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Nicholas Chim, Changhua Shi, Sujay P Sau, Ali Nikoomanzar, John C Chaput
Darwinian evolution experiments carried out on xeno-nucleic acid (XNA) polymers require engineered polymerases that can faithfully and efficiently copy genetic information back and forth between DNA and XNA. However, current XNA polymerases function with inferior activity relative to their natural counterparts. Here, we report five X-ray crystal structures that illustrate the pathway by which α-(L)-threofuranosyl nucleic acid (TNA) triphosphates are selected and extended in a template-dependent manner using a laboratory-evolved polymerase known as Kod-RI...
November 27, 2017: Nature Communications
Fernando Orden Rueda, Michal Bista, Matthew D Newton, Anne U Goeppert, M Emanuela Cuomo, Euan Gordon, Felix Kröner, Jon A Read, Jonathan D Wrigley, David Rueda, Benjamin J M Taylor
The CRISPR-Cas9 RNA-guided endonuclease system allows precise and efficient modification of complex genomes and is continuously developed to enhance specificity, alter targeting and add new functional moieties. However, one area yet to be explored is the base chemistry of the associated RNA molecules. Here we show the design and optimisation of hybrid DNA-RNA CRISPR and tracr molecules based on structure-guided approaches. Through careful mapping of the ribose requirements of Cas9, we develop hybrid versions possessing minimal RNA residues, which are sufficient to direct specific nuclease activity in vitro and in vivo with reduced off-target activity...
November 20, 2017: Nature Communications
Ali Nikoomanzar, Matthew R Dunn, John C Chaput
Engineered polymerases that can copy genetic information between DNA and xeno-nucleic acids (XNA) hold tremendous value as reagents in future biotechnology applications. However, current XNA polymerases function with inferior activity relative to their natural counterparts, indicating that current polymerase engineering efforts would benefit from new benchmarking assays. Here, we describe a highly parallel, low-cost method for measuring the average rate and substrate specificity of XNA polymerases in a standard qPCR instrument...
December 5, 2017: Analytical Chemistry
Chengcheng Qu, Mingkai Ma, Wenli Chen, Peng Cai, Qiaoyun Huang
Surface complexation modeling, isothermal titration calorimetry, and batch adsorption were employed to characterize the adsorption of Cu onto montmorillonite, Pseudomonas putida X4, and their composites at mass ratios of 2:1, 6:1, and 12:1, respectively. Different enthalpy values were found for Cu adsorption to permanent (-6.43kJ/mol) and variable charge sites (8.51kJ/mol) on montmorillonite. The component additivity (CA) method was used to predict the adsorption of Cu on the composites by combining end member models for montmorillonite and P...
December 31, 2017: Science of the Total Environment
Ali Nikoomanzar, Matthew R Dunn, John C Chaput
Polymerase engineering is making it possible to synthesize xeno-nucleic acid polymers (XNAs) with diverse backbone structures and chemical functionality. The ability to copy genetic information back and forth between DNA and XNA has led to a new field of science known as synthetic genetics, which aims to study the genetic concepts of heredity and evolution in artificial genetic polymers. Since many of the polymerases needed to synthesize XNA polymers are not available commercially, researchers must express and purify these enzymes as recombinant proteins from E...
June 19, 2017: Current Protocols in Nucleic Acid Chemistry
Stella Diafa, Damien Evéquoz, Christian J Leumann, Marcel Hollenstein
The selection of artificial genetic polymers with tailor-made properties for their application in synthetic biology requires the exploration of new nucleosidic scaffolds that can be used in selection experiments. Herein, we describe the synthesis of a bicyclo-DNA triphosphate (i.e., 7',5'-bc-TTP) and show its potential to serve for the generation of new xenonucleic acids (XNAs) based on this scaffold. 7',5'-bc-TTP is a good substrate for Therminator DNA polymerase, and up to seven modified units can be incorporated into a growing DNA chain...
March 31, 2017: Chemistry, An Asian Journal
Jen-Yu Liao, Irina Anosova, Saikat Bala, Wade D Van Horn, John C Chaput
G-rich sequences can adopt four-stranded helical structures, called G-quadruplexes, that self-assemble around monovalent cations like sodium (Na(+) ) and potassium (K(+) ). Whether similar structures can be formed from xeno-nucleic acid (XNA) polymers with a shorter backbone repeat unit is an unanswered question with significant implications on the fold space of functional XNA polymers. Here, we examine the potential for TNA (α-l-threofuranosyl nucleic acid) to adopt a four-stranded helical structure based on a planar G-quartet motif...
