Site-specific recombinases: molecular machines for the Genetic Revolution

2016 ◽  
Vol 473 (6) ◽  
pp. 673-684 ◽  
Author(s):  
Femi J. Olorunniji ◽  
Susan J. Rosser ◽  
W. Marshall Stark
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Molecular Machines ◽  
Molecular Tools ◽  
Site Specific ◽  
Important Group ◽  
Current State ◽  
Genetic Revolution ◽  
Improved Performance ◽  
Novel Applications

The fields of molecular genetics, biotechnology and synthetic biology are demanding ever more sophisticated molecular tools for programmed precise modification of cell genomic DNA and other DNA sequences. This review presents the current state of knowledge and development of one important group of DNA-modifying enzymes, the site-specific recombinases (SSRs). SSRs are Nature's ‘molecular machines’ for cut-and-paste editing of DNA molecules by inserting, deleting or inverting precisely defined DNA segments. We survey the SSRs that have been put to use, and the types of applications for which they are suitable. We also discuss problems associated with uses of SSRs, how these problems can be minimized, and how recombinases are being re-engineered for improved performance and novel applications.

scholarly journals Antarctic bryophyte research—current state and future directions

2021 ◽  
Vol 43 (1) ◽  
Author(s):  
PAULO E.A.S. CÂMARA ◽  
MICHELINE CARVALHO-SILVA ◽  
MICHAEL STECH
Keyword(s):  
Dna Sequences ◽  
Molecular Data ◽  
Molecular Tools ◽  
Future Directions ◽  
Moss Species ◽  
Current State ◽  
Molecular Studies ◽  
The Antarctic ◽  
New Phase ◽  
Antarctic Moss

Botany is one of the oldest sciences done south of parallel 60 °S, although few professional botanists have dedicated themselves to investigating the Antarctic bryoflora. After the publications of liverwort and moss floras in 2000 and 2008, respectively, new species were described. Currently, the Antarctic bryoflora comprises 28 liverwort and 116 moss species. Furthermore, Antarctic bryology has entered a new phase characterized by the use of molecular tools, in particular DNA sequencing. Although the molecular studies of Antarctic bryophytes have focused exclusively on mosses, molecular data (fingerprinting data and/or DNA sequences) have already been published for 36 % of the Antarctic moss species. In this paper we review the current state of Antarctic bryological research, focusing on molecular studies and conservation, and discuss future questions of Antarctic bryology in the light of global challenges.

scholarly journals Characterization of squalene synthase gene from Gymnema sylvestre R. Br.

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Kuldeepsingh A. Kalariya ◽  
Ram Prasnna Meena ◽  
Lipi Poojara ◽  
Deepa Shahi ◽  
Sandip Patel
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Competitive Inhibition ◽  
Sequence Data ◽  
Homology Model ◽  
Squalene Synthase ◽  
Gymnema Sylvestre ◽  
Gardenia Jasminoides ◽  
Ramachandran Plots ◽  
Flanking Regions

Abstract Background Squalene synthase (SQS) is a rate-limiting enzyme necessary to produce pentacyclic triterpenes in plants. It is an important enzyme producing squalene molecules required to run steroidal and triterpenoid biosynthesis pathways working in competitive inhibition mode. Reports are available on information pertaining to SQS gene in several plants, but detailed information on SQS gene in Gymnema sylvestre R. Br. is not available. G. sylvestre is a priceless rare vine of central eco-region known for its medicinally important triterpenoids. Our work aims to characterize the GS-SQS gene in this high-value medicinal plant. Results Coding DNA sequences (CDS) with 1245 bp length representing GS-SQS gene predicted from transcriptome data in G. sylvestre was used for further characterization. The SWISS protein structure modeled for the GS-SQS amino acid sequence data had MolProbity Score of 1.44 and the Clash Score 3.86. The quality estimates and statistical score of Ramachandran plots analysis indicated that the homology model was reliable. For full-length amplification of the gene, primers designed from flanking regions of CDS encoding GS-SQS were used to get amplification against genomic DNA as template which resulted in approximately 6.2-kb sized single-band product. The sequencing of this product through NGS was carried out generating 2.32 Gb data and 3347 number of scaffolds with N50 value of 457 bp. These scaffolds were compared to identify similarity with other SQS genes as well as the GS-SQSs of the transcriptome. Scaffold_3347 representing the GS-SQS gene harbored two introns of 101 and 164 bp size. Both these intronic regions were validated by primers designed from adjoining outside regions of the introns on the scaffold representing GS-SQS gene. The amplification took place when the template was genomic DNA and failed when the template was cDNA confirmed the presence of two introns in GS-SQS gene in Gymnema sylvestre R. Br. Conclusion This study shows GS-SQS gene was very closely related to Coffea arabica and Gardenia jasminoides and this gene harbored two introns of 101 and 164 bp size.

