scholarly journals Bilingual Peptide Nucleic Acids: Encoding the Languages of Nucleic Acids and Proteins in a Single Self-Assembling Biopolymer

Author(s):  
Colin Swenson ◽  
Arventh Velusamy ◽  
Hector Argueta-Gonzalez ◽  
Jennifer Heemstra

<div> <div> <div> <p>Nucleic acids and proteins are the fundamental biopolymers that support all life on Earth. Nucleic acids store large amounts of information in nucleobase sequences while peptides and proteins utilize diverse amino acid functional groups to adopt complex structures and perform wide-ranging activities. Although Nature has evolved machinery to read the nucleic acid code and translate it into amino acid code, the extant biopolymers are restricted to encoding amino acid or nucleotide sequences separately, limiting their potential applications in medicine and biotechnology. Here we describe the design, synthesis, and stimuli-responsive assembly behavior of a bilingual biopolymer that integrates both amino acid and nucleobase sequences into a single peptide nucleic acid (PNA) scaffold to enable tunable storage and retrieval of tertiary structural behavior and programmable molecular recognition capabilities. Incorporation of a defined sequence of amino acid side-chains along the PNA backbone yields amphiphiles having a “protein code” that directs self-assembly into micellar architectures in aqueous conditions. However, these amphiphiles also carry a “nucleotide code” such that subsequent introduction of a complementary RNA strand induces a sequence-specific disruption of assemblies through hybridization. Together, these properties establish bilingual PNA as a powerful biopolymer that combines two information systems to harness structural responsiveness and sequence recognition. The PNA scaffold and our synthetic system are highly generalizable, enabling fabrication of a wide array of user-defined peptide and nucleotide sequence combinations for diverse future biomedical and nanotechnology applications. </p> </div> </div> </div>

2019 ◽  
Author(s):  
Colin Swenson ◽  
Arventh Velusamy ◽  
Hector Argueta-Gonzalez ◽  
Jennifer Heemstra

<div> <div> <div> <p>Nucleic acids and proteins are the fundamental biopolymers that support all life on Earth. Nucleic acids store large amounts of information in nucleobase sequences while peptides and proteins utilize diverse amino acid functional groups to adopt complex structures and perform wide-ranging activities. Although Nature has evolved machinery to read the nucleic acid code and translate it into amino acid code, the extant biopolymers are restricted to encoding amino acid or nucleotide sequences separately, limiting their potential applications in medicine and biotechnology. Here we describe the design, synthesis, and stimuli-responsive assembly behavior of a bilingual biopolymer that integrates both amino acid and nucleobase sequences into a single peptide nucleic acid (PNA) scaffold to enable tunable storage and retrieval of tertiary structural behavior and programmable molecular recognition capabilities. Incorporation of a defined sequence of amino acid side-chains along the PNA backbone yields amphiphiles having a “protein code” that directs self-assembly into micellar architectures in aqueous conditions. However, these amphiphiles also carry a “nucleotide code” such that subsequent introduction of a complementary RNA strand induces a sequence-specific disruption of assemblies through hybridization. Together, these properties establish bilingual PNA as a powerful biopolymer that combines two information systems to harness structural responsiveness and sequence recognition. The PNA scaffold and our synthetic system are highly generalizable, enabling fabrication of a wide array of user-defined peptide and nucleotide sequence combinations for diverse future biomedical and nanotechnology applications. </p> </div> </div> </div>


2020 ◽  
Vol 16 ◽  
pp. 2017-2025
Author(s):  
Goutam Ghosh ◽  
Gustavo Fernández

Peptide-based biopolymers represent highly promising biocompatible materials with multiple applications, such as tailored drug delivery, tissue engineering and regeneration, and as stimuli-responsive materials. Herein, we report the pH- and concentration-dependent self-assembly and conformational transformation of the newly synthesized octapeptide PEP-1. At pH 7.4, PEP-1 forms β-sheet-rich secondary structures into fractal-like morphologies, as verified by circular dichroism (CD), Fourier-transform infrared (FTIR) spectroscopy, thioflavin T (ThT) fluorescence spectroscopy assay, and atomic force microscopy (AFM). Upon changing the pH value (using pH 5.5 and 13.0), PEP-1 forms different types of secondary structures and resulting morphologies due to electrostatic repulsion between charged amino acids. PEP-1 can also form helical or random-coil secondary structures at a relatively low concentration. The obtained pH-sensitive self-assembly behavior of the target octapeptide is expected to contribute to the development of novel drug nanocarrier assemblies.


