What is happening when you crosslink a sample of DNA?
357315
I think you may need to rephrase the question.  What are you crosslinking the DNA to?  Usually you use the term crosslinking when you are trying to map where a protein interacts with the DNA.  This is done with UV light.  Exposure to UV light causes lesions in DNA.  Two Major types are 8-oxoguanosine and thymine dimers.  If a protein is bound to the DNA, it will protect the guanosine bases from becoming oxidized.  If you add a reagent that cleaves the 8-oxoG's, then you can map the difference in the cleavage pattern.  If a G is not cleaved when the protein is bound to the DNA, then you know that the protein interacts with that G.  \n\nHere's a link to a protocol, but its for RNA, simular idea though\n\nhttp://www.bioprotocol.com/protocolstools/protocol.jhtml;jsessionid=KZJTNAD1G4YANR3FQLMSFEWHUWBNQIV0?id=p517
851316
I think I might be qualified to answer this question.\n\nDNA is separated in an electrophoretic field based on the size of the molecules.  \n\nImagine wet spaghetti strands (all different sizes) passing through a thick block of Swiss cheese.   Agarose electrophoresis is based on the ability of the smaller molecules to pass through holes easier than the larger molecules.\nThe smaller the mass, the more nimble it is, and the quicker it can manage all those "Swiss cheese" holes that agarose gels naturally have.\n\nOnce the DNA has run through the gel for a sufficient amount of time, you can stain the gel (actually you can stain the gel as the DNA moves through the gel too).  \n\nThe stain (the classic one is ethidium bromide, but there are others) has a propensity to squeeze itself between nucleotides on both strands.  When it is exposed to a transilluminator light  with a specific wavelength, the ethidium bromide will fluoresce and can be photographed for a permanent record.  \n\nAnalysis is typically based on running controls (positive and negative controls) and a size ladder along with the "unknown" PCR amplicon.  Usually I can predict the size of my unknown amplicon before I run the reaction. \n\nI can then choose a size ladder that will at least give me a rough idea of the size of my amplicon I expect. The ladder also allows me to observe any other false amplicons created during the PCR.  Additionally, some like to estimate how much PCR amplicon was generated in the reaction by comparing the intensity of the size ladder with the intensity of the amplicon. \n\nI hope I was able to help in answering your question.  Hoping YOU spread the good Karma!
1138370
That DNA of different sizes will migrate through a gel at different speeds.\n\nDNA is charged, so applying an electric current will cause the DNA to migrate down the gel, the smaller the piece, the faster it goes.  So you can separete pieces of different lengths, or estimate the size of your band by comparing to a standard ladder.
249178
Are you asking about DNA causing itself to be assembled?
111490
Ahh...thats easy...After putting the DNA in the holes, and turning on the electric field, DNAs move to the (+) pole because they have a (-) charge....Small DNAs move faster and they separate so the result is seen on the gel...
1093732
When you do a maxi-prep, there are several steps for eliminating possible contaminants including, chromosomal DNA, RNA, and protein. If you are using the Birnboim and Doly method of alkaline SDS, then the first few steps are crucial. When the cells are lysed in alkali and SDS, the high pH degrades the cellular RNA and causes the chromosomal and plasmid DNA to denature. If you mix excessively during this step you can, and do, shear the chromosomal DNA and allow for fragments that can subsequently be carried on during the process. In the renaturation step, when you adjust the pH back to near neutrality, you cause the denatured DNA to attempt to re-anneal. For the supercoiled plasmids this is relatively easy because their complementary strands are in close proximity. For chromosomal DNA, they essentially collapse in the presence of the precipitating proteins and they do not effectively re-anneal. When you spin out the white "junk" after neutralization, you are removing the vast majority of the chromosomal DNA, as long as you did not shear it during the earlier steps.\n\nThese features only apply to the alkaline SDS method of plasmid preparation. If you use the boiling SDS method, or the "cleared lysate" method, the problems, and solutions, are different.
93644
I use a 1 KB DNA ladder for electrophoresis and it comes with a paper to actually tell you which band represents which size fragment. Maybe you could look on the tech company's website. If you do not need to know the actual fragment size of each band, maybe you could just compare to make sure the band you need is there in the first place.
62320
well, hope these help:\n\nhttp://www.bbc.co.uk/dna/h2g2/A388217\n\nhttp://www.chemistrysurvival.com/
429879
Each half of the double-helix sort-of "unzips" during replication.  Since each of the bases is kind of like a jigsaw-puzzle piece, the two strands can then wind back up, if supplied with the appropriate free bases, to form two identical copies of the original DNA strand.\n\nNeat, huh?
