Genetic Music System with Synthetic Biology

This article introduces GeMS, a system for music composition informed by synthetic biology. GeMS generates music with simulations of genetic processes, such as transcription, translation, and protein folding, with which biological systems render chains of amino acids from DNA strands. The system comprises the following components: the Miranda machine, the rhythmator, and the pitch processor. The Miranda machine is an abstract Turing-machine-like processor, which manipulates a sequence of DNA symbols according to a set of programming instructions. This process generates a pool of new DNA strands, which are subsequently translated into rhythms. GeMS represents the musical equivalent of amino acids in terms of rhythms, referred to as rhythmic codons. This enables the rhythmator to convert DNA sequences into rhythmic sequences. The pitch processor generates pitches for such rhythmic sequences. It is inspired by the phenomenon of protein folding. The pitch processor considers orientation information of DNA instructions yielded by the Miranda machine in order to activate algorithms for generating pitches. A musical composition, entitled Artibiotics, for percussion ensemble and electronic instruments, is presented to demonstrate the system.

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A Synthetic Biology Approach Using Engineered Bacteria to Detect Perfluoroalkyl Substance (PFAS) Contamination in Water

Military Medicine ◽

10.1093/milmed/usaa367 ◽

2021 ◽

Vol 186 (Supplement_1) ◽

pp. 801-807

Author(s):

Nathaniel A Young ◽

Ryan L Lambert ◽

Angela M Buch ◽

Christen L Dahl ◽

Jackson D Harris ◽

...

Keyword(s):

Synthetic Biology ◽

Dna Sequences ◽

Detection System ◽

The United States ◽

Detection Methods ◽

Health Concern ◽

Contaminated Water ◽

Engineered Bacteria ◽

Synthetic Biology Approach ◽

Rhodococcus Jostii

ABSTRACT Introduction Per- and polyfluoroalkyl substances (PFAS) are a class of synthetic compounds used industrially for a wide variety of applications. These PFAS compounds are very stable and persist in the environment. The PFAS contamination is a growing health issue as these compounds have been reported to impact human health and have been detected in both domestic and global water sources. Contaminated water found on military bases poses a potentially serious health concern for active duty military, their families, and the surrounding communities. Previous detection methods for PFAS in contaminated water samples require expensive and time-consuming testing protocols that limit the ability to detect this important global pollutant. The main objective of this work was to develop a novel detection system that utilizes a biological reporter and engineered bacteria as a way to rapidly and efficiently detect PFAS contamination. Materials and Methods The United States Air Force Academy International Genetically Engineered Machine team is genetically engineering Rhodococcus jostii strain RHA1 to contain novel DNA sequences composed of a propane 2-monooxygenase alpha (prmA) promoter and monomeric red fluorescent protein (mRFP). The prmA promoter is activated in the presence of PFAS and transcribes the mRFP reporter. Results The recombinant R. jostii containing the prmA promoter and mRFP reporter respond to exposure of PFAS by activating gene expression of the mRFP. At 100 µM of perfluorooctanoic acid, the mRFP expression was increased 3-fold (qRT-PCR). Rhodococcus jostii without exposure to PFAS compounds had no mRFP expression. Conclusions This novel detection system represents a synthetic biology approach to more efficiently detect PFAS in contaminated samples. With further refinement and modifications, a similar system could be readily deployed in the field around the world to detect this critical pollutant.

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Time-dependent communication between multiple amino acids during protein folding

Chemical Science ◽

10.1039/d0sc07025d ◽

2021 ◽

Vol 12 (16) ◽

pp. 5944-5951

Author(s):

Song-Ho Chong ◽

Sihyun Ham

Keyword(s):

Amino Acids ◽

Protein Folding ◽

Transition State ◽

Time Dependent ◽

Transition Path ◽

Contact Formation ◽

Molecular Origin

Cooperativity in contact formation among multiple amino acids starts to develop upon entering the folding transition path and attains a maximum at the folding transition state, providing the molecular origin of the two-state folding behavior.