March 2017: Biopolymers
Ozlem Yaren, Kevin M Bradley, Patricia Moussatche, Shuichi Hoshika, Zunyi Yang, Shu Zhu, Stephanie M Karst, Steven A Benner
Noroviruses are the major cause of global viral gastroenteritis with short incubation times and small inoculums required for infection. This creates a need for a rapid molecular test for norovirus for early diagnosis, in the hope of preventing the spread of the disease. Non-chemists generally use off-the shelf reagents and natural DNA to create such tests, suffering from background noise that comes from adventitious DNA and RNA (collectively xNA) that is abundant in real biological samples, especially feces, a common location for norovirus...
November 2016: Journal of Virological Methods
Weixin Yan, Aiguo Zhang, Michael J Powell
Gastrointestinal stromal tumors (GISTs) have been recognized as a biologically distinctive type of tumor, different from smooth muscle and neural tumors of the gastrointestinal tract. The identification of genetic aberrations in proto-oncogenes that drive the growth of GISTs is critical for improving the efficacy of cancer therapy by matching targeted drugs to specific mutations. Research into the oncogenic mechanisms of GISTs has found that these tumors frequently contain activating gene mutations in either platelet-derived growth factor receptor A (PDGFRA) or a receptor tyrosine protein associated with a mast cell growth factor receptor encoded by the KIT gene...
July 21, 2016: Chinese Journal of Cancer
Ozlem Yaren, Lyudmyla G Glushakova, Kevin M Bradley, Shuichi Hoshika, Steven A Benner
This paper combines two advances to detect MERS-CoV, the causative agent of Middle East Respiratory Syndrome, that have emerged over the past few years from the new field of "synthetic biology". Both are based on an older concept, where molecular beacons are used as the downstream detection of viral RNA in biological mixtures followed by reverse transcription PCR amplification. The first advance exploits the artificially expanded genetic information systems (AEGIS). AEGIS adds nucleotides to the four found in standard DNA and RNA (xNA); AEGIS nucleotides pair orthogonally to the A:T and G:C pairs...
October 2016: Journal of Virological Methods
Matthew R Dunn, John C Chaput
Recent advances in polymerase engineering have enabled the replication of xenonucleic acid (XNA) polymers with backbone structures distinct from those found in nature. By introducing a selective amplification step into the replication cycle, functional XNA molecules have been isolated by in vitro selection with binding and catalytic activity. Despite these successes, coding and decoding genetic information in XNA polymers remains limited by the fidelity and catalytic efficiency of engineered XNA polymerases...
October 4, 2016: Chembiochem: a European Journal of Chemical Biology
Soumadwip Ghosh, Rajarshi Chakrabarti
Xenonucleic acids are synthetic nucleic acid analogues that are potential candidates for antisense or antigene therapy owing to their higher thermal and enzymatic stability compared to that of naturally occurring ones at physiological conditions. We investigate the binding and unzipping of xylonucleic acid (XNA) containing xylose (a stereoisomer of ribose) sugar in its backbone assisted by a single walled carbon nanotube (SWCNT) using extensive atomistic molecular dynamics simulations. Our simulations confirm XNA to undergo faster unzipping compared to a double stranded RNA with the same nucleobase sequence which is presumably due to the near orthogonal base pairing arrangement of the constituent nucleobases of XNA at physiologically relevant conditions (in terms of temperature and salt concentration)...
April 21, 2016: Journal of Physical Chemistry. B
Alexander I Taylor, Fabienne Beuron, Sew-Yeu Peak-Chew, Edward P Morris, Piet Herdewijn, Philipp Holliger
Nanoscale objects of increasing complexity can be constructed from DNA or RNA. However, the scope of potential applications could be enhanced by expanding beyond the moderate chemical diversity of natural nucleic acids. Here, we explore the construction of nano-objects made entirely from alternative building blocks: synthetic genetic polymers not found in nature, also called xeno nucleic acids (XNAs). Specifically, we describe assembly of 70 kDa tetrahedra elaborated in four different XNA chemistries (2'-fluro-2'-deoxy-ribofuranose nucleic acid (2'F-RNA), 2'-fluoroarabino nucleic acids (FANA), hexitol nucleic acids (HNA), and cyclohexene nucleic acids (CeNA)), as well as mixed designs, and a ∼600 kDa all-FANA octahedron, visualised by electron microscopy...
June 16, 2016: Chembiochem: a European Journal of Chemical Biology
Matheus Froeyen, Rania Abu el Asrar, Mikhail Abramov, Piet Herdewijn
As part of a selection strategy for artificial nucleic acids (XNA) (to be considered as potential new information systems in vivo), we have carried out a modelling study on cyclohexanyl nucleic acids (CNA) duplexes and hairpins. CNA may form a duplex as well as hairpin structures, having the carbocyclic nucleosides in the (4)C1 conformation (with equatorial basis). The geometry of ds CNA is close to that of a HNA:RNA duplex. We demonstrated that CNA triphosphates function as a substrate for polymerases. Modelling experiments indicate that the monomers are probably presented to the polymerase in the (1)C4 conformation...
