|
| |
| | Bio 572: Restriction Endonucleases |
 | | Some restriction enzymes exhibit what are called "relaxed" specificity or "star" activity when they are used under the wrong buffer conditions. | | | From what species do you think EcoRI is derived? | | | A cautionary note about restriction enzyme buffer conditions is appropriate at this point. |
|
http://escience.ws/b572/L5/L5.htm
(2369 words)
|
|
| |
| | Support, restriction enzymes: Troubleshooting |
| | Reaction conditions for each enzyme are indicated in the product's Certificate of Analysis. | | | Cleavage by some restriction enzymes may be affected by EcoKI or EcoBI methylation. | | | Under certain conditions (low ionic strength, high pH of the reaction buffer, high enzyme concentration, Mn instead of Mg organic solvents), some restriction enzymes relax their substrate specificity. |
|
http://www.fermentas.com/techinfo/re/troubleshoot.htm
(1508 words)
|
|
| |
| | Molecular Biology - Restriction Enzymes |
| | For the researchers, the results of this experiment suggested two things. | | | In these experiments, bacteriophages were incubated with the different strains of E. | | | Overall, restriction endonucleases are quite variable in the DNA ends that they produce upon cleavage, for example leaving overhangs at the 5' (as in EcoRI in figure 2), a 3' overhang, or no overhang at all (referred to as "blunt" ends). |
|
http://www.bioteach.ubc.ca/MolecularBiology/RestrictionEndonucleases
(1808 words)
|
|
| |
| | Restriction enzyme-generated siRNA (REGS) vectors and libraries. |
| | Functional studies of the PI(3)-kinase signalling pathway employing synthetic and expressed siRNA. | | | Cyan indicates the constructs that were possible but not isolated. | | | The process uses restriction enzymes to digest double-stranded cDNAs into multiple fragments and limit their size to 21 nt, small enough to avoid the interferon response. |
|
http://www.euchromatin.org/Sen01.htm
(5658 words)
|
|
| |
| | Restriction Enzymes Web Page |
| | I acknowledge Dr. Richard Roberts and Dana Macelis for their help from REBASE at New England Biolabs. | | | This page and the Restriction Enzymes lists was created and maintained by Tim Tolley. | | | To see a color code table for Html visit Here: |
|
http://internalmed.wustl.edu/divisions/enzymes
(41 words)
|
|
| |
| | Restriction Enzymes - Glossary |
| | Although E. coli is ubiquitous among humans, some strains of this bacterium do cause human disease. | | | Enzymes change the rate of the reactions without being used up in the reaction. | | | Restriction enzyme: An endonuclease which recognizes a specific sequence of bases in a DNA molecule. |
|
http://www.accessexcellence.org/AE/AEC/CC/enzyme_glossary.html
(728 words)
|
|
| |
| | Digestion of Plasmid DNA |
| | One of the most important reaction conditions which varies between different restriction enzymes is the salt (usually NaCl) concentration. | | | Each restriction enzyme requires specific reaction conditions for optimum activity. | | | Restriction endonucleases such as EcoRI recognize specific palindromic sequences and cleave a phosphodiester bond on each strand at that sequence. |
|
http://csm.jmu.edu/biology/courses/bio480_580/mblab/restrict.html
(540 words)
|
|
| |
| | Restriction enzyme - Wikipedia, the free encyclopedia |
| | The term restriction comes from the fact that these enzymes were discovered in E. coli strains that appeared to be restricting the infection by certain bacteriophages. | | | Many of the procedures of molecular biology and genetic engineering rely on restriction enzymes. | | | So no matter the context in which a gene naturally appears, there is probably a pair of restriction enzymes that can snip it out, and which will produce ends that enable the gene to be spliced into a plasmid (i.e. |
|
http://en.wikipedia.org/wiki/Restriction_enzymes
(981 words)
|
|
| |
| | Restriction enzyme definition - Medical Dictionary definitions of popular medical terms |
| | Restriction enzyme definition - Medical Dictionary definitions of popular medical terms | | | Restriction enzymes were originally discovered and characterized by the molecular biologists Werner Arber, Hamilton O. Smith, and Daniel Nathans who shared the 1978 Nobel prize in medicine. | | | Types I and III enzymes are similar in that both restriction and methylase activities are carried out by one large enzyme complex, in contrast to the type II system, in which the restriction enzyme is independent of its methylase. |
|
http://www.medterms.com/script/main/art.asp?articlekey=5337
(583 words)
|
|
| |
| | RESTRICTION DIGESTS |
| | You will use these enzymes in future experiments. | | | This concentration is usually greater than is needed to digest your DNA fragment but for your first tests, use this concentration. | | | Promega and Gibco/BRL catalogs are excellent sources of information about the restriction enzymes that they sell including the correct conditions for digestion. |