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

Molecules ◽

10.3390/molecules23112748 ◽

2018 ◽

Vol 23 (11) ◽

pp. 2748 ◽

Cited By ~ 5

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.

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Real-time kinetic studies of Mycobacterium tuberculosis LexA-DNA interaction

Bioscience Reports ◽

10.1042/bcj20210434 ◽

2021 ◽

Author(s):

Chitral Chatterjee ◽

Soneya Majumdar ◽

Sachin Deshpande ◽

Deepak Pant ◽

Saravanan Matheshwaran

Keyword(s):

Amino Acids ◽

Mycobacterium Tuberculosis ◽

Dna Binding ◽

Kinetic Parameters ◽

Dna Sequences ◽

Kinetic Studies ◽

Dna Interaction ◽

Damage Repair ◽

Inducible Genes ◽

Kinetics Of

Transcriptional repressor, LexA, regulates the “SOS” response, an indispensable bacterial DNA damage repair machinery. Compared to its E.coli ortholog, LexA from Mycobacterium tuberculosis (Mtb) possesses a unique N-terminal extension of additional 24 amino acids in its DNA binding domain (DBD) and 18 amino acids insertion at its hinge region that connects the DBD to the C-terminal dimerization/autoproteolysis domain. Despite the importance of LexA in “SOS” regulation, Mtb LexA remains poorly characterized and the functional importance of its additional amino acids remained elusive. In addition, the lack of data on kinetic parameters of Mtb LexA-DNA interaction prompted us to perform kinetic analyses of Mtb LexA and its deletion variants using Bio-layer Interferometry (BLI). Mtb LexA is seen to bind to different “SOS” boxes, DNA sequences present in the operator regions of damage-inducible genes, with comparable nanomolar affinity. Deletion of 18 amino acids from the linker region is found to affect DNA binding unlike the deletion of the N-terminal stretch of extra 24 amino acids. The conserved RKG motif has been found to be critical for DNA binding. Overall, this study provides insights into the kinetics of the interaction between Mtb LexA and its target “SOS” boxes. The kinetic parameters obtained for DNA binding of Mtb LexA would be instrumental to clearly understand the mechanism of “SOS” regulation and activation in Mtb.

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Arac/XylS family of transcriptional regulators

Microbiology and Molecular Biology Reviews ◽

10.1128/mmbr.61.4.393-410.1997 ◽

1997 ◽

Vol 61 (4) ◽

pp. 393-410

Author(s):

M T Gallegos ◽

R Schleif ◽

A Bairoch ◽

K Hofmann ◽

J L Ramos

Keyword(s):

Amino Acids ◽

Dna Sequences ◽

Carbon Metabolism ◽

Binding Sites ◽

Alpha Helix ◽

Transcriptional Regulators ◽

Biochemical Data ◽

Dimerization Domain ◽

Multiple Alignments ◽

The Family

The ArC/XylS family of prokaryotic positive transcriptional regulators includes more than 100 proteins and polypeptides derived from open reading frames translated from DNA sequences. Members of this family are widely distributed and have been found in the gamma subgroup of the proteobacteria, low- and high-G + C-content gram-positive bacteria, and cyanobacteria. These proteins are defined by a profile that can be accessed from PROSITE PS01124. Members of the family are about 300 amino acids long and have three main regulatory functions in common: carbon metabolism, stress response, and pathogenesis. Multiple alignments of the proteins of the family define a conserved stretch of 99 amino acids usually located at the C-terminal region of the regulator and connected to a nonconserved region via a linker. The conserved stretch contains all the elements required to bind DNA target sequences and to activate transcription from cognate promoters. Secondary analysis of the conserved region suggests that it contains two potential alpha-helix-turn-alpha-helix DNA binding motifs. The first, and better-fitting motif is supported by biochemical data, whereas existing biochemical data neither support nor refute the proposal that the second region possesses this structure. The phylogenetic relationship suggests that members of the family have recruited the nonconserved domain(s) into a series of existing domains involved in DNA recognition and transcription stimulation and that this recruited domain governs the role that the regulator carries out. For some regulators, it has been demonstrated that the nonconserved region contains the dimerization domain. For the regulators involved in carbon metabolism, the effector binding determinants are also in this region. Most regulators belonging to the AraC/XylS family recognize multiple binding sites in the regulated promoters. One of the motifs usually overlaps or is adjacent to the -35 region of the cognate promoters. Footprinting assays have suggested that these regulators protect a stretch of up to 20 bp in the target promoters, and multiple alignments of binding sites for a number of regulators have shown that the proteins recognize short motifs within the protected region.