259305
U meant for denaturing the DNA strands  Mainly verymuch important role playing in the   polymerization  chain reaction for amplifiaction of the DNA synthesis . When DNA get separated while in the melting temp .Forward and reverse primers  complimentary sequences will bind  to the DNA strands while in the annealing temp, it leads to the DNA synthesis.
1098660
Your question isn't easy to read, but i think i understand it enough. There is one mole of 1kbp DNA strand with an EcoR1 restriction site in the middle. The amount of 5'ends produced when you addd EcoR1 to the DNA will be double because you will be effectively cutting the DNA in half. I hope this is what you were asking
730267
Mass-spectrometry (MS) is the only technique that gives true quantitative answers with extremely high certainty, but MS of DNA is uncommon and hard to do.  A more typical approach would be to "run a gel" separate the different fragments based on size: you have a porous matrix, you place the mixture of DNA pieces on one end, you apply a voltage.  Since the DNA is charged it migrates on the gel, but the bigger pieces are hindered by the matrix (the gel).  You then run a "standard" side-by-side with your unknown mixture--something with a mixture of a few fragments on known size.  Typically these "standard ladders" which are commercially available come in increments, e.g. 100 bp, 500 bp, 1000 bp, etc.  So you will be able to tell the size is between those fragment lengths (e.g. that a band from your unknown mixture is between 100 and 500 bp) with very high certainty, but you do not know the exact length with any certainty.\n\nAlternatively you can sequence DNA--this is very easy and cheap now-a-days, and has a very high-certainty.  So after doing a gel you can cut out the different bands and have them sequenced individually.  Both steps--the gel and the sequencing--are very routine, cheap, and reliable.
944540
Probing is based on hybridization techniques.  \n\nIf you will allow, I will describe some of the basics in this commonly used assay.\n\nLet's say, for example that you wanted to know if a genome from a particular person contained a mutation.  And that you already knew what the mutation sequence was.  \n\nYou would purchase an probe (a short stretch of DNA that would be at least 20 bases long, that's been modified with a indicator molecule) in the anti-sense sequence of what your probing.  \n\nIn theory, when the anti-sense sequence (or more commonly called the probe), finds its sense sequence, it will bind to it match (this is the hybridization step).\n\nThe indicator molecule that is co-valently attached to the probe would be something like a radio-isotope, or a fluorescent molecule.  It is used to visually indicate that the probe has, indeed, found it's complimentary sequence.  \n\nWhere the hybridization takes place has changed through out the years.  \n\nClassically the assay was performed in an agarose gel, where the DNA would travel according to its size.  Then the probe would be washed over the agarose gel, and allowed to hybridize to the genomic DNA.  \n\nI never did it this way (so I may be missing a step).  I did mine on glass slides.  \n\nThere a lot variations on this step.  Some where the probe is immobilized and fixed in location, and some where the "test" DNA is immobilized and fixed in location.\n\nIt is improtant to know which one is immobilized. Because then you know which way to orient things. \n\nAlso it is really important to control the salt concentration during the hybridization step. A high salt concentration (along with other factors like low temperature, pH) encourages DNA (probe and "test" DNA) to bind together.  I'll say it again:  High salts encourage specific hybridization to occur.\n\nDuring this hybridization step, you'll also be adding an enzyme which will co-valently (and permanently) bind the probe to the DNA.\n\nAfter a good amount time, allowing for hybridization and co-valent attachment to occur, you'll do some wash steps.  The wash steps remove any unbound probe (the probe is always added in huge amounts compared to your "test" DNA) from the assay.  \n\nThis step is also critical, because it will allow you to "read" the final results with greater acuity.  In other words, you'll have less false positive results.\n\nThe wash steps are done with lower salt concentrations.  Just the opposite of the hybridization step, with the goal of removing any probes that have inadvertently attached to the "test" DNA imperfectly without co-valent attachment.\n\nNow its time to read the results. The "read out" method is based on the molecule you attached to your probe. So if you had a fluorescent probe, you will use a fluorescent reader.  If you chose an isotope, you'll use a radio-graphic technique.\n\nEarlier I mentioned this example would be a method to detect a mutation in the genome of a patient (but you vary this method to detect a lot of different things).  So if you saw something "glowing" in your read out, then you could assume that the patient had the mutation.  If you saw no "glow" then you could assume the patient did not possess the mutation.\n\nIn reality, when one visualizes a positive result, they usually follow it up with a more sensitive test.  \n\nProbing nucleic acids is a quick way to screen for one thing on many samples. \n\nBut it can be a good way to probe one sample for many different things.  You would be limited by how many unique indicator molecules you can have (and afford) to have on your many probes that would give you unique signal.\n\nI had fun thinking about your question.  Please pass on the good Karma!
