Genetic information storage and processing rely on just two polymers, DNA RNA, yet whether their role reflects evolutionary history or fundamental functional constraints is currently unknown. With the use of polymerase evolution design, we show that genetic can be stored in recovered from six alternative polymers based simple nucleic acid architectures not found nature [xeno-nucleic acids (XNAs)]. We also select XNA aptamers, which bind targets with high affinity specificity, demonstrating...

In an effort to expand the binding and recognition capabilities of aptamers, a nucleoside triphosphate modified with phenol that mimics side chain tyrosine was used in selection DNA aptamers against live bacteria. Of multiple were isolated Escherichia coli DH5α cells, one aptamer displays high selectivity affinity for target cells is greatly enriched phenol-modified dU nucleotides (dUy, 47.5%). When same sequences are synthesized TTP, no observed. Taken together, these findings highlight...

T4 DNA ligase is capable of ligating XNA in the presence 10% w/v PEG8000 and 3 M betaine.

Pradimicin S (PRM-S) is a highly water-soluble, negatively charged derivative of the antibiotic pradimicin A (PRM-A) in which terminal xylose moiety has been replaced by 3-sulfated glucose. PRM-S does not prevent human immunodeficiency virus (HIV) adsorption on CD4(+) T cells, but it blocks entry into its target cells. It inhibits wide variety HIV-1 laboratory strains and clinical isolates, HIV-2, simian (SIV) various cell culture systems (50% 90% effective concentrations [EC(50)s EC(90)s]...

Abstract Objectives This study aimed to assess the antiviral properties of a unique lectin (NICTABA) produced by tobacco plant, Nicotiana tabacum. Methods Cellular assays were used investigate activity NICTABA and Urtica dioica agglutinin (UDA). Surface plasmon resonance (SPR) studies performed sugar specificity interactions both lectins with envelope glycoproteins HIV-1. Results The N-acetyl-d-glucosamine (GlcNAc)-binding exhibited broad-spectrum against several families enveloped viruses...

On the basis of interesting inhibitory properties that lectins show against HIV-replication through their interaction with glycoprotein 120 (gp120), we here describe design, synthesis, and anti-HIV evaluation three series 1,3,5-triazine derivatives (monomers, dimers, trimers) functionalized aromatic amino acids meant to mimic interactions establish gp120. While monomers were inactive HIV replication, dimers showed limited activity is, however, considerably more significant in trimers series,...

Abstract Insertions and deletions (indels) are known to affect function, biophysical properties substrate specificity of enzymes, they play a central role in evolution. Despite such clear significance, this class mutation remains an underexploited tool protein engineering with few available platforms capable systematically generating analysing libraries varying sequence composition length. We present novel DNA assembly platform (InDel assembly), based on cycles endonuclease restriction...

Modified DNAzyme selections typically depend on recopying catalytically active modified DNA (mDNA) into cDNA in a PCR amplification step. However mDNA is often poor template PCR. Herein we propose selection method which the active, strand covalently linked to unmodified from it was polymerized. Following selection, amplified instead of mDNA. This circumvents

Therminator is the hero when it comes to enzymatic production of phosphonomethyl–threosyl oligonucleotides with a non-natural 3′–2′ linkage (see scheme). The ability polymerase catalyze condensation diphosphate derivatives nucleosides give modified oligomers promises be quite general. Such are useful tools in synthetic biology because innate stability phosphonate linkage. Supporting information for this article available on WWW under...

The enzymatic recognition of six-membered ring nucleoside triphosphates--in particular the 6'-triphosphates (beta-D-glucopyranosyl)thymine, (2',3'-dideoxy-beta-D-glucopyranosyl)thymine, (3',4'-dideoxy-beta-D-glucopyranosyl)thymine and (2',3'-dideoxy-beta-D-glucopyranosyl)adenine--was investigated. Despite facts that pyranose nucleic acids obtained by polymerisation these monomers do not hybridise in solution with DNA geometry a strand natural duplex differs from acid, elongation all four...

Directed evolution has been remarkably successful at expanding the chemical and functional boundaries of biology. That progress is heavily dependent on robustness flexibility available selection platforms, given significant cost to (re)develop a platform target new desired function. Bacterial cell display track record as viable strategy for engineering mesophilic enzymes, enzyme activity can be probed directly free from interference cellular milieu, but its adoption lagged behind other...

Six 1′,5′-anhydrohexitol uridine triphosphates were synthesized with aromatic substitutions appended via a carboxamide linker to the 5-position of their bases. An improved method for obtaining such 5-substituted hexitol nucleosides and nucleotides is described. The incorporation profile nucleotide analogues into DNA duplex overhang using recently evolved XNA polymerases compared. Long, mixed HNA sequences featuring base modifications are generated. apparent binding affinity four enzyme, rate...

Abstract 5′‐O‐Phosphonomethyl‐2′‐deoxyadenosine (PMdA) proved to be a good substrate of the Therminator polymerase. In this article, we investigated whether A, C, T and U analogues phosphonate nucleoside (PMdN) series can function as substrates natural DNA polymerases. PMdT PMdU could only polymerized enzymatically limited extent. Nevertheless, PMdA PMdC incorporated into duplex with complete chain elongation by all polymerases tested. A mixed sequence four nucleotides containing modified...

Abstract Insertions and deletions (indels) are known to affect function, biophysical properties substrate specificity of enzymes, they play a central role in evolution. Despite such clear significance, this class mutation remains an underexploited tool protein engineering with no available platforms capable systematically generating or analysing libraries varying sequence composition length. We present novel DNA assembly platform (InDel assembly), based on cycles endonuclease restriction...

Ein Therminator als Held bei der enzymatischen Produktion von Phosphonomethyl-Threosyl-Oligonucleotiden mit nichtnatürlicher 3′-2′-Verknüpfung (siehe Bild): Die Therminator-Polymerase scheint die Kondensation Diphosphatderivaten Nucleosiden zu modifizierten Oligomeren allgemein katalysieren. Solche Oligonucleotide sind für synthetische Biologie wegen ihrer stabilen Phosphonatbrücke wichtig.

Abstract T4 DNA ligase in high concentrations of certain crowding agents and cosolutes catalyzes the synthesis a series backbone‐modified oligonucleotides that are difficult to obtain chemically. Backbone‐modified nucleic acids often enzymatically chemically more stable, making them interesting as potential diagnostic or therapeutic agents, biosafety tool, nanotechnology. In this article, we describe small‐scale experiment probe efficiency ligation reaction modified presence 3 M betaine 10%...

The 2'-N-formamide derivatives of adenosine, cytidine, and 9-beta-d-arabinofuranosyladenine were synthesized tested (as triphosphate) for their substrate capacities the HCV NS5B polymerase.

Abstract Although directed evolution has been remarkably successful at expanding the chemical and functional boundaries of biology, it is limited by robustness flexibility available selection platforms – traditionally designed around a single desired function with scope for alternative applications. We report SNAP as quantitative reporter bacterial cell display, which enabled fast troubleshooting systematic development platform. In addition, we demonstrate that even weak interactions between...

Abstract By measuring a DNA polymerase incorporation reaction on very short time scale (5 ms to 10 s) and with high enzyme concentration, the isolated event of single nucleotide can be analyzed. Practically, this is done using quench‐flow instrument, which allows rapid mixing enzyme‐primer/template substrate, after quenched We describe how titrate active site, determine, via scouting experiment, rate‐limiting step in polymerization reaction, measure apparent k pol , K d(DNA) d(N) burst or...