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Some theoretical aspects of reprogramming the standard genetic code

10.1101/2020.09.12.294553 ◽

2020 ◽

Author(s):

Kuba Nowak ◽

Paweł Błażej ◽

Małgorzata Wnetrzak ◽

Dorota Mackiewicz ◽

Paweł Mackiewicz

Keyword(s):

Amino Acids ◽

Genetic Code ◽

Dna Sequences ◽

Theoretical Perspective ◽

Optimal Number ◽

Optimal Size ◽

Coding System ◽

Standard Genetic Code ◽

Nucleotide Mutation ◽

Code Extension

1AbstractReprogramming of the standard genetic code in order to include non-canonical amino acids (ncAAs) opens a new perspective in medicine, industry and biotechnology. There are several methods of engineering the code, which allow us for storing new genetic information in DNA sequences and transmitting it into the protein world. Here, we investigate the problem of optimal genetic code extension from theoretical perspective. We assume that the new coding system should encode both canonical and new ncAAs using 64 classical codons. What is more, the extended genetic code should be robust to point nucleotide mutation and minimize the possibility of reversion from new to old information. In order to do so, we follow graph theory to study the properties of optimal codon sets, which can encode 20 canonical amino acids and stop coding signal. Finally, we describe the set of vacant codons that could be assigned to new amino acids. Moreover, we discuss the optimal number of the newly incorporated ncAAs and also the optimal size of codon blocks that are assigned to ncAAs.

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A set of experimentally validated, mutually orthogonal primers for combinatorially specifying genetic components

Synthetic Biology ◽

10.1093/synbio/ysx008 ◽

2018 ◽

Vol 3 (1) ◽

Cited By ~ 1

Author(s):

Subu K Subramanian ◽

William P Russ ◽

Rama Ranganathan

Keyword(s):

Synthetic Biology ◽

High Throughput ◽

Dna Sequences ◽

Gene Synthesis ◽

Modular Architecture ◽

Design And Synthesis ◽

Genetic Components ◽

Polymerase Chain ◽

Polymerase Chain Reaction Primers ◽

Microarray Chips

Abstract The design and synthesis of novel genes and deoxyribonucleic acid (DNA) sequences is a central technique in synthetic biology. Current methods of high throughput gene synthesis use pooled oligonucleotides obtained from custom-designed DNA microarray chips, and rely on orthogonal (non-interacting) polymerase chain reaction primers to specifically de-multiplex, by amplification, the precise subset of oligonucleotides necessary to assemble a full length gene. The availability of a large validated set of mutually orthogonal primers is therefore a crucial reagent for high-throughput gene synthesis. Here, we present a set of 166 20-nucleotide primers that are experimentally verified to be non-interacting, capable of specifying 13 695 unique genes. These primers represent a valuable resource to the synthetic biology community for specifying genetic components that can be assembled through a scalable and modular architecture.

