Solid-phase synthesis of pseudo-complementary peptide nucleic acids

Bulletin of the Chemical Society of Japan

Yoshimoto

Sisido

et al. 2017

Self Cite

275

131

In this review, we introduce two kinds of bio-related nanoarchitectonics, DNA nanoarchitectonics and cellmacromolecular nanoarchitectonics, both of which are basically controlled by chemical strategies. The former DNA-based approach would represent the precise nature of the nanoarchitectonics based on the strict or "digital" molecular recognition between nucleic bases. This part includes functionalization of single DNAs by chemical means, modification of the main-chain or side-chain bases to achieve stronger DNA binding, DNA aptamers and DNAzymes. It also includes programmable assemblies of DNAs (DNA Origami) and their applications for delivery of drugs to target sites in vivo, sensing in vivo, and selective labeling of biomaterials in cells and in animals. In contrast to the digital molecular recognition between nucleic bases, cell membrane assemblies and their interaction with macromolecules are achieved through rather generic and "analog" interactions such as hydrophobic effects and electrostatic forces. This cell-macromolecular nanoarchitectonics is discussed in the latter part of this review. This part includes bottom-up and top-down approaches for constructing highly organized cell-architectures with macromolecules, for regulating cell adhesion pattern and their functions in twodimension, for generating three-dimensional cell architectures on micro-patterned surfaces, and for building synthetic/natural macromolecular modified hybrid biointerfaces.

Section: Binding To Double-stranded Dnamentioning

confidence: 99%

Chemistry Can Make Strict and Fuzzy Controls for Bio-Systems: DNA Nanoarchitectonics and Cell-Macromolecular Nanoarchitectonics

Bulletin of the Chemical Society of Japan

Yoshimoto

Sisido

et al. 2017

Self Cite

275

131

“…The site specificity and target site of this artificial DNA cutter can be almost freely modulated; therefore, this cutter should be useful in developing new biotechnology. For instance, viruses with single-stranded genomes can be manipulated to produce 59 Lohse et al 60 and Komiyama et al 61 ).…”

Section: Site-selective Scission Of Double-stranded Dna By the Combinmentioning

confidence: 99%

“…16,56,57 This cutter is composed of two pcPNAs [58][59][60][61] and Ce(IV)/EDTA ( Figure 11). The pcPNAs used are designed to be laterally shifted to one another by five nucleobases.…”

Section: Site-selective Scission Of Double-stranded Dna By the Combinmentioning

confidence: 99%

Artificial site-selective DNA cutters to manipulate single-stranded DNA

Aiba

2012

Polym J

Self Cite

Recent progress regarding the development of artificial site-selective DNA cutters by chemical approaches are reviewed herein, with a special focus on site-selective cutters for single-stranded DNA. We employ a Ce(IV)/EDTA complex to serve as the catalyst, because it efficiently and selectively cuts single-stranded DNA. Using two complementary oligonucleotide additives, a gap structure is formed at the target site in the single-stranded DNA substrate. Owing to the substrate specificity of Ce(IV)/ EDTA, the gap site is preferentially hydrolyzed, resulting in a site-selective DNA scission. The scission site is easily determined using the Watson-Crick base-pairing rule; thus, both the sequence and scission specificity can be tuned according to demand. The site-selective scission is greatly promoted by attaching a multiphosphonate to the termini of the oligonucleotide additives and placing this ligand at the gap site. The scission fragments can be connected with foreign DNA using ligase, and the recombinant DNA expresses the corresponding protein in E. coli. INTRODUCTIONThe role of DNA in storing and carrying genetic information is essential for the function and development of all living organisms. If the information stored within DNA can be rewritten by scientists, numerous applications in a variety of fields will be possible. On this basis, chemists, biochemists and biologists have long attempted to rewrite the information encoded within DNA using various approaches. One direct and straightforward approach to precisely alter the information contained by DNA is the site-selective scission of DNA at a target site, 1-11 followed by the appropriate manipulation of the DNA at this local site.Currently, in molecular biology, DNA is manipulated by the 'cut-and-paste' method. In this approach, DNA is first cut at a predetermined site by naturally occurring restriction enzymes, and the resultant fragment is connected with another DNA fragment using ligases. Here, the target gene is inserted, deleted or altered. This strategy is satisfactorily effective so long as small DNAs such as plasmids (composed of several thousand base pairs) are targeted. Unfortunately, this technology is insufficient for manipulating large DNAs; however, our interests have been gradually focusing on the manipulation of genomic DNAs of higher organisms. The key problem is the low site specificity of naturally occurring restriction enzymes (most of them recognize 4 to 8-bp DNA sequences). Statistically, the scission site of a restriction enzyme with 6-bp

