two points. Full article
(This article belongs to the Special Issue DNA-Templated Synthesis)
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