E-Mail Alert

Add your e-mail address to receive forthcoming issues of this journal:

Journal Browser

Journal Browser

Special Issue "DNA-Templated Synthesis"

Quicklinks

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

Deadline for manuscript submissions: closed (30 November 2011)

Special Issue Editor

Guest Editor
Prof. Dr. Satoshi Obika

Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
E-Mail
Phone: +81-6-6879-8200
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)

View options order results:
result details:
Displaying articles 1-6
Export citation of selected articles as:

Research

Jump to: Review

Open AccessArticle Site-Specific Incorporation of Functional Components into RNA by an Unnatural Base Pair Transcription System
Molecules 2012, 17(3), 2855-2876; doi:10.3390/molecules17032855
Received: 16 December 2011 / Revised: 22 February 2012 / Accepted: 24 February 2012 / Published: 7 March 2012
Cited by 15 | PDF Full-text (4033 KB)
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)
Figures

Open AccessArticle Enzyme Treatment-Free and Ligation-Independent Cloning Using Caged Primers in Polymerase Chain Reactions
Molecules 2012, 17(1), 328-340; doi:10.3390/molecules17010328
Received: 28 October 2011 / Revised: 26 December 2011 / Accepted: 27 December 2011 / Published: 30 December 2011
Cited by 6 | PDF Full-text (723 KB) | Supplementary Files
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)
Open AccessArticle Template Directed Reversible Photochemical Ligation of Oligodeoxynucleotides
Molecules 2012, 17(1), 163-178; doi:10.3390/molecules17010163
Received: 29 November 2011 / Revised: 21 December 2011 / Accepted: 22 December 2011 / Published: 27 December 2011
Cited by 5 | PDF Full-text (887 KB)
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)
Open AccessArticle Cleavage of Oligonucleotides Containing a P3’→N5’ Phosphoramidate Linkage Mediated by Single-Stranded Oligonucleotide Templates
Molecules 2011, 16(12), 10695-10708; doi:10.3390/molecules161210695
Received: 1 November 2011 / Revised: 9 December 2011 / Accepted: 13 December 2011 / Published: 20 December 2011
PDF Full-text (503 KB) | Supplementary Files
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)
Open AccessArticle DNA-Templated Preparation of Gold Nanoparticles
Molecules 2011, 16(10), 8143-8151; doi:10.3390/molecules16108143
Received: 6 September 2011 / Revised: 19 September 2011 / Accepted: 20 September 2011 / Published: 27 September 2011
Cited by 11 | PDF Full-text (937 KB) | Supplementary Files
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)

Review

Jump to: Research

Open AccessReview Oligonucleotide-Templated Reactions for Sensing Nucleic Acids
Molecules 2012, 17(3), 2446-2463; doi:10.3390/molecules17032446
Received: 10 February 2012 / Revised: 23 February 2012 / Accepted: 24 February 2012 / Published: 29 February 2012
Cited by 23 | PDF Full-text (479 KB)
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)

Journal Contact

MDPI AG
Molecules Editorial Office
St. Alban-Anlage 66, 4052 Basel, Switzerland
molecules@mdpi.com
Tel. +41 61 683 77 34
Fax: +41 61 302 89 18
Editorial Board
Contact Details Submit to Molecules
Back to Top