Macvector Serial

Serial Cloner also lets you build text restriction map and quickly format it to add multi-frame translation or only show single cutters for example. Since version 2.1, Sequence Features are visible in the Sequence Map.The graphic map of Serial Cloner is really Graphic as you can easily select and extract a fragment or show single, double or multiple cutter all in the same window. All the features are displayed on the map using user-modifiable colors; the features can be manually entered, imported from GenBank or automatically found after scanning by Serial Cloner. The Collection of Features to be scanned for can be defined and modified by the user, imported and exported.Version 2.5 now allows to open protein sequences, align protein sequences and reverse translate proteins using defined codon biais tables. Serial Cloner has been developed to provide a light yet powerful molecular biology software to both Macintosh and Windows users. A Linux version is also distributed. Serial Cloner reads and write DNA Strider-compatible files and import and export files in the universal FASTA format.

Serial Cloner also import files saved in the Vector NTI, MacVector, ApE, DNAstar, pDRAW32 and GenBank formats. Import from VectorNTI multi-file format is also supported. Powerful graphical display tools and simple interfaces help the analysis and construction steps in a very intuitive way. Serial Cloner 2.5, handles Annotations and Features both in the sequence and in the Graphic Map and can automatically scan for sequence Features. PCR-based fragment or synthetic adaptors. ShRNA constructions based on pre-defined scaffolds are also automated.

Finally, you can assemble fragments, obtained by PCR, adaptor/shRNA synthesis or simply by graphically selecting fragments between restriction sites. Just select, blunt if you need, and click the Ligate button.

An additional interface allows easy Gateway(tm) cloning for both BP and LR reactions. Finally, Serial Cloner provides an interface to align two sequences using a local algorithm or the BLAST2Seq NCBI server. Features are now visible when aligning locally.

You will also find a Restriction Enzyme library management interface, Additional tools, like a web browser for direct import of NCBI and EMBL entries, a virtual cutter to prepare restriction analysis or a silent restriction map generator to find how to introduce restriction sites without modifying the translated peptide are also provided. It is also posible to send directly BLAST request at the NCBI and obtain the result inside a Web interface. Serial Cloner 2.5 now allows to import codon frequency tables from the internet using a Web interface.

It also allows to generate sense and antisense sequences to be obtained after bi-sulfite conversion.

Illustration of a bacterium showing chromosomal DNA and plasmids. Not to scale.A plasmid is a small molecule within a cell that is physically separated from and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in; however, plasmids are sometimes present in. In nature, plasmids often carry genes that benefit the survival of the organism, such as by providing. While the chromosomes are big and contain all the essential genetic information for living under normal conditions, plasmids usually are very small and contain only additional genes that may be useful in certain situations or conditions.

Artificial plasmids are widely used as in, serving to drive the replication of sequences within host organisms. In the laboratory, plasmids may be introduced into a cell via.Plasmids are considered, units of DNA capable of replicating autonomously within a suitable host. However, plasmids, like, are not generally classified as. Plasmids are transmitted from one bacterium to another (even of another species) mostly through. This host-to-host transfer of genetic material is one mechanism of, and plasmids are considered part of the. Unlike viruses, which encase their genetic material in a protective protein coat called a, plasmids are 'naked' DNA and do not encode genes necessary to encase the genetic material for transfer to a new host. However, some classes of plasmids encode the necessary for their own transfer.

The size of the plasmid varies from 1 to over 200 k, and the number of identical plasmids in a single can range anywhere from one to thousands under some circumstances. Contents.History The term plasmid was introduced in 1952 by the American to refer to 'any extrachromosomal hereditary determinant.'

