Synthetic Approaches to Biology

Abstract

Nanobiotechnology and synthetic biology are emerging as novel fields that integrate research from science and technology to create novel organisms with new desired properties. We present here the new revolutionary methods of synthetic biology that enable us to engineer gene control circuits, edit genomes, and create de novo whole genomes. The creation of new genomes that function in the cell means that we can create new organisms that are different from those observed in nature. The synthetic genomes can contain novel combinations of genes that offer the opportunities to create novel biological species that possess predefined combination of properties. Therefore, the synthetic genomes can be regarded as a new kind of materials. The methods for whole genome assemble applied so far combined several in vitro and in vivo steps that possess certain technical limitations and shortcomings. In this chapter, we discuss all technical aspects of assembling novel genomes and their current limitations. The genome editing technologies that have been developed over the last several years based on the CRISPR-Cas system is also discussed. In addition, we present major RNA-based methods for design of gene control circuits both in prokaryotes and eukaryotes, including humans.

Antisense and Functional Nucleic Acids in Rational Drug Development

“…One of these ASOs, PNA, can bind to the promoter and inhibit transcription (5). PNA can bind to one of the DNA strands (6) and induce the transcription of pre-mRNA-3 (7). ASOs present in the nucleus can hybridize to complementary sequences of pre-mNA-3 (8); hybridizing of LNA leads to 5'-capping inhibition (9); hybridizing of PNA leads to splicing inhibition of mRNA-3 (10); hybridizing of PS-DNA leads to the formation of a chimeric structure that is a substrate for RNase H, which recognizes, binds and cleaves mRNA-3 (11).…”

“…The binding activates RISC and induces cleavage of mRNA-1 (5). RISC-ssRNA complex can also bind to non-coding mRNA-3 (6), which leads to the prevention of translation (7). RNA interference can be affected by incorporating a non-coding mRNA-4 from the cytoplasm inside the cytosol (8).…”

“…5). The synthesized pre-mRNA-2 complement the ribozyme sequence and binds it (6). When bound to the pre-mRNA-2, the ribozyme is activated and cleaved at the cleavage site (black arrow).…”

“…The binding of RNAP to the other promoter site triggers (4) the transcription of pre-mRNA-2 (5). The synthesized pre-mRNA-2 complement the ribozyme sequence and binds it (6). When bound to the pre-mRNA-2, the ribozyme is activated and cleaved at the cleavage site (black arrow).…”

“…At the same time, new natural mechanisms for the control of gene expression have been discovered based on various types of RNAs, including micro(mi)RNAs, small interfering(si)RNAs, riboswitches [ 1 ], and ribozymes. There are currently four different nucleic acid engineering strategies to inhibit the expression of specific RNAs in the cell, such as siRNAs [ 2 ], antisense oligonucleotides (ASOs) [ 3 ], ribozymes [ 4 , 5 ], and CRISPR-Cas9 systems [ 6 ]. All tools used for nucleic acid-based drug development are inherited based on rational design methods, being novel and the main point of this review.…”