16328
DNA testing can be pretty accurate, but it depends on how many sequences they test.  If you read my test procedure explanation you will understand why DNA is used.\n\nFirst, Carbohydrates and lipids are pretty much identical between all people.  A few people have metabolic disorders that result in a build up of certain carbs, but generally it would be useless to test for the specific carb or lipid present, because they are the same for everyone.\n\nProteins do differ among people, but not as much as DNA does.  DNA provides the information telling ribosomes how to put proteins together in people, but only a small portion of DNA is ever tranlsated to protein.  Most of your DNA is junk, and the big DNA differences between two people are in this junk DNA, so that is what is used for DNA testing.\n\nThis is an explanation of how it is typically done:\n\nThe way DNA testing works is by measuring the lengths of DNA segments between two endonuclease cleavage sites.  An endonuclease is an enzyme that will cleave DNA at a particular sequence of bases.  Some specific cleavage sites exist in the DNA of all people.  In between two specific cleavage sites, you may have a sequence of tandem repeat DNA.  For example le us say your DNA looks like this:\n(Cleave) gene1-TGTGTGTGTGTG-gene2 (Cleave)\nWe will denote this length of tandem repeat segment as (TG)6.  My DNA may have a tandem repeat segment may be (TG)10, in which case the segment of DNA between the two cleavage points is longer for me than it is for you.  This additional length also makes it heavier.\n\nNow let us make a suspend lots of copies of this particular segment of your DNA in a fluid and make another suspension with my DNA.  \n\nLet us also say that we know that everyone has a sequence of TG repeats at least 6 repeats long.  The complement to this sequence is:\nACACACACACAC -> (AC)6\nWe could create a radio labelled (AC)6 probe and sprinkle it into the suspension with your DNA, the suspension with my DNA, and a suspension with unknown DNA.  This probe would bind to the DNA in all three solutions, but my DNA segment would still be heavier than yours, because it contains 10 repeats, even if only 6 are bound to the probe.\n\nWe now place some of the suspension of your DNA at a point on an adsorbent surface.  The suspnsion will travel along the surface, but at some point the DNA will stick to the surface.  If it is heavier it will stick sooner.  With good equipment all DNA of a certain length will stick at the same spot (or short line)\n\nSince my DNA is heavier than yours, mine will travel less far.  The unknown DNA will travel either as far as your DNA does or as far as my DNA does, and that will tell whose DNA it is.\n\nThe way you view the DNA on the adsorbent surface is with a film that will darken when exposed to our radio labelled probe.  You place this film on top of the adsorbent bed with the DNA samples and three small spots (or short lines) will show.  The distance the unknown DNA travelled in comparison to your DNA and mine tells us whose DNA it is.\n\nInvestigators do this with evidence; only they use many different tandem repeat segments scattered throughout the genome.  The more segments used, the lower the probability of a coincidence.
203875
Usually described as about 2 meters for all of the dna in one human cell.  This actually consists of many separate strands of dna.
838778
To be honest with you i don't quite understand your question, it is often that restriction enzymes are used to create genomic library for which you look into the overlapping sequence and then be able to determine which fragment is next to which. If that is what you have done, you should have used the fragmented DNA sequence to determine the orginall DNA sequence that you digested it with the enzyme, to confirm the sequence you ahve found is correct, you can use PCR, you got the hypothetical sequence, thus by making primers from the start and the end of the sequence (doesn't matter which way round) you should have amplify the same sequence which you started with, you got the amplified DNA (same as the orginal DNA because you used primers that complemented the very start and the very end of the sequence which you found out after the restruction enzyme mapping) run it on gel electrophoresis with a DNA size marker that will include the size of DNA you have sequenced, if the amplified DNA size is the same as the sequence you have found from restriction mapping, that means your primers did complemented from the start and the end, that means the sequence you thought is actually the correct sequnece.\nI am sorry, i don't think i am making this clear enough, but anyway, that's the best i can think of.
1127492
These types of DNA are used to create a much more accurate diagnosis of DNA samples lef tfrom teh crime\n\nemail me a kkstrong0@yahoo.com if you have further questions and ill try to tell you what i know