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What makes DNA sticky-ends sticky?

What makes DNA sticky-ends sticky?


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


The sticky ends are sticky because they have complementary bases. Typically used restriction enzymes cut the two complementary DNA strands at different spots, generating 'overhang', or sticky ends:

These overhangs allow for perfect base pairing (C with G, A with T), which is the result of hydrogen bonding. Just like water molecules show strong affinity to each other or other molecules with -OH and -H groups (e.g., alcohol), hydrogen bonds between nucleotides glues the ends together.

The principles of base-pairing has been nicely answered by @MadScientist in "Why does A pair with T and G with C?"


What are sticky ends. There is no substance that is attached making the DNA ends "sticky". What has actually happened is an overhang of at least a few nucleotides. Blunt ends are another kind of cut, but have no overhanging residues.

Why are sticky ends sticky? Restriction enzymes usually cut these ends deliberately so that a four nucleotides are overhanging on the 5' end of the double strand. These are complementary to other overhangs and because they are less stable than a bound double strand region, and are able to hydrogen bond easily with complementary bases, they are easier to attach with a ligase.

Below is an image of the base pairs interacting via H bonds.


The "substance" is hydrogen bonds (H-bonds), or rather the potential to form them. Each of the unpaired A/T bases in the sticky ends have the potential to form 2 H-bonds with a complementary T/A, and each of the unpaired G/C bases have the potential to form 3 H-bonds with a complementary C/G.

From the perspective of a biophysicist, H-bonds are often thought of as being the strongest intermolecular interactions. I personally think that it's a little bit lazy and unphysical to see things this way, but the prevailing view in the field is that H-bonds determine specificity in all macromolecular interactions (e.g. the specificity that causes a single DNA strand to bind mostly to complementary DNA strands and poorly to random DNA strands).


What is the role of sticky ends in recombinant DNA?

The ends of the strand are either sticky or blunt so they can be attach to other DNA. Explain how the creation of "sticky ends" by restriction enzymes is useful in producing a recombinant DNA molecule. Sticky ends want to bond to create base pairs and thus a new molecule with the same DNA.

Furthermore, what are the sticky ends of a plasmid? The overhangs, called "sticky ends", are what allow the vector and insert to bind to each other. When the sticky ends are compatible, meaning that the overhanging base pairs on the vector and insert are complementary, the two pieces of DNA connect and ultimately are fused by the ligation reaction.

Also Know, what do sticky ends do?

Using sticky ends helps scientists ensure the DNA sequences they are working with can be joined together easily. They fit together perfectly, like pieces of a puzzle. The restriction enzyme EcoRI makes sticky ends when it cuts DNA.

What are sticky ends in DNA quizlet?

Sticky ends are when the enzymes make staggered cuts in the two strands. Cuts that are not directly opposite of each other. Sticky ends are most useful in rDNA because they can be used to join two different pieces of DNA that were cut by the same restriction enzyme.


What is a sticky end in biology?

noun Genetics, Biotechnology. a single-stranded end of DNA or RNA having a nucleotide base sequence complementary to that of another strand, enabling the two strands to be connected by base pairing: produced in the laboratory with the use of restriction enzymes for genetic engineering purposes.

Secondly, what is the difference between blunt ends and sticky ends? Answer: Blunt and sticky ends areresult of restriction endonuclease action on double stranded DNA. Sticky Ends &ndash are staggered ends on a DNA molecule with short, single-stranded overhangs. Blunt Ends are a straight cut, down through the DNA that results in a flat pair of bases on the ends of the DNA.

Also know, what are sticky ends used for?

Restriction enzymes cut double-stranded DNA in half. Depending on the restriction enzyme, the cut can result in either a sticky end or a blunt end. Sticky ends are more useful in molecular cloning because they ensure that the human DNA fragment is inserted into the plasmid in the right direction.

'sticky' ends. A 'sticky' end is produced when the restriction enzyme cuts at one end of the sequence, between two bases on the same strand, then cuts on the opposite end of the complementary strand. This will produce two ends of DNA that will have some nucleotides without any complementary bases.


‘sticky’ ends

A restriction enzyme can cut DNA at a specific sequence of nucleotides usually 4, 6 or 8 nucleotides long. This may result in symmetrical cleavage leading to blunt ends or assymetrical cleavage causing 'sticky' ends. A 'sticky' end is produced when the restriction enzyme cuts at one end of the sequence, between two bases on the same strand, then cuts on the opposite end of the complementary strand. This will produce two ends of DNA that will have some nucleotides without any complementary bases. A restriction enzyme will only cut at a specific sequence and it recognises palindromic sequence that is, sequences that are the same whether they are read forwards or backwards (For example words like Hannah and Race car are palindromes). These 'sticky' ends allow the insertion of 'foreign' DNA into the host genome. By cutting the plasmid with the same restriction enzyme, the same 'sticky ends' are produced. For example, complementary bases of the plasmid can pair with those of the host DNA and form hydrogen bonds which anneal the two strands together. However, there will still be nicks in the phosphodiester bonds which form the rigid phosphate backbone of DNA. In this scenario DNA ligase can be added which will form the phosphodiester bonds between the recombinant strands. The genes carried on the plasmid will now be incorporated into the host's genome, creating a recombinant plasmid. However, the gene of interest can sometimes be inserted into the plasmid in the wrong orientation.