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DNA Origami Nanomachines

Molecules ◽

10.3390/molecules23071766 ◽

2018 ◽

Vol 23 (7) ◽

pp. 1766 ◽

Cited By ~ 26

Author(s):

Masayuki Endo ◽

Hiroshi Sugiyama

Keyword(s):

Dna Sequences ◽

Molecular Motors ◽

Molecular Machines ◽

Dna Origami ◽

Dna Nanostructures ◽

Molecular Systems ◽

Nanoscale Structures ◽

Research Fields ◽

Dna Strands ◽

External Stimuli

DNA can assemble various molecules and nanomaterials in a programmed fashion and is a powerful tool in the nanotechnology and biology research fields. DNA also allows the construction of desired nanoscale structures via the design of DNA sequences. Structural nanotechnology, especially DNA origami, is widely used to design and create functionalized nanostructures and devices. In addition, DNA molecular machines have been created and are operated by specific DNA strands and external stimuli to perform linear, rotational, and reciprocating movements. Furthermore, complicated molecular systems have been created on DNA nanostructures by arranging multiple molecules and molecular machines precisely to mimic biological systems. Currently, DNA nanomachines, such as molecular motors, are operated on DNA nanostructures. Dynamic DNA nanostructures that have a mechanically controllable system have also been developed. In this review, we describe recent research on new DNA nanomachines and nanosystems that were built on designed DNA nanostructures.

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Selection intensity for codon bias.

Genetics ◽

10.1093/genetics/138.1.227 ◽

1994 ◽

Vol 138 (1) ◽

pp. 227-234 ◽

Cited By ~ 7

Author(s):

D L Hartl ◽

E N Moriyama ◽

S A Sawyer

Keyword(s):

Amino Acids ◽

Dna Sequences ◽

Codon Bias ◽

Enteric Bacteria ◽

Average Intensity ◽

Ancestral State ◽

Selection Intensity ◽

Coding Region ◽

Effective Population ◽

Synonymous Codons

Abstract The patterns of nonrandom usage of synonymous codons (codon bias) in enteric bacteria were analyzed. Poisson random field (PRF) theory was used to derive the expected distribution of frequencies of nucleotides differing from the ancestral state at aligned sites in a set of DNA sequences. This distribution was applied to synonymous nucleotide polymorphisms and amino acid polymorphisms in the gnd and putP genes of Escherichia coli. For the gnd gene, the average intensity of selection against disfavored synonymous codons was estimated as approximately 7.3 x 10(-9); this value is significantly smaller than the estimated selection intensity against selectively disfavored amino acids in observed polymorphisms (2.0 x 10(-8)), but it is approximately of the same order of magnitude. The selection coefficients for optimal synonymous codons estimated from PRF theory were consistent with independent estimates based on codon usage for threonine and glycine. Across 118 genes in E. coli and Salmonella typhimurium, the distribution of estimated selection coefficients, expressed as multiples of the effective population size, has a mean and standard deviation of 0.5 +/- 0.4. No significant differences were found in the degree of codon bias between conserved positions and replacement positions, suggesting that translational misincorporation is not an important selective constraint among synonymous polymorphic codons in enteric bacteria. However, across the first 100 codons of the genes, conserved amino acids with identical codons have significantly greater codon bias than that of either synonymous or nonidentical codons, suggesting that there are unique selective constraints, perhaps including mRNA secondary structures, in this part of the coding region.

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3. Proteins

Biochemistry: A Very Short Introduction ◽

10.1093/actrade/9780198833871.003.0003 ◽

2021 ◽

pp. 34-51

Author(s):

Mark Lorch

Keyword(s):

Amino Acids ◽

Protein Folding ◽

Protein Structure ◽

Protein Structures ◽

Structure And Function ◽

Vast Array ◽

A Cell ◽

Cellular Machinery ◽

And Function ◽

The Relationship

This chapter examines proteins, the dominant proportion of cellular machinery, and the relationship between protein structure and function. The multitude of biological processes needed to keep cells functioning are managed in the organism or cell by a massive cohort of proteins, together known as the proteome. The twenty amino acids that make up the bulk of proteins produce the vast array of protein structures. However, amino acids alone do not provide quite enough chemical variety to complete all of the biochemical activity of a cell, so the chapter also explores post-translation modifications. It finishes by looking as some dynamic aspects of proteins, including enzyme kinetics and the protein folding problem.

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