The term's early usage included any bacterial genetic material that exists extrachromosomally for at least part of its replication cycle, but because that description includes bacterial viruses, the notion of plasmid was refined over time to comprise genetic elements that reproduce autonomously.Later in 1968, it was decided that the term plasmid should be adopted as the term for extrachromosomal genetic element, and to distinguish it from viruses, the definition was narrowed to genetic elements that exist exclusively or predominantly outside of the chromosome and can replicate autonomously. Properties and characteristics. There are two types of plasmid integration into a host bacteria: Non-integrating plasmids replicate as with the top instance, whereas, the lower example, can integrate into the host.In order for plasmids to replicate independently within a cell, they must possess a stretch of DNA that can act as an. The self-replicating unit, in this case the plasmid, is called a. A typical bacterial replicon may consist of a number of elements, such as the gene for plasmid-specific replication initiation protein (Rep), repeating units called, boxes, and an adjacent AT-rich region. Smaller plasmids make use of the host replicative enzymes to make copies of themselves, while larger plasmids may carry genes specific for the replication of those plasmids.

A few types of plasmids can also insert into the host chromosome, and these integrative plasmids are sometimes referred to as in prokaryotes.Plasmids almost always carry at least one gene. Many of the genes carried by a plasmid are beneficial for the host cells, for example: enabling the host cell to survive in an environment that would otherwise be lethal or restrictive for growth. Some of these genes encode traits for antibiotic resistance or resistance to heavy metal, while others may produce that enable a bacterium to colonize a host and overcome its defences, or have specific metabolic functions that allow the bacterium to utilize a particular nutrient, including the ability to degrade recalcitrant or toxic organic compounds. Plasmids can also provide bacteria with the ability to. Some plasmids, however, have no observable effect on the phenotype of the host cell or its benefit to the host cells cannot be determined, and these plasmids are called cryptic plasmids.Naturally occurring plasmids vary greatly in their physical properties. Their size can range from very small mini-plasmids of less than a 1 kilobase pairs (Kbp), to very large megaplasmids of several megabase pairs (Mbp).

At the upper end, little can differentiate between a megaplasmid and a. Plasmids are generally circular, but examples of linear plasmids are also known. These linear plasmids require specialized mechanisms to replicate their ends.Plasmids may be present in an individual cell in varying number, ranging from one to several hundreds. The normal number of copies of plasmid that may be found in a single cell is called the, and is determined by how the replication initiation is regulated and the size of the molecule. Larger plasmids tend to have lower copy numbers.

Low-copy-number plasmids that exist only as one or a few copies in each bacterium are, upon, in danger of being lost in one of the segregating bacteria. Such single-copy plasmids have systems that attempt to actively distribute a copy to both daughter cells. These systems, which include the and, are often referred to as the or partition function of a plasmid.Classifications and types.

Electron micrograph of a bacterial DNA plasmid (chromosome fragment)Plasmids may be classified in a number of ways. Plasmids can be broadly classified into conjugative plasmids and non-conjugative plasmids. Conjugative plasmids contain a set of transfer or tra genes which promote sexual conjugation between different cells. In the complex process of, plasmid may be transferred from one bacterium to another via sex encoded by some of the tra genes (see figure). Non-conjugative plasmids are incapable of initiating conjugation, hence they can be transferred only with the assistance of conjugative plasmids.

An intermediate class of plasmids are mobilizable, and carry only a subset of the genes required for transfer. They can parasitize a conjugative plasmid, transferring at high frequency only in its presence.Plasmids can also be classified into incompatibility groups. A microbe can harbour different types of plasmids, but different plasmids can only exist in a single bacterial cell if they are compatible.

If two plasmids are not compatible, one or the other will be rapidly lost from the cell. Different plasmids may therefore be assigned to different incompatibility groups depending on whether they can coexist together. Incompatible plasmids (belonging to the same incompatibility group) normally share the same replication or partition mechanisms and can thus not be kept together in a single cell.Another way to classify plasmids is by function. There are five main classes:.