2018 ◽  
Vol 14 ◽  
pp. 114-129 ◽  
Author(s):  
Mattias Bood ◽  
Sangamesh Sarangamath ◽  
Moa S Wranne ◽  
Morten Grøtli ◽  
L Marcus Wilhelmsson

Förster resonance energy transfer (FRET) between a donor nucleobase analogue and an acceptor nucleobase analogue, base–base FRET, works as a spectroscopic ruler and protractor. With their firm stacking and ability to replace the natural nucleic acid bases inside the base-stack, base analogue donor and acceptor molecules complement external fluorophores like the Cy-, Alexa- and ATTO-dyes and enable detailed investigations of structure and dynamics of nucleic acid containing systems. The first base–base FRET pair, tCO–tCnitro, has recently been complemented with among others the adenine analogue FRET pair, qAN1–qAnitro, increasing the flexibility of the methodology. Here we present the design, synthesis, photophysical characterization and use of such base analogues. They enable a higher control of the FRET orientation factor, κ 2, have a different distance window of opportunity than external fluorophores, and, thus, have the potential to facilitate better structure resolution. Netropsin DNA binding and the B-to-Z-DNA transition are examples of structure investigations that recently have been performed using base–base FRET and that are described here. Base–base FRET has been around for less than a decade, only in 2017 expanded beyond one FRET pair, and represents a highly promising structure and dynamics methodology for the field of nucleic acids. Here we bring up its advantages as well as disadvantages and touch upon potential future applications.


2018 ◽  
Vol 115 (7) ◽  
pp. E1391-E1400 ◽  
Author(s):  
Yihuang Chen ◽  
Zewei Wang ◽  
Yanjie He ◽  
Young Jun Yoon ◽  
Jaehan Jung ◽  
...  

The ability to dynamically organize functional nanoparticles (NPs) via the use of environmental triggers (temperature, pH, light, or solvent polarity) opens up important perspectives for rapid and convenient construction of a rich variety of complex assemblies and materials with new structures and functionalities. Here, we report an unconventional strategy for crafting stable hairy NPs with light-enabled reversible and reliable self-assembly and tunable optical properties. Central to our strategy is to judiciously design amphiphilic star-like diblock copolymers comprising inner hydrophilic blocks and outer hydrophobic photoresponsive blocks as nanoreactors to direct the synthesis of monodisperse plasmonic NPs intimately and permanently capped with photoresponsive polymers. The size and shape of hairy NPs can be precisely tailored by modulating the length of inner hydrophilic block of star-like diblock copolymers. The perpetual anchoring of photoresponsive polymers on the NP surface renders the attractive feature of self-assembly and disassembly of NPs on demand using light of different wavelengths, as revealed by tunable surface plasmon resonance absorption of NPs and the reversible transformation of NPs between their dispersed and aggregated states. The dye encapsulation/release studies manifested that such photoresponsive NPs may be exploited as smart guest molecule nanocarriers. By extension, the star-like block copolymer strategy enables the crafting of a family of stable stimuli-responsive NPs (e.g., temperature- or pH-sensitive polymer-capped magnetic, ferroelectric, upconversion, or semiconducting NPs) and their assemblies for fundamental research in self-assembly and crystallization kinetics of NPs as well as potential applications in optics, optoelectronics, magnetic technologies, sensory materials and devices, catalysis, nanotechnology, and biotechnology.


2015 ◽  
Vol 3 (4) ◽  
pp. 627-635 ◽  
Author(s):  
Tao Peng ◽  
Hwankyu Lee ◽  
Sierin Lim

Controlling the self-assembly behavior of caged proteins expands their potential applications in nanotechnology.