April 15, 2016: Bioorganic & Medicinal Chemistry
Matthew R Dunn, Carine Otto, Kathryn E Fenton, John C Chaput
The ability to synthesize and propagate genetic information encoded in the framework of xeno-nucleic acid (XNA) polymers would inform a wide range of topics from the origins of life to synthetic biology. While directed evolution has produced examples of engineered polymerases that can accept XNA substrates, these enzymes function with reduced activity relative to their natural counterparts. Here, we describe a biochemical strategy that enables the discovery of engineered polymerases with improved activity for a given unnatural polymerase function...
May 20, 2016: ACS Chemical Biology
Dennis Rataj, Sonja Werwitzke, Birgitt Haarmeijer, Michael Winkler, Wolf Ramackers, Björn Petersen, Heiner Niemann, Annegret Wünsch, Andrea Bähr, Nikolai Klymiuk, Eckhard Wolf, Jan-Michael Abicht, David Ayares, Andreas Tiede
BACKGROUND: Xenogeneic thrombotic microangiopathy (TMA) and acute vascular rejection (AVR) prevent long-term survival of porcine xenografts after transplantation into non-human primates. Preformed xenoreactive natural antibodies (XNA) cause endothelial damage and activate the complement system. Mechanisms of xenogeneic coagulation and platelet activation are only poorly characterized. METHODS: A microfluidic flow chamber was used to study platelet activation and thrombus formation of human platelet-rich plasma (PRP) upon perfusion over wild-type (WT) or α-1,3- galactosyltransferase knockout (GTKO) and human CD46 (hCD46) transgenic porcine aortic endothelial cells (PAEC)...
March 2016: Xenotransplantation
Irina Anosova, Ewa A Kowal, Matthew R Dunn, John C Chaput, Wade D Van Horn, Martin Egli
Synthetic genetics is a subdiscipline of synthetic biology that aims to develop artificial genetic polymers (also referred to as xeno-nucleic acids or XNAs) that can replicate in vitro and eventually in model cellular organisms. This field of science combines organic chemistry with polymerase engineering to create alternative forms of DNA that can store genetic information and evolve in response to external stimuli. Practitioners of synthetic genetics postulate that XNA could be used to safeguard synthetic biology organisms by storing genetic information in orthogonal chromosomes...
February 18, 2016: Nucleic Acids Research
Irani Alves Ferreira-Bravo, Christopher Cozens, Philipp Holliger, Jeffrey J DeStefano
Using a Systematic Evolution of Ligands by Exponential Enrichment (SELEX) protocol capable of selecting xeno-nucleic acid (XNA) aptamers, a 2'-deoxy-2'-fluoroarabinonucleotide (FANA) aptamer (referred to as FA1) to HIV-1 reverse transcriptase (HIV-1 RT) was selected. FA1 bound HIV-1 RT with KD,app values in the low pM range under different ionic conditions. Comparisons to published HIV-1 RT RNA and DNA aptamers indicated that FA1 bound at least as well as these aptamers. FA1 contained a 20 nucleotide 5' DNA sequence followed by a 57 nucleotide region of FANA nucleotides...
November 16, 2015: Nucleic Acids Research
Alexander I Taylor, Philipp Holliger
This protocol describes the directed evolution of artificial endonuclease and ligase enzymes composed of synthetic genetic polymers (XNAzymes), using 'cross-chemistry selective enrichment by exponential amplification' (X-SELEX). The protocol is analogous to (deoxy)ribozyme selections, but it enables the development of fully substituted catalysts. X-SELEX is initiated by the synthesis of diverse repertoires (here 10(14) different sequences), using xeno nucleic acid (XNA) polymerases, on DNA templates primed with DNA, RNA or XNA oligonucleotides that double as substrates, allowing selection for XNA-catalyzed cleavage or ligation...
October 2015: Nature Protocols
Lyudmyla G Glushakova, Nidhi Sharma, Shuichi Hoshika, Andrea C Bradley, Kevin M Bradley, Zunyi Yang, Steven A Benner
Nucleic acid (NA)-targeted tests detect and quantify viral DNA and RNA (collectively xNA) to support epidemiological surveillance and, in individual patients, to guide therapy. They commonly use polymerase chain reaction (PCR) and reverse transcription PCR. Although these all have rapid turnaround, they are expensive to run. Multiplexing would allow their cost to be spread over multiple targets, but often only with lower sensitivity and accuracy, noise, false positives, and false negatives; these arise by interactions between the multiple nucleic acid primers and probes in a multiplexed kit...
November 15, 2015: Analytical Biochemistry
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