Examples of DNA in the following topics:
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- Prokaryotic DNA is replicated by DNA polymerase III in the 5' to 3' direction at a rate of 1000 nucleotides per second.
- In prokaryotes, three main types of polymerases are known: DNA pol I, DNA pol II, and DNA pol III.
- DNA pol III is the enzyme required for DNA synthesis; DNA pol I and DNA pol II are primarily required for repair.
- DNA polymerase III uses this primer to synthesize the daughter DNA strand.
- DNA polymerase I replaces the RNA primer with DNA.
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- DNA protection or "footprinting" analysis is a powerful technique for identifying the nucleotides involved in a protein-DNA interaction.
- DNA protection or footprinting is a technique from molecular biology/biochemistry that detects DNA-protein interaction using the fact that a protein bound to DNA will often protect that DNA from enzymatic cleavage.
- This makes it possible to locate a protein binding site on a particular DNA molecule.
- The cleavage pattern of the DNA in the absence of a DNA binding protein, typically referred to as free DNA, is compared to the cleavage pattern of DNA in the presence of a DNA binding protein.
- If the protein binds DNA, the binding site is protected from enzymatic cleavage.
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- Whole-genome DNA-binding analysis is a powerful tool for analyzing epigenetic modifications and DNA sequences bound to regulatory proteins.
- After cell lysis, the DNA is fragmented by sonication.
- DNA bound by the protein will be coprecipitated and enriched, compared to DNA not bound by the respective protein.
- Two different fluorescence labels are used to label the IP DNA, and a hybridization-control DNA, respectively.
- Usually, total DNA before IP (input DNA) is used as hybridization control.
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- DNA replication uses a semi-conservative method that results in a double-stranded DNA with one parental strand and a new daughter strand.
- Watson and Crick's discovery that DNA was a two-stranded double helix provided a hint as to how DNA is replicated.
- In dispersive replication, after replication both copies of the new DNAs would somehow have alternating segments of parental DNA and newly-synthesized DNA on each of their two strands.
- DNA from cells grown exclusively in 15N produced a lower band than DNA from cells grown exclusively in 14N.
- So each "daughter" DNA actually consists of one "old" DNA strand and one newly-synthesized strand.
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- Eukaryotic DNA is packed into bundles of chromosomes, each consisting of a linear DNA molecule coiled around basic (alkaline) proteins called histones, which wind the DNA into a more compact form.
- In addition, prokaryotes have plasmids, which are smaller pieces of circular DNA that can replicate separately from prokaryotic genomic DNA.
- A major DNA difference between eukaryotes and prokaryotes is the presence of mitochondrial DNA (mtDNA) in eukaryotes.
- The mtDNA is composed of significantly fewer base pairs than nuclear DNA and encodes only a few dozen genes, depending on the organism.
- Eukaryotic DNA is stored in a nucleus, whereas prokaryotic DNA is in the cytoplasm in the form of a nucleoid.
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- The classical chain-termination method requires a single-stranded DNA template, a DNA primer, a DNA polymerase, normal deoxynucleotidetriphosphates (dNTPs), and modified nucleotides (dideoxyNTPs) that terminate DNA strand elongation .
- Following rounds of template DNA extension from the bound primer, the resulting DNA fragments are heat denatured and separated by size using gel electrophoresis.
- The DNA bands may then be visualized by autoradiography or UV light and the DNA sequence can be directly read off the X-ray film or gel image.
- Automated DNA-sequencing instruments (DNA sequencers) can sequence up to 384 DNA samples in a single batch (run) in up to 24 runs a day.
- The four DNA bases are represented by different colours which are interpreted by the software to give the DNA sequence above.
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- Noncoding DNA are sequences of DNA that do not encode protein sequences but can be transcribed to produce important regulatory molecules.
- In genomics and related disciplines, noncoding DNA sequences are components of an organism's DNA that do not encode protein sequences.
- The amount of noncoding DNA varies greatly among species.
- For example, over 98% of the human genome is noncoding DNA, while only about 2% of a typical bacterial genome is noncoding DNA.
- The amount of total genomic DNA varies widely between organisms, and the proportion of coding and noncoding DNA within these genomes varies greatly as well.
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- Each helicase unwinds and separates the DNA helix into single-stranded DNA.
- Once RNA primer has been synthesized at the template DNA, primase exits, and DNA polymerase extends the new strand with nucleotides complementary to the template DNA.
- DNA polymerase halts when it reaches a section of DNA template that has already been replicated.
- Once the primers are removed, a free-floating DNA polymerase lands at the 3' end of the preceding DNA fragment and extends the DNA over the gap.
- The DNA fragments are joined by DNA ligase (not shown).
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- When cloning genomic DNA, the DNA to be cloned is extracted from the organism of interest.
- For cloning of genomic DNA, the DNA to be cloned is extracted from the organism of interest.
- DNA for cloning experiments may also be obtained from RNA using reverse transcriptase (complementary DNA or cDNA cloning), or in the form of synthetic DNA (artificial gene synthesis). cDNA cloning is usually used to obtain clones representative of the mRNA population of the cells of interest, while synthetic DNA is used to obtain any precise sequence defined by the designer.
- Typically, this is done by cleaving the vector DNA and foreign DNA with the same restriction enzyme.
- The two resulting DNA strands make up the template DNA for the next cycle, thus doubling the amount of DNA duplicated for each new cycle.
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- Both the packaging of DNA around histone proteins, as well as chemical modifications to the DNA or proteins, can alter gene expression.
- Histones package and order DNA into structural units called nucleosome complexes, which can control the access of proteins to the DNA regions.
- The tags do not alter the DNA base sequence, but they do alter how tightly wound the DNA is around the histone proteins .
- The DNA molecule itself can also be modified.
- Nucleosomes can slide along DNA.