Rapid Amplification of Uncharacterized Transposon-tagged DNA Sequences from Genomic DNA

Yeast ◽  
1997 ◽  
Vol 13 (3) ◽  
pp. 233-240 ◽  
Author(s):  
KRISTIN T. CHUN ◽  
HOWARD J. EDENBERG ◽  
MARK R. KELLEY ◽  
MARK G. GOEBL
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Rapid Amplification

scholarly journals Distribution of sequence-dependent curvature in genomic DNA sequences

FEBS Letters ◽  
1997 ◽  
Vol 406 (1-2) ◽  
pp. 69-74 ◽  
Author(s):  
Andrei Gabrielian ◽  
Kristian Vlahovicek ◽  
Sándor Pongor
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Sequence Dependent

scholarly journals Thermodynamic Model for B-Z Transition of DNA Induced by Z-DNA Binding Proteins

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 2748 ◽  
Author(s):  
Ae-Ree Lee ◽  
Na-Hyun Kim ◽  
Yeo-Jin Seo ◽  
Seo-Ree Choi ◽  
Joon-Hwa Lee
Keyword(s):  
Dna Binding ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Multiple Sequence ◽  
Left Handed ◽  
Transition Mechanism ◽  
Dna Strands ◽  
Z Dna

Z-DNA is stabilized by various Z-DNA binding proteins (ZBPs) that play important roles in RNA editing, innate immune response, and viral infection. In this review, the structural and dynamics of various ZBPs complexed with Z-DNA are summarized to better understand the mechanisms by which ZBPs selectively recognize d(CG)-repeat DNA sequences in genomic DNA and efficiently convert them to left-handed Z-DNA to achieve their biological function. The intermolecular interaction of ZBPs with Z-DNA strands is mediated through a single continuous recognition surface which consists of an α3 helix and a β-hairpin. In the ZBP-Z-DNA complexes, three identical, conserved residues (N173, Y177, and W195 in the Zα domain of human ADAR1) play central roles in the interaction with Z-DNA. ZBPs convert a 6-base DNA pair to a Z-form helix via the B-Z transition mechanism in which the ZBP first binds to B-DNA and then shifts the equilibrium from B-DNA to Z-DNA, a conformation that is then selectively stabilized by the additional binding of a second ZBP molecule. During B-Z transition, ZBPs selectively recognize the alternating d(CG)n sequence and convert it to a Z-form helix in long genomic DNA through multiple sequence discrimination steps. In addition, the intermediate complex formed by ZBPs and B-DNA, which is modulated by varying conditions, determines the degree of B-Z transition.

scholarly journals Genomic DNA sequences of mitochondrial tRNA genes in fungiPenicillium chrysogenumKCTC1262: tRNAarg, tRNAasnand tRNAtyrgenes

1992 ◽  
Vol 20 (21) ◽  
pp. 5842-5842
Author(s):  
Joonho Sheen ◽  
Seungmoak Kim ◽  
Yung Hee Kho ◽  
Kyung Sook Bae
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Trna Genes ◽  
Mitochondrial Trna ◽  
Mitochondrial Trna Genes

Extended Molecular Evolutionary Biology: Artificial Life Bridging the Gap Between Chemistry and Biology

1993 ◽  
Vol 1 (1_2) ◽  
pp. 39-60 ◽  
Author(s):  
P. Schuster
Keyword(s):  
Molecular Evolution ◽  
Artificial Life ◽  
Evolutionary Biology ◽  
State Of The Art ◽  
Test Tube ◽  
Base Pairs ◽  
Current State ◽  
Stability Of Structures ◽  
Novel Applications ◽  
Variation And Selection

Molecular evolution provides an ample field for the extension of Nature's principles towards novel applications. Several examples are discussed here, among them are evolution in the test tube, nucleotide chemistry with new base pairs and new backbones, enzyme-free replication of polynucleotides and template chemistry aiming at replicating structures that have nothing in common with the molecules from nature. Molecular evolution in the test tube provides a uniquely simple system for the study of evolutionary phenomena: genotype and phenotype are two features of one and the same RNA molecule. Then fitness landscapes are nothing more than combined mappings from sequences to structures and from structures to functions, the latter being expressed in terms of rate constants. RNA landscapes are presented as examples for which an access to phenomena in reality by mathematical analysis and computer simulations is feasible. New questions concerning stability of structures in evolution can be raised and quantitative answers are given. Evolutionary biotechnology is a spin-off from molecular evolution. Darwin's principle of variation and selection is applied to design novel biopolymers with predetermined functions. Different approaches to achieve this goal are discussed and a survey of the current state of the art is given.

scholarly journals Chitosan Applications on Pharmaceutical Sciences: A Review

2019 ◽  
Vol 9 (3) ◽  
pp. 167-181
Author(s):  
Cintia Alejandra Briones Nieva ◽  
Mercedes Villegas ◽  
Alicia Graciela Cid ◽  
Analía Irma Romero ◽  
José María Bermúdez
Keyword(s):  
New Technologies ◽  
Immunological Response ◽  
Biological Properties ◽  
Future Research ◽  
Pharmaceutical Sciences ◽  
Chemical Derivatization ◽  
Current State ◽  
Pharmaceutical Applications ◽  
Novel Applications ◽  
State Of Art

Background: Chitosan (CS) is a biomaterial derived from chitin, known for its excellent biological properties. One of the most interesting features of CS is its potential for chemical derivatization, which makes it a versatile material and allows to expand its applications. In the last years, the interest on this polymer and its pharmaceutical applications has notably increased. This biopolymer is being widely studied for its interesting properties, such as bioadhesion, antimicrobial activity, biocompatibility, and biodegradability. Other promising properties of CS include its modulation of immunological response, hemostasis, and wound and bone healing activity. Objective: In this work, a critical review is performed covering its conventional and novel applications, specially focused on pharmaceutical area, providing a clear picture of the current state of art to serve as a basis to direct future research in this field. Conclusion: Despite all the qualities of this polymer, there are only few CS-based products in the market, so it is a priority to enhance the research to develop new technologies and CS-based systems to enforce this biopolymer in the industry.

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