Fertility, which contain tra genes. They are capable of and result in the expression of sex pili. Resistance (R) plasmids, which contain genes that provide resistance against. Historically known as R-factors, before the nature of plasmids was understood. Col plasmids, which contain genes that code for, that can kill other bacteria. Degradative plasmids, which enable the digestion of unusual substances, e.g.

And. Virulence plasmids, which turn the bacterium into a.Plasmids can belong to more than one of these functional groups.Vectors. Further information:Artificially constructed plasmids may be used as in. These plasmids serve as important tools in genetics and biotechnology labs, where they are commonly used to clone and amplify (make many copies of) or particular genes. A wide variety of plasmids are commercially available for such uses. The gene to be replicated is normally inserted into a plasmid that typically contains a number of features for their use. These include a gene that confers resistance to particular antibiotics ( is most frequently used for bacterial strains), an to allow the bacterial cells to replicate the plasmid DNA, and a suitable site for cloning (referred to as a ).DNA structural instability can be defined as a series of spontaneous events that culminate in an unforeseen rearrangement, loss, or gain of genetic material.

Such events are frequently triggered by the transposition of mobile elements or by the presence of unstable elements such as non-canonical (non-B) structures. Accessory regions pertaining to the bacterial backbone may engage in a wide range of structural instability phenomena. Well-known catalysts of genetic instability include direct, inverted, and tandem repeats, which are known to be conspicuous in a large number of commercially available cloning and expression vectors. Insertion sequences can also severely impact plasmid function and yield, by leading to deletions and rearrangements, activation, down-regulation or inactivation of neighboring gene expression.

Therefore, the reduction or complete elimination of extraneous noncoding backbone sequences would pointedly reduce the propensity for such events to take place, and consequently, the overall recombinogenic potential of the plasmid. Main article:Plasmids are the most-commonly used bacterial cloning vectors. These cloning vectors contain a site that allows DNA fragments to be inserted, for example a or polylinker which has several commonly used to which DNA fragments may be. After the gene of interest is inserted, the plasmids are introduced into bacteria by a process called.

These plasmids contain a, usually an antibiotic resistance gene, which confers on the bacteria an ability to survive and proliferate in a selective growth medium containing the particular antibiotics. The cells after transformation are exposed to the selective media, and only cells containing the plasmid may survive. In this way, the antibiotics act as a filter to select only the bacteria containing the plasmid DNA. The vector may also contain other or to facilitate selection of plasmid with cloned insert. Bacteria containing the plasmid can then be grown in large amounts, harvested, and the plasmid of interest may then be isolated using various methods of.A plasmid cloning vector is typically used to clone DNA fragments of up to 15. To clone longer lengths of DNA, with lysogeny genes deleted, or are used.Protein production.

Main article:Plasmid may also be used for gene transfer into human cells as potential treatment in so that it may express the protein that is lacking in the cells. Some strategies of require the insertion of therapeutic at pre-selected target sites within the human.

Plasmid vectors are one of many approaches that could be used for this purpose. (ZFNs) offer a way to cause a site-specific double-strand break to the DNA genome and cause. Plasmids encoding ZFN could help deliver a therapeutic gene to a specific site so that cell damage, cancer-causing mutations, or an immune response is avoided. Disease models Plasmids were historically used to genetically engineer the embryonic stem cells of rats to create rat genetic disease models. The limited efficiency of plasmid-based techniques precluded their use in the creation of more accurate human cell models. However, developments in recombination techniques, and, have enabled the creation of a new generation of.Episomes.

'Episome' redirects here. For the album by Bill Laswell, Otomo Yoshihide and Tatsuya Yoshida, see.The term episome was introduced by and in 1958 to refer to extra-chromosomal genetic material that may replicate autonomously or become integrated into the chromosome. Since the term was introduced, however, its use has shifted, as plasmid has become the preferred term for autonomously replicating extrachromosomal DNA. At a 1968 symposium in London some participants suggested that the term episome be abandoned, although others continued to use the term with a shift in meaning.Today some authors use episome in the context of prokaryotes to refer to a plasmid that is capable of integrating into the chromosome.