|
http://fp.bio.utk.edu/mycology/Techniques/MT-restriction_digests.htm
(819 words)
|
|
| |
| | Restriction Enzyme Analysis of DNA-Student Handout |
| | Other restriction enzymes can be used to further characterize a particular DNA molecule. | | | These are often called cohesive ends, as these single-stranded overhangs could potentially come together again through complementary base-pairing. | | | A particular restriction enzyme will cleave DNA at that recognition sequence and nowhere else. |
|
http://biotech.biology.arizona.edu/labs/DNA_analysis_RE_student.html
(972 words)
|
|
| |
| | Restriction enzyme digestion of DNA (basic method) |
| | This is when the enzyme cuts at sites other than its cognate element. | | | If you are doing many digests then it may be worthwhile to make up a pre-mix in order to save on pipetting. | | | I have done many 1000s of restriction digests and have never experienced trouble due to star activity. |
|
http://www.methodbook.net/dna/restrdig.html
(1140 words)
|
|
| |
| | Restriction Enzymes - Background |
| | Scientists, now knowing the molecular structure of the hereditary molecule, could begin both to elucidate and to manipulate its function. | | | Importantly, these enzymes make it possible to create entirely new kinds of DNA molecules and, equally important, to manipulate the functioning of the genes located on these new molecules. | | | The positions of these two cuts, both in relation to each other, and to the recognition sequence itself, are determined by the identity of the restriction endonuclease used to cleave the molecule in the first place. |
|
http://www.accessexcellence.org/AE/AEC/CC/restriction.html
(1191 words)
|
|
| |
| | Background Information |
| | For example, the commonly used enzyme Bam HI comes from the bacterium Bacillus amylophilus, and Sau 3A comes from Staphylococcus aureus. | | | Many, but by no means all, Restriction Enzymes recognize exact sequences of bases 6 nucleotides long (you will often hear enzymes like this referred to as "6-cutters"). | | | A palindrome is a sequence which is read the same on both strands in the 5' --> 3' direction. |
|
http://www.life.uiuc.edu/molbio/background/background.html
(789 words)
|
|
| |
| | RE Resource |
| | This resource assists researchers in choosing the appropriate enzyme for each application. | | | Restriction enzymes (REs) that are most useful for molecular biology applications possess two essential attributes: high sequence specificity and precision cutting. | | | Our Restriction Enzymes Resource is an interactive tool, designed to speed your research applications, for identifying REs and RE recognition sites. |
|
http://www.promega.com/guides/re_guide
(212 words)
|
|
| |
| | Gel Electrophoresis of DNA |
| | Electrophoresis is a technique used in the laboratory that results in the separation of charged molecules. | | | DNA is a negatively charged molecule, and is moved by electric current through a matrix of agarose. | | | You have now digested a piece of DNA with Restriction Enzymes, separated the digested fragments by Agarose Gel Electrophoresis on a gel you poured, and analyzed and documented your results. |
|
http://www.life.uiuc.edu/molbio/geldigest/electro.html
(390 words)
|
|
| |
| | Restriction Enzymes |
| | Products with flush ends or 5' or 3' overhanging single-stranded ends may be produced. | | | Recognition sequences for many enzymes are the same on both strands. | | | Restriction endonucleases are protein enzymes that recognize specific nucleotide sequences and cleave both strands of the DNA containing those sequences. |
|
http://opbs.okstate.edu/~melcher/MG/MGW4/MG421.html
(217 words)
|
|
| |
| | [No title] |
| | Restriction enzymes are purchased from Bethesda Research Laboratories, New England Biolabs, or United States Biochemicals. | | | Inactivate the enzyme(s) by heating at 70-100degC for 10 minutes or by phenol extraction (see the vendor's catalog to determine the degree of heat inactivation for a given enzyme). | | | In general, it is best to use a strain lacking Mcr and Mrr systems when cloning genomic DNA from an organism with methylcytosine such as mammals, higher plants, and many prokaryotes.(11) |
|
http://www.genome.ou.edu/protocol_book/protocol_partI.html
(3791 words)
|
|
| |
| | Restriction of Lambda DNA |
| | A restriction enzyme (also known as an endonuclease) will search for a specific sequence of base pairs. | | | Therefore, from a plasmid map a research scientist can determine which enzymes can most effectively be used to cut out the gene in order to transfer that gene to another plasmid. | | | The DNA arrangement may appear many times, thereby providing the fragments that we are able to separate. |
|
http://ep.llnl.gov/bep/science/10/sLamb.html
(1805 words)
|
|
| |