“…20 Furthermore, the selective scission site is determined only by WatsonCrick rule. Thus, artificial cutters required for aimed DNA manipulation can be straightforwardly designed and synthesized in terms of (i) sequence of targeted scission site, (ii) size of DNA substrate, and (iii) magnitude of desired site-specificity.…”

Section: Features Of Artificial Restriction Dna Cutter As a New Tool mentioning

confidence: 99%

“…In pcPNA, poly(N-aminoethylglycine) backbone is used in place of poly(deoxyribose-phosphodiester) backbone of DNA (the structure is presented in Figure 4). 4,20,21 Furthermore, conventional nucleobases A and T are replaced by modified nucleobases 2,6-diaminopurine (D) 21 and 2-thiouracil (Us), 4 respectively, in order to promote the invasion (see below). In most of the cases, lysine residues are bound to the Nand/or C-termini of pcPNAs to increase the water-solubility and also to promote the binding to DNA (this modification is not necessarily an absolute requisite).…”

mentioning

confidence: 99%

Design and Applications of Artificial Restriction DNA Cutters for Site-Selective Scission of Genomes

Bulletin of the Chemical Society of Japan

Sumaoka

2012

Self Cite

By combining Ce(IV)/EDTA complex and pseudo-complementary peptide nucleic acid (pcPNA), an artificial restriction DNA cutter which hydrolyzes targeted phosphodiester linkages in double-stranded DNA has been developed. The targeted site in the DNA is activated by two strands of pcPNA and selectively hydrolyzed by the Ce(IV) complex. The DNA cutter required for aimed manipulation can be straightforwardly designed and obtained in terms of (i) the sequence of targeted selective scission, (ii) size of DNA substrate, and (iii) magnitude of desired site-specificity. The sitespecificity can be high enough to cut the whole genome of human beings (3 © 10 9 base-pairs) at one predetermined site. Off-target scissions at the sites of analogous sequences hardly take place. With the use of this specificity, targeted gene can be engineered in human cells through homologous recombination. Other potential applications of this cutter, as well as recent attempts to improve its activity and specificity, are also discussed. Significance of Site-Selective Scission of DNASite-selective scission of DNA is a key step in biotechnology and molecular biology. For a long time, target DNA for our manipulation has been restricted to small DNA such as plasmids which are composed of 30005000 base-pairs (bp). In order to cut them at a desired site, naturally occurring restriction enzymes, which recognize 4-or 6-bp sequence, have been used. The resultant scission fragments are combined with other fragments with the use of another enzyme ligase. With outstanding developments in relevant fields, however, target DNA of our manipulation is gradually shifting from plasmids to genomes which are directly responsible for the memory of genetic information. Unfortunately, the site-specificity of naturally occurring restriction enzymes is too low to manipulate genomes which are by several orders of magnitude larger than plasmids. For example, human genome is composed of 3 © 10 9 bp. If this DNA of enormous size is treated with a restriction enzyme recognizing a 6-bp sequence, the scission occurs at too many sites (statistically, the scission site of this enzyme should appear at every 4 6 (= 4096) bp, and the number of scission sites in this genome should be larger than half million). Precise manipulation is impossible under these conditions. In order to cut genomes selectively at a desired site, we apparently need artificial cutters which recognize a longer sequence. If one should like to cut human genomes at one site and manipulate them precisely, the length of recognition site of the cutter should be at least 16 bp (note that 4 16 > 3 © 10 9). The importance of these artificial DNA cutters having higher and tunable site-specificity has been widely recognized for a long time, and many researchers have devoted efforts to this subject.1 As a result, remarkable progress has already been accomplished, especially in the design of non-protein molecules which selectively bind to target site in doublestranded DNA. Peptide nucleic acids (PNAs) developed by Nielsen 2...