Manipulation Of DNA Sequences Research Articles

Investigating the Frontiers of Genetic Regulation and Unlocking the Secrets of Gene Expression: The Power of RNA-based Therapeutics

Advancements in genome editing have revolutionized the field of biotechnology by enabling precise manipulation of DNA sequences. The ability to edit genes has significant implications for treating genetic diseases and developing novel therapeutics. Despite the considerable progress made in genome editing, there are still concerns over its off-target effects and ethical considerations, which have spurred the exploration of alternative approaches. In this context, we present a paper on antisense technology, an innovative biological approach that has the potential to regulate gene expression by halting the translation process of mRNA and suppressing protein production. We highlight the limitations of current genome editing technologies and the need for more targeted and personalized approaches to treat genetic disorders. Antisense technology employs artificially synthesized oligonucleotides or small RNA sequences to target specific genes and inhibit their expression. This approach provides greater specificity and control over gene expression, making it a highly promising therapeutic option for various diseases such as cancer, cardiovascular diseases, and viral infections. We discuss the current status of antisense technology, its potential future prospects, as well as the challenges and opportunities that need to be addressed to fully exploit its potential. Overall, our paper aims to shed light on the significance of antisense technology in the field of biotechnology and its potential to revolutionize gene expression regulation. By providing an overview of this innovative approach, we hope to inspire further research in this area and pave the way for novel and more effective therapies for genetic disorders.

Applications and Major Achievements of Genome Editing in Vegetable Crops: A Review.

The emergence of genome-editing technology has allowed manipulation of DNA sequences in genomes to precisely remove or replace specific sequences in organisms resulting in targeted mutations. In plants, genome editing is an attractive method to alter gene functions to generate improved crop varieties. Genome editing is thought to be simple to use and has a lower risk of off-target effects compared to classical mutation breeding. Furthermore, genome-editing technology tools can also be applied directly to crops that contain complex genomes and/or are not easily bred using traditional methods. Currently, highly versatile genome-editing tools for precise and predictable editing of almost any locus in the plant genome make it possible to extend the range of application, including functional genomics research and molecular crop breeding. Vegetables are essential nutrient sources for humans and provide vitamins, minerals, and fiber to diets, thereby contributing to human health. In this review, we provide an overview of the brief history of genome-editing technologies and the components of genome-editing tool boxes, and illustrate basic modes of operation in representative systems. We describe the current and potential practical application of genome editing for the development of improved nutritious vegetables and present several case studies demonstrating the potential of the technology. Finally, we highlight future directions and challenges in applying genome-editing systems to vegetable crops for research and product development.

Mechanistic modelling of a recombinase‐based two‐input temporal logic gate

Site-specific recombinases (SSRs) mediate efficient manipulation of DNA sequences in vitro and in vivo. In particular, serine integrases have been identified as highly effective tools for facilitating DNA inversion, enabling the design of genetic switches that are capable of turning the expression of a gene of interest on or off in the presence of a SSR protein. The functional scope of such circuitry can be extended to biological Boolean logic operations by incorporating two or more distinct integrase inputs. To date, mathematical modelling investigations have captured the dynamical properties of integrase logic gate systems in a purely qualitative manner, and thus such models are of limited utility as tools in the design of novel circuitry. Here, the authors develop a detailed mechanistic model of a two-input temporal logic gate circuit that can detect and encode sequences of input events. Their model demonstrates quantitative agreement with time-course data on the dynamics of the temporal logic gate, and is shown to subsequently predict dynamical responses relating to a series of induction separation intervals. The model can also be used to infer functional variations between distinct integrase inputs, and to examine the effect of reversing the roles of each integrase on logic gate output.

Capturing, sharing and analysing biophysical data from protein engineering and protein characterization studies

Large amounts of data are being generated annually on the connection between the sequence, structure and function of proteins using site-directed mutagenesis, protein design and directed evolution techniques. These data provide the fundamental building blocks for our understanding of protein function, molecular biology and living organisms in general. However, much experimental data are never deposited in databases and is thus ‘lost’ in journal publications or in PhD theses. At the same time theoretical scientists are in need of large amounts of experimental data for benchmarking and calibrating novel predictive algorithms, and theoretical progress is therefore often hampered by the lack of suitable data to validate or disprove a theoretical assumption. We present PEAT (Protein Engineering Analysis Tool), an application that integrates data deposition, storage and analysis for researchers carrying out protein engineering projects or biophysical characterization of proteins. PEAT contains modules for DNA sequence manipulation, primer design, fitting of biophysical characterization data (enzyme kinetics, circular dichroism spectroscopy, NMR titration data, etc.), and facilitates sharing of experimental data and analyses for a typical university-based research group. PEAT is freely available to academic researchers at http://enzyme.ucd.ie/PEAT.