| | Restriction Enzyme Mapping by Atomic Force Microscopy |
| | These maps are also useful in conjunction with other bound proteins to determine positions of specific elements (e. | | | This EcoRI enzyme was unlike most restriction enzymes however, because it bound to the DNA but was deficient in cutting activity. | | | Even with infrequent cutting enzymes such as NotI, and using pulse-gel electrophoretic set-ups, it was becoming difficult to determine the relative orientation and alignment of fragments from large clones. |
|
http://homer.ornl.gov/cbps/mappage.htm
(233 words)
|
|
| |
| | Restriction Maps |
| | Complicated double digest patterns may be resolvable by computer analysis. | | | These molecules can be digested with restriction enzymes in situ on the glass slides. | | | Comparison of restriction maps was often used to establish the overlap of clones in contig mapping. |
|
http://opbs.okstate.edu/~melcher/MG/MGW1/MG11231.html
(334 words)
|
|
| |
| | [No title] |
| | For use with the CSHL sequence analysis programs. | | | Reports any notable changes since the previous REBASE version, such as any enzyme name changes, announcements of new REBASE formats, new commercial suppliers, corrections, etc. Automatically sent to each subscriber of any of our formats. | | | Each enzyme is followed by its reference information. |
|
http://www.itc.virginia.edu/achs/molbio/databases/REBASE206.txt
(2921 words)
|
|
| |
| | Restriction Enzyme Digest and Gel Electrophoresis Field Trip--Background |
| | Molecular biology laboratory skills and equipment, as well as laboratory safety, will be discussed and used in this lab. | | | If you encounter technical problems with this site, please e-mail the webmaster. | | | The reaction is incubated at the enzyme's optimum temperature to digest the DNA. |
|
http://www.btci.org/k12/bft/red_background.html
(834 words)
|
|
| |
| | Webcutter 2.0 |
| | Find sites which may be introduced by silent mutagenesis | | | lease indicate which enzymes to include in the analysis | | | Degenerate sequences Analyze restriction maps of sequences containing ambiguous nucleotides like N, Y, and R. Circular sequences Choose whether to treat your sequence as linear or circular |
|
http://www.firstmarket.com/cutter/cut2.html
(379 words)
|
|
| |
| | Restriction Enzyme Analysis of DNA-Teacher Guide |
| | Students will have time to set up the restriction enzyme reactions, but not to stop the reactions. | | | Recognition and cleavage sites used by some common restriction enzymes: | | | Be sure the students record the number of their electrophoresis unit on their lab handout. |
|
http://biotech.biology.arizona.edu/labs/DNA_analysis_RE_teacher.html
(1340 words)
|
|
| |
| | Genome Glossary |
| | Variation between individuals in DNA fragment sizes cut by specific restriction enzymes; polymorphic sequences that result in RFLPs are used as markers on both physical maps and genetic linkage maps. | | | A specific nucleotide sequence of DNA at which a particular restriction enzyme cuts the DNA. | | | Bacteria contain over 400 such enzymes that recognize and cut more than 100 different DNA sequences. |
|
http://www.ornl.gov/TechResources/Human_Genome/glossary/glossary_r.html
(579 words)
|
|
| |
| | Refining Restriction Enzyme Genome Maps - Revesz (ResearchIndex) |
| | 0.3: Experiment 3 - Restriction Enzyme Digestion and Agarose Gel.. | | | Abstract: A genome map is an ordering of a set of clones according to their believed position on a DNA string. | | | Online articles have much greater impact More about CiteSeer.IST Add search form to your site Submit documents Feedback |
|
http://citeseer.ist.psu.edu/16968.html
(640 words)
|
|
| |
| | Restriction Enzyme Mapping 4 |
| | Below is a description and examples of three methods used to organize restriction enzyme location on DNA fragments. | | | Maps of restriction enzyme cleavage sites are useful in planning not only cloning projects but also in gene identification, forensics, sequencing and mutagenesis projects. | | | When a fragment of DNA with an unknown restriciton map is cloned into a vector containing many flanking restriction enzyme sites, it is fairly easy to identify the location of most single cuts within the unknown portion. |
|
http://bioweb.wku.edu/courses/biol350/REmaps4/Review.html
(389 words)
|
|
| |
| | NEBcutter V2.0 |
| | By default, only enzymes available from NEB are used, but other sets may be chosen. | | | You need to have cookies enabled in your browser for this feature to work. | | | This tool will take a DNA sequence and find the large, non-overlapping open reading frames using the E.coli genetic code and the sites for all Type II restriction enzymes that cut the sequence just once. |
|
http://tools.neb.com/NEBcutter2/index.php
(133 words)
|
|
| |
| | Webcutter news |