These steps are commonly used in the lab [1] .

…..GAATTC…..
…..CTTAAG…..
After using restiction enzymes to cut at specific sites:


Molecular Biology Techniques

1. Mutate a gene
e.g. to test the function of a particular aa or domain → it tells you if that aa or domain is important for the protein's function
--> You can also create animal models for human diseases to test treatments

2. Add a gene
E.g. add a reporter construct

You can then observe the phenotype of organism when gene's RNA has been destroyed, which implies what normal function of gene is

Only works in worms, plants, and fungi

1. Denature double-stranded nucleotides in a source

2. Add probe (complementary to sequence of interest and labeled (the probe is radioactive or fluorescent))

Probe complementary to mRNA

Transfer molecules to nitrocellulose paper

Cut genomic DNA with restriction enzyme (chromosomes are way too big to fit through gel)

Even after digestion with a restriction enzyme, genomic DNA is just a smear (too many bands all of different sizes)

use mRNA from different cell/tissue types

Probe = DNA complementary to mRNA

1. Cut genomic DNA w/restriction enzyme (to make it a more manageable size) → but where they cut has no relationship to the beginnings or ends of genes

2. Ligate DNA fragments into a plasmid

3. Transform the plasmids into bacteria

Grow bacteria colonies on a petri dish → each colony contains a different piece of DNA from the genome

Put nitrocellulose paper on top of the petri dish → some of the colonies stick to the paper in the same pattern that they are on the petri dish

Lyse bacteria and denature DNA

Reverse transcriptase: synthesizes DNA using an RNA template

Use a Poly(T) primer: TTTTTTTTTTT

---> dsDNA = cDNA, complementary to mRNA that we started with

2. Genes can be fragmented so that parts of the genes are often spread throughout different clones in the library

1. only includes coding sequences
---> Easier to study coding sequences

Disadvantages of cDNA: You can't study regulatory sequences (transcription factor binding sites are not part of coding region so are not included)

Copy # is proportional to transcription level (greater number of copies suggests the gene is being transcribed more in that tissue)

---> a gene being expressed at low levels will be hard to find in the cDNA library (there will be very few clones of it)

From Textbook:
Genomic clones represent a random sample of all of the DNA sequences found in an organism's genome and, with very rare exceptions, will contain the same sequences regardless of the cell type from which the DNA came. Also, genomic clones from eukaryotes contain large amounts of noncoding DNA, repetitive DNA sequences, introns, regulatory DNA, and spacer DNA sequences that code for proteins will make up only a few percent of the library.

By contrast, cDNA clones contain predominantly protein- coding sequences, and only those for genes which have been transcribed into mRNA in the cells from which the cDNA was made. As different types of cells produce distinct sets of mRNA molecules, each yields a different cDNA library. Furthermore, patterns of gene expression change during development, so cells at different stages in their development will also yield different cDNA libraries.


What makes DNA sticky-ends sticky? - Biology

DNA end or sticky end refers to the properties of the end of a molecule of DNA or a recombinant DNA molecule. The concept is important in molecular biology, especially in cloning or when subcloning insert DNA into vector DNA. All the terms can also be used in reference.
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. able to base pair with any DNA molecule containing the complementary sticky end. . This is cut by the restriction enzyme EcoRI, producing sticky ends. .
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Information about sticky end in the free online English dictionary and . sticky end - an end of DNA in which one strand of the double helix extends a few .
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Information about sticky ends in the free online English . sticky end - an end of DNA in which one strand of the double helix extends a few .
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sticky end an end of DNA in which one strand of the double helix extends a few units beyond the . What is the sticky end of the female part of a flower .
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Note: click on a word meaning below to see its connections and related words. The noun sticky end has one meaning: Meaning #1 : an end of DNA in which
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Sticky ends. Sticky ends . I) generate ends with a short single-stranded sequences. Such ends are called sticky ends. Related. Blunt ends Overhang. Other .
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Sticky Ends are A. produced by the action of DNA ligase. B. produced by PCR. C. always long sequences of a single nucleotide. D. used by mRNA to attach to ribosomes. .
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Scientists from Duke University have recently demonstrated a new method for assembling large, low-cost DNA nanostructures, in part by reusing the "sticky-ends," the .
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The first type, the "generic" sticky-end, binds with only one helix instead of the normal two. . type, the "specific" sticky-end, provides a stronger .
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Definition of Sticky end . A B C D E F G H I J K L M N O P Q R S T U V W X Y Z. Search for Sticky end in these other databases too. Definition of Sticky end : .
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What makes DNA sticky-ends sticky? - Biology