2011 ◽  
Vol 361 (2) ◽  
pp. 587-593 ◽  
Author(s):  
Hana Svobodová ◽  
Nonappa ◽  
Zdeněk Wimmer ◽  
Erkki Kolehmainen

2020 ◽  
Author(s):  
David M. Fialho ◽  
Suneesh C. Karunakaran ◽  
Katherine W. Greeson ◽  
Isaac Martínez ◽  
Gary B. Schuster ◽  
...  

AbstractThe mechanism by which genetic polymers spontaneously formed on the early Earth is currently unknown. The RNA World hypothesis implies that RNA oligomers were produced prebiotically, but the demonstration of this process has proven challenging. Alternatively, RNA may be the product of evolution and some, or all, of its chemical components may have been preceded by functionally analogous moieties that were more readily accessible under plausible early-Earth conditions. We report a new class of nucleic acid analog, depsipeptide nucleic acid, which displays several properties that make it an attractive candidate for the first informational polymer to arise on the Earth. The monomers of depsipeptide nucleic acids can form under plausibly prebiotic conditions. These monomers oligomerize spontaneously when dried from aqueous solutions to form nucleobase-functionalized depsipeptides. Once formed, these depsipeptide nucleic acid oligomers are capable of complementary self-assembly, and are resistant to hydrolysis in the assembled state. These results suggest that the initial formation of primitive, self-assembling, informational polymers may have been relatively facile.


Author(s):  
Tommaso Fraccia ◽  
Tony Z. Jia

<p>Phase separation of nucleic acids and proteins is a ubiquitous phenomenon regulating sub-cellular compartment structure and function. While complex coacervation of flexible single stranded nucleic acids is broadly investigated, coacervation of double stranded DNA (dsDNA) is less studied because of its propensity to generate solid precipitates. Here, we reverse this perspective by showing that short dsDNA and poly-L-lysine coacervates can escape precipitation while displaying a surprisingly complex phase diagram, including the full set of liquid crystal (LC) mesophases observed to date in bulk dsDNA. LC-coacervate structure was characterized upon variations in temperature and monovalent salt, DNA and peptide concentrations, which allow continuous transitions between all accessible phases. A deeper understanding of LC-coacervates can gain insights to decipher structures and phase transition mechanisms within biomolecular condensates, to design stimuli-responsive multi-phase synthetic compartments with different degrees of order and to exploit self-assembly driven cooperative prebiotic evolution of nucleic acids and peptides.</p>


2022 ◽  
Author(s):  
Munusamy Krishnamurthy ◽  
Philip Hope ◽  
P Ramar ◽  
A. A. Boopathi ◽  
Srinivasan Sampath ◽  
...  

Photo-catalysts offer a simple catalytic method with widespread applications like degradation of polluting dyes, hydrogen generation from water, etc., in the presence of a photon source like sunlight. The development of a second-generation photo-catalyst in the form of a nanocomposite is an integral part of research to improve the practical usefulness and efficiency of the process. A systematic study using the active material with controlled functional groups is required to understand the process in detail as well as to develop efficient photocatalytic systems. In this paper, we report the design, synthesis, detailed physicochemical studies, and self-assembly of interesting materials where fullerenes have been functionalized with polycyclic, aromatic, conjugated, butterfly-shaped molecules like Tetrabenzofluorene (TBF) using a well-known click chemistry approach. Detailed analyses using spectroscopic, electrochemical, and microscopic or X-ray diffraction (single crystal) techniques were undertaken for a clear understanding of their photophysical or self-assembly behavior. The functionalized fullerene material was mainly used so that comparative results could be presented where two units (mono adduct) or twelve units (hexakis adduct) of TBF molecules were attached separately. These comparative studies were beneficial for unambiguous interpretation of results and drawing definitive conclusions regarding the energy transfer with cascade-type systems. Finally, those results were useful for the logical understanding of photo-catalytic experiments using those designer fullerene materials.


Author(s):  
David M. Fialho ◽  
Suneesh C. Karunakaran ◽  
Katherine W. Greeson ◽  
Isaac Martínez ◽  
Gary B. Schuster ◽  
...  

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