| | In addition to restriction site mapping, Webcutter 2 also performs degenerate digests, including the option of finding restriction sites that can be introduced into a sequence by silent mutagenesis ("silent cutters"). | | | Students will learn to read a DNA sequencing gel, use computer resources like BLAST searching and Webcutter to identify the sequence and predict a restriction map, design an analytical restriction digest, and finally go to the bench to set their digests and run them on an agarose gel. | | | pWEB I have licensed Webcutter to be part of a teacher's kit about manipulating DNA with restriction enzymes that will be published by the Carolina Biological Supply Co. in the summer of 1998. |
|
http://www.ccsi.com/firstmarket/cutter
(326 words)
|
|
| |
| | R |
| | Hairlike structure that serves as a root for bryophytes, fern prothallia, and certain fungi and lichens. | | | A virus whose genome consists of RNA which, after infection, is copied by reverse transcriptase into DNA. | | | An enzyme that cuts DNA molecules at, or close to, a certain sequence of nucleotides. |
|
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/R/R.html
(265 words)
|
|
| |
| | Technical Reference, New England Biolabs |
| | InBase, The New England Biolabs Intein Database—Inteins are self-splicing proteins that can also act as homing endonucleases and mediate DNA cleavage at the intein insertion site in inteinless alleles. | | | The Restriction Enzyme Database (REBASE)—contains a complete listing of all known restriction endonucleases, including: recognition sequences, methylation sensitivity, commercial availability and references. |
|
http://www.neb.com/nebecomm/tech_reference
(148 words)
|
|
| |
| | Restriction Enzyme Buffer |
| | Most enzymes can use REact buffers; however, some are made up separately. | | | Use fresh Milli-Q water, siliconized or sterile glassware or disposable plastic ware to make the following stock solutions up fresh (discard after use), combine to make 5 ml of 10X reaction buffers, put 1 ml in to each of 5 microfuge tubes (MFTs) and store the current one at -20C and the rest at -70C. |
|
http://wheat.pw.usda.gov/homepage/lazo/methods/lazo/restricb.html
(418 words)
|
|
| |
| | Restriction Endonuclease Buffer Data Base: Multi-Cut |
| | Multi-Cut does not promote any specific restriction enzyme manufacturer | | | Multi-Cut searches through activity data from the catalogs of several major restriction endonuclease manufacturers and finds buffers that will work with all of the endonucleases in the reaction. | | | It finds compatible buffers for a list of enzymes that you want to use in a multiple restriction endonuclease digest. |
|
http://users.mis.net/~colinw/buffer.html
(89 words)
|
|
| |
| | RestrictionMapper version 3 |
| | Welcome to RestrictionMapper - on line restriction mapping the easy way. |
|
http://www.restrictionmapper.org
(11 words)
|
|
| |
| | TACG |
| | The 'magnitude' of the recognition sequence depends on the number of defined bases that make up the site. | | | You can cut off any size in 10^n increments (as you might want to cut off very large fragments if you were doing chromosomal digests). | | | Those enzymes sequences' patterns that 'sum' to the equivalent of at least the given magnitude pass the test |
|
http://bioweb.pasteur.fr/seqanal/interfaces/tacg.html
(532 words)
|
|
| |
| | Welcome to biomirror.org.nz - the New Zealand BioMirror |
| | Commercial restrictions may apply to data sets listed on this page. | | | * Commercial use restrictions on SWISS-PROT and PROSITE: Publishers of the SWISS-PROT and PROSITE data sets ask that all commercial users participate in the funding of these important data by paying a license fee. | | | Please check data sets' homepages and documentation for details. |
|
http://www.cebl.auckland.ac.nz/biomirror
(227 words)
|
|
| |
| | Promega - Cloning - Restriction Enzymes |
| | This Table (pdf, 72kb) may be used to quickly select the best buffer for digestions using multiple restriction enzymes. | | | Each Promega restriction enzyme is supplied with a 10X Reaction Buffer, which is optimized to give 100% activity with that enzyme. | | | A comprehensive resource detailing everything you need to know about restriction enzymes. |
|
http://www.promega.com/techserv/apps/cloning/cloning1.htm
(104 words)
|
|
| |
| | New England Biolabs |
| | A better enzyme than SAP at a better price. | | | Add a Free Sample (M0289G) to your order. | | | To access your account, log in or register. |
|
http://www.neb.com/nebecomm/products/category1.asp
(25 words)
|
|
| |
| | Dr Garrett M. Morris |
| | Course on Biotechnology and Enzyme Technology from Newcastle University, UK, which relies heavily on Rasmol and Kinemages. | | | REBASE - The Restriction Enzyme Database, includes recognition sequences. | | | Hypertextbook on Biology from MIT: go to the list of chapters. |
|
http://www.scripps.edu/mb/olson/people/gmm
(3985 words)
|
|
|