The integrative plasmids may be replicated and stably maintained in a cell through multiple generations, but always at some stage they exist as an independent plasmid molecule. In the context of eukaryotes, the term episomes is used to mean a non-integrated extrachromosomal closed circular DNA molecule that may be replicated in the nucleus. Viruses are the most common examples of this, such as, and, but some are plasmids.

Other examples include aberrant chromosomal fragments, such as, that can arise during artificial gene amplifications or in pathologic processes (e.g., cancer cell transformation). Episomes in eukaryotes behave similarly to plasmids in prokaryotes in that the DNA is stably maintained and replicated with the host cell. Cytoplasmic viral episomes (as in infections) can also occur. Some episomes, such as herpesviruses, replicate in a mechanism, similar to bacterial phage viruses.

Others replicate through a bidirectional replication mechanism ( Theta type plasmids). In either case, episomes remain physically separate from host cell chromosomes.

Several cancer viruses, including and, are maintained as latent, chromosomally distinct episomes in cancer cells, where the viruses express that promote cancer cell proliferation. In cancers, these episomes passively replicate together with host chromosomes when the cell divides. When these viral episomes initiate to generate multiple virus particles, they in general activate cellular defense mechanisms that kill the host cell.Plasmid maintenance.

Main article:Some plasmids or microbial hosts include an or postsegregational killing system (PSK), such as the (host killing/suppressor of killing) system of plasmid R1 in. This variant produces both a long-lived and a short-lived. Several types of plasmid addiction systems (toxin/ antitoxin, metabolism-based, ORT systems) were described in the and used in biotechnical (fermentation) or biomedical (vaccine therapy) applications. Daughter cells that retain a copy of the plasmid survive, while a daughter cell that fails to inherit the plasmid dies or suffers a reduced growth-rate because of the lingering poison from the parent cell.

Finally, the overall productivity could be enhanced.In contrast, virtually all biotechnologically used plasmids (such as pUC18, pBR322 and derived vectors) do not contain toxin-antitoxin addiction systems and thus need to be kept under antibiotic pressure to avoid plasmid loss.Yeast plasmids naturally harbour various plasmids. Notable among them are 2 μm plasmids — small circular plasmids often used for of yeast — and linear pGKL plasmids from, that are responsible for.Other types of plasmids are often related to yeast cloning vectors that include:. Yeast integrative plasmid (YIp), yeast vectors that rely on integration into the host chromosome for survival and replication, and are usually used when studying the functionality of a solo gene or when the gene is toxic. Also connected with the gene URA3, that codes an enzyme related to the biosynthesis of pyrimidine nucleotides (T, C);. Yeast Replicative Plasmid (YRp), which transport a sequence of chromosomal DNA that includes an origin of replication.

These plasmids are less stable, as they can get lost during the budding.Plasmid DNA extraction As alluded to above, plasmids are often used to purify a specific sequence, since they can easily be purified away from the rest of the genome. For their use as vectors, and for, plasmids often need to be isolated.There are several methods to from bacteria, the archetypes of which are the and the maxiprep/ bulkprep. The former can be used to quickly find out whether the plasmid is correct in any of several bacterial clones. The yield is a small amount of impure plasmid DNA, which is sufficient for analysis by and for some cloning techniques.In the latter, much larger volumes of bacterial suspension are grown from which a maxi-prep can be performed. In essence, this is a scaled-up miniprep followed by additional purification. This results in relatively large amounts (several hundreds micrograms) of very pure plasmid DNA.In recent times, many commercial kits have been created to perform plasmid extraction at various scales, purity, and levels of automation.