Computer Manipulation of DNA and Protein Sequences

This unit outlines a variety of methods by which DNA sequences can be manipulated by computers. Procedures for entering sequence data into the computer and assembling raw sequence data into a contiguous sequence are described first, followed by a description of methods of analyzing and manipulating sequences--e.g., verifying sequences, constructing restriction maps, designing oligonucleotides, identifying protein-coding regions, and predicting secondary structures. This unit also provides information on the large amount of software available for sequence analysis. The appendix to this unit lists some of the commercial software, shareware, and free software related to DNA sequence manipulation. The goal of this unit is to serve as a starting point for researchers interested in utilizing the tremendous sequencing resources available to the computer-knowledgeable molecular biology laboratory.

Leftward ribosome frameshifting at a hungry codon

Previous experiments have shown that limitation for certain aminoacyl-tRNA species results in phenotypic suppression of a subset of frameshift mutant alleles, including members in both the (+) and (−) incorrect reading frames. Here, we demonstrate that such phenotypic suppression can occur through a ribosome reading frame shift at a hungry AAG codon calling for lysyl-tRNA in short supply. Direct amino acid sequence analysis of the product and DNA sequence manipulation of the gene demonstrate that the ribosome frameshift occurs through a movement of one base to the left, so as to decode the triplet overlapping the hungry codon from the left or 5′ side, followed by continued normal translation in the new, shifted reading frame.

A program for the graphic representation and manipulation of DNA sequences.

We have developed a program for the graphic representation and manipulation of DNA sequences. The program (named CARTE from the French for 'map') is intended as a tool in the planning and analysis of recombinant DNA experiments. DNA sequences are represented as standard restriction maps, using any desired combination of restriction enzymes. Features of interest, such as promoters or coding sequences, can be highlighted. The sequence can be manipulated to mimic cloning, using deletions, insertions or replacements at specified sites. This process is facilitated by the simultaneous display of a graphic map of the entire sequence, a detailed picture of the work in progress, and a menu of functions.

Two computer programs for rapid entry of DNA sequence data.

Two computer programs for the IBM personal computer are described for rapid and accurate entry of DNA sequence data. The DNA sequence files produced can be used directly by the DNA sequence manipulation programs by R. Staden (the DataBase system), the University of Wisconsin Genetics Computer Group, DNASTAR, or D.Mount. The first program, DIGISEQ, utilizes a sonic digitizer for semi-automation of sequence entry. To enter the DNA sequence each band of a gel reading is touched by the stylus of the sonic digitizer. DIGISEQ corrects for both changes in lane width and lane curvature. The algorithm is extremely efficient and rarely requires re-entering the centers of the lanes. The second program, TYPESEQ, uses only the keyboard for input. The keyboard is reconfigured to place nucleotides and ambiguity codes under the fingers of one hand, corresponding to the order of the nucleotides on the gel defined by the user. Both programs produce individual tones for each nucleotide, and certain ambiguity codes. This verifies input of the correct nucleotide or ambiguity code, and thus eliminates the need to visually check the screen display during sequence entry.

Data structures for DNA sequence manipulation.

Two data structures designated Fragment and Construct are described. The Fragment data structure defines a continuous nucleic acid sequence from a unique genetic origin. The Construct defines a continuous sequence composed of sequences from multiple genetic origins. These data structures are manipulated by a set of software tools to simulate the construction of mosaic recombinant DNA molecules. They are also used as an interface between sequence data banks and analytical programs.

Computer analysis and manipulation of DNA sequences

Abstract Programs are described for the efficient analysis of large numbers of DNA sequences for the recurrence of particular short segments. These programs include routines for the determination of oligonucletide frequencies, and for the analysis for perfect and imperfect palindromic sequences with either mirror or two-fold symmetry, as well as for inverted repeat sequences at remote loci. Other routines are included for locating perfect or imperfect matching sequences of any length and of either specified or unspecified sequences in the same or in different molecules. The latter routines are especially useful for locating repeated sequences obscured by random divergence. A number of additional programs are provided for more basic analysis or for cosmetic management of sequences. A routine is included for generating a numbered listing of primary and complementary strands, in selectable order, from an unformatted database. Another routine plots with sequence length the variation in percent G-C or the variation of a particular nearest neighbor or collection of nearest neighbors. Still other routines allow for the determination of translation reading frames and restriction maps.