DNA end or sticky end refers to the . Longer overhangs are called cohesive ends or sticky ends. . For example, these two " sticky" ends are compatible: .
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These are called "sticky ends" because they are able to base pair with any DNA . This is cut by the restriction enzyme EcoRI, producing sticky ends. .
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Information about sticky end in the free online English dictionary and . sticky end - an end of DNA in which one strand of the double helix extends a few .
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Information about sticky ends in the free online English . sticky end - an end of DNA in which one strand of the double helix extends a few .
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DNA end This article relies largely or entirely upon a single source. . For example, these two "sticky" ends are compatible: .
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Sticky ends. Sticky ends . I) generate ends with a short single-stranded sequences. Such ends are called sticky ends. Related. Blunt ends Overhang. Other .
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Scientists from Duke University have recently demonstrated a new method for assembling large, low-cost DNA nanostructures, in part by reusing the "sticky-ends," the .
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Sticky ends are ends on one or more DNA molecule s that have short, overhanging, . You'll come to a sticky end. Cohesive. Benight. complimentary. molecule. DNA .
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Name the bonds that are formed when sticky ends anneal and those that are formed when blunt ends anneal.
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This results in both ends having a single stranded area called sticky ends. . this space that the new piece of DNA is added, attaching to the sticky ends. .
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The tails are called "sticky-ends" because they can combine with each other. . Two complimentary sticky ends will naturally fit together like toy Lego blocks. .
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Hybridization between sticky ends associates two DNA molecules together. . These motifs, when carrying sticky ends, have been self-assembled into well .
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Using Bacteria

A common method in genetic engineering is to find a gene for a useful product (e.g. insulin) and get a microorganism to produce it.

This is done using a vector which carry things between species. In the case of using bacteria, the vector is the plasmid which is a circle of DNA found in bacterial cytoplasm. It can easily be opened up and a DNA fragment inserted into it.

The vector can be encouraged to enter the cell by heat shock where the temperature is raised rapidly from 0 to 40°C or you also could use electroporation where a high voltage is used to disrupt the cell membrane.

The above steps show how the gene is added to a plasmid. The plasmid already has a gene for antibiotic resistance to Tetracycline and Ampicillin as shown by the black areas. Then a restriction endonuclease is introduced that will cut the gene in between the Tetracycline resistance gene and an insulin gene is added.

At the bottom of the diagram shows the possible outcomes of this situation. Plasmid A shows there has been no change because the plasmid rejoined up after being but or was never cut. Plasmid B shows that the insulin gene has been accepted into the the sticky ends and now disrupts the Tetra resistance gene. Plasmid C shows that the insulin gene has curled up into the it's own little plasmid.

There is another situation of plasmid, which is the same as B, however instead of an insulin gene disrupting the Tetra resistance gene, it is another gene fragment (that we aren't interested in. However for simplicity of explanation this has been omitted.

In step 3 the different bacteria with these plasmid are cultured. Using a process called replica plating where a piece of velvet is put on top of the master plate bacteria, then transfered to make a copy onto the next. The cultures are next grown on a plate containing Ampicillin, this will kill the bacteria without the resistance to the gene, i.e bacteria with plasmid C (ring on insulin) and bacteria without our plasmid at all.

What is left on the Amp plate will be bacteria with plasmids A and B (see diagram above this one). These are now transfered to a final plate containing Tetracycline . This will kill bacteria containing plasmid B because the Tetra. resistance gene has been disrupted by the insulin gene. Now all we have to do is compare the bacterial colonies to see where the insulin containing bacteria are.


Cohesive (sticky) ends and their significance in genetic engineering, Paul Berg

Interviewee: Paul Berg. Cohesive (sticky) ends and their significance in genetic engineering.

Cohesive end in this particular context means that if you take two DNAs that have single strands protruding from their ends, and if these single strands are able to pair with each other by the same rules that DNA strands are held together, then these two molecules could come together. And what Janet showed was that if two DNAs were cut with this particular enzyme, called Eco R-1, then they could be joined and fused together to make recombinant DNAs. And that was a hugely important discovery, because it bypassed the need of the complicated procedures that we had developed in order to bring two molecules together.

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Different Enzymes Can Give The Same Sticky End

Restriction sites are located throughout the genome of organisms, but are not evenly spaced. In plasmids, they can be engineered to be located right next to each other. Scientists who want to cut out a fragment of human DNA from the human genome must find restriction sites that are in front and in back of the region of the fragment. In addition to ensuring that a DNA fragment is inserted in the right direction, different sticky end enzymes can create the same sticky end even though they recognize different restriction sequences. For example, BamHI, BglII, and Sau3A have different recognition sequences but produce the same GATC sticky end. This increases the likelihood that there will be sticky end restriction sites that flank your human gene of interest.


Watch the video: Lektion: DNA och RNA (May 2022).