Commercial services can prepare plasmid DNA at quoted prices below $300/mg in milligram quantities and $15/mg in gram quantities (early 2007 ).Conformations Plasmid DNA may appear in one of five conformations, which (for a given size) run at different speeds in a gel during. The conformations are listed below in order of electrophoretic mobility (speed for a given applied voltage) from slowest to fastest:. Nicked open-circular DNA has one strand cut. Relaxed circular DNA is fully intact with both strands uncut, but has been enzymatically relaxed (supercoils removed).

This can be modeled by letting a twisted extension cord unwind and relax and then plugging it into itself. Linear DNA has free ends, either because both strands have been cut or because the DNA was linear in vivo. This can be modeled with an electrical extension cord that is not plugged into itself.

Macvector Serial Number

(or covalently closed-circular) DNA is fully intact with both strands uncut, and with an integral twist, resulting in a compact form. This can be modeled by twisting an and then plugging it into itself. Supercoiled DNA is like supercoiled DNA, but has unpaired regions that make it slightly less compact; this can result from excessive alkalinity during plasmid preparation.The rate of migration for small linear fragments is directly proportional to the voltage applied at low voltages. At higher voltages, larger fragments migrate at continuously increasing yet different rates.

Thus, the resolution of a gel decreases with increased voltage.At a specified, low voltage, the migration rate of small linear DNA fragments is a function of their length. Large linear fragments (over 20 kb or so) migrate at a certain fixed rate regardless of length. This is because the molecules 'resperate', with the bulk of the molecule following the leading end through the gel matrix. Are frequently used to analyse purified plasmids.

Macvector Serial Number

These enzymes specifically break the DNA at certain short sequences. The resulting linear fragments form 'bands' after. It is possible to purify certain fragments by cutting the bands out of the gel and dissolving the gel to release the DNA fragments.Because of its tight conformation, supercoiled DNA migrates faster through a gel than linear or open-circular DNA.Software for bioinformatics and design The use of plasmids as a technique in is supported. These programs record the sequence of plasmid vectors, help to predict cut sites of, and to plan manipulations. Examples of software packages that handle plasmid maps are ApE, GeneConstructionKit, Geneious, LabGenius, Lasergene, pDraw32, Serial Cloner, VectorFriends, and WebDSV. These software help conduct entire experiments in silico before doing wet experiments. Plasmid collections Many plasmids have been created over the years and researchers have given out plasmids to plasmid databases such as the non-profit organisations.

One can find and request plasmids from those databases for research.Researcher also often upload plasmid sequences to the, from which sequences of specific plasmids can be retrieved.See also. Piechaczek C, Fetzer C, Baiker A, Bode J, Lipps HJ (January 1999). Nucleic Acids Research. 27 (2): 426–8.

Bode J; Fetzer CP; Nehlsen K; Scinteie M; Hinrichsen B-H; Baiker A; Piechazcek C; Benham C; Lipps HJ (2001). Gene Ther Mol Biol. Archived from (PDF) on 30 May 2009. Nehlsen K, Broll S, Bode J (2006). Gene Ther Mol Biol. Archived from (PDF) on 30 May 2009. Ehrhardt A, Haase R, Schepers A, Deutsch MJ, Lipps HJ, Baiker A (June 2008).

Current Gene Therapy. 8 (3): 147–61. Archived from on 26 September 2011. Argyros O, Wong SP, Niceta M, Waddington SN, Howe SJ, Coutelle C, Miller AD, Harbottle RP (December 2008). 'Persistent episomal transgene expression in liver following delivery of a scaffold/matrix attachment region containing non-viral vector'. Gene Therapy. 15 (24): 1593–605.

Wong SP, Argyros O, Coutelle C, Harbottle RP (August 2009). Current Opinion in Molecular Therapeutics. 11 (4): 433–41. Archived from on 17 September 2011.

Haase R, Argyros O, Wong SP, Harbottle RP, Lipps HJ, Ogris M, Magnusson T, Vizoso Pinto MG, Haas J, Baiker A (March 2010). BMC Biotechnology. 10: 20.External links.