Endonucleases are enyzmes (usually derived from bacterial sources) which cleave DNA at defined "restriction" sites.

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Restriction enzymes, how are the recognition sequences determined?

How were the recognition sequences (e.g. GAATTC of EcoRI, GGATCC of BamHI) characterised? Text books only list the recognition ...
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How to cut out a specific named gene from plant DNA

Suppose one has extracted RNA from a plant, converted it to the corresponding cDNA & amplified it but now wants to cut out a particular, already-sequenced gene out from it, how does one proceed? ...
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Enzymes and plasmids

A high school class has analyzed plasmids by the help of restriction enzymes and electrophoresis. The class got delivered two different plasmids, pBR 322 and pC 508. These two plasmids were going to ...
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RAD sequencing: choosing the appropriate enzyme?

I’m studying Darwin’s finches genome and I say in some articles that the researchers used restriction enzymes to cut the DNA in their double digest RAD protocol. They are using EcoRI and MseI (GAATTC ...
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What happen if we inject restriction enzyme into the blood

Just a curious question, if we extract restriction enzyme and inject it to our body, what happen? Does antibody recognize and block it? Can restriction enzyme pass over cell membrane and destroy the ...
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Freezing after restriction digest

Brief question: I have performed a double digest with heat inactivated restriction enzymes with no star activity. I usually purify the DNA (PCR inserts and linearised vector) using a kit or gel ...
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Batch several sequences for absent restriction sites

I have a collection of about 120 7kB sequences I would like to check for ether a list of specific restriction sites, or what restriction sites might be absent in all of them. Is there a app or ...
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Restriction sites

I would like to know: how many restriction sites does a restriction enzyme use on a DNA molecule? In other words: If a sequence on a plasmid contains the following bases: ATTGCAGTCTG and I want ...
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What makes DNA sticky-ends sticky?

When restriction enzymes jaggedly cut double stranded DNA it results in so called sticky ends. What is the substance that makes the DNA sticky?
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Cleavage of RNA by restriction enzymes?

Six restriction enzymes discussed in Sequence-specific cleavage of RNA by Type II restriction enzymes (Murray et al.) have the ability to detect and cut RNA strands with that enzyme's recognition ...
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Do restriction enzymes on read 3' to 5'?

Every chart of palindromic restriction enzymes I've seen lists their restriction sites from 5' to 3', something like this: EcoR1 cuts GAATTC between the G and A: 5' NNNGAATTCNNN 3' --> ...
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Does mung bean nuclease cleave a phosphate group when it's chewing off 5' or 3' ssDNA ends?

I'm looking to create blunt ends from sticky ends with mung bean nuclease for subsequent ligation. Does anyone know full mechanism by which mung bean nuclease will do this? In particular after the ...
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Are restriction enzymes active at −20 °C?

I have digested my DNA with NotI enzyme and put it in the −20 °C freezer without heat inactivating it. Can restriction enzymes work at −20 °C? Should I expect STAR activity?
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Molecular Cloning- Blunt end restriction endonucleases

I work in a microbiology lab where we do a lot of cloning. I have always used restriction endonucleases to cleave the DNA to have sticky ends and not blunt ends. I currently am working on a project ...
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How many Type II restrictions enzymes are currently available (commercially) [closed]

How many Type II restrictions enzymes are currently available (commercially) for purchase as of the date of this posting (September 1, 2014)
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How do Type I restriction enzymes work?

According to NCBI, type I REases have a specific target sequence but randomly make cuts at sites far from the target sequence. How does the restriction enzyme travel from the target sequence to the ...
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What does 'H' in BamHI stand for?

It's not explained on the wikipedia page. So if, apparently, 'H' is not relevant, why is it part of the name? And if it is relevant, why is it not explained?
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How was Restriction Site of EcoRI sequenced?

The sequence of restriction site of EcoRI - GAATTC was identified in the early 1970s, before Sanger Sequencing was invented.(1977) How was the restriction site of EcoRI sequenced ?
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Restriction endonucleases are found in?

Quoting from : Scientific American July 1975 The Manipulation of genes by Stanley Cohen : Restriction endonucleases (and modification methylases) are widespread in microorganisms; genes for ...
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Removing a restriction site and introducing other at its place

What would you do if you want to remove an EcoRI restriction site and introduce BamHI restriction site at apprx. the same location ? One of the answers in my textbook was : To construct a DNA ...
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DNA fingerprinting

I would like to make my own DNA fingerprint - just for fun to have my "autoportrait":). I was looking around a bit and all the commercial kits you can have are very expensive. Can you suggest me a ...
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Why restriction enzymes cut (usually) at palindromic sequences?

Restriction enzymes usually cut only at palindromic sequences. Is there any specific reason for that ? Is there any advantage for bacteria if it cuts up virus at this type of sequences ?
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What can cause incompatible sticky ends to be ligated?

Actual question I have reason to believe (details see below) that in a ligation I carried out, an EcoRI sticky end (EcoRI: G'AATT_C) and an XmaI sticky end (XmaI: C'CCGG_G) were somehow ligated ...
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Gel electrophoresis question

Leena is a molecular biology student. She purifies two fragments of DNA, 800 and 300 base pairs long. These were obtained from a plasmid after digesting it with HindIII. Each of these fragments has a ...
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What is the advantage of restriction enzymes cutting only at specific sites?

Bacteriophages have sequences which often do not have specific sites for restriction enzymes of bacteria to cut at and so can attack the bacteria. Wouldn't it be better if bacteria had something ...
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How effective are restriction enzymes in protecting bacteria?

Bacteria use restriction enzymes to cut DNA of bacteriophages. Virus mutates really fast. Won't a point mutation in restriction site render the restriction enzymes of the bacteria useless ? So how ...
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What are common causes of unexpected ligation products?

I digested two plasmids, one with EcoRI and AgeI and the other with EcoRI and XmaI. Digests looked as expected, so I purified the respective fragments and set up the T4 DNA ligation (AgeI and XmaI ...
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Can viruses protect themselves against restriction enzymes?

Restriction enzymes cut the DNA of bacteriophages. Have bacteriophages evolved any mechanism to protect themselves from it ?
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How prevalent is Taq polymerase in adding 3' A overhangs to the PCR product?

I am conducting a mutagenesis on a gene in vivo of which I need to ligate into an expression vector. The primers I have designed overlap restriction sites of which I plan to use to ligate into the ...
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Restriction Mapping of Plasmid Assignment

pUWL22 is a circular, double stranded, 10.5 kb plasmid. It contains a gene encoding an enzyme that confers ampicillin resistance in the host bacterium. Cloning into the kpn I and Sst I sites ...
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Primer design for introduction of restriction sites flanking a gene of interest

I am wondering what the correct method for primer design to introduce restriction sites. Specifically between two methods. 1) Primer first partially hybridises to the gene, has a mis-match where the ...
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Why do restriction enzymes tend to have an even number of bases in their recognition site?

When reading my textbook I noticed that in all examples but one from eight the recognition site was an even number of bases. I wondered if this was just a co-incidence, so I took the data from this ...