A template is the sequence of DNA or RNA that directs the synthesis of a complementary sequence. A primer is the initial segment of a polymer that is to be extended on which elongation depends.
DNA polymerase cannot initiate primer synthesis. Consequently, an RNA polymerase, called primase, synthesizes a short sequence of RNA that is used as a primer by the DNA polymerase.
Okazaki fragments are short segments of DNA that are synthesized on the lagging stand of DNA. These fragments are subsequently joined by DNA ligase to form a continuous segment of DNA.
When DNA is being synthesized at the replication fork, the leading strand is synthesized continuously in the 5′-to-
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The nucleotides used for DNA synthesis have the triphosphate attached to the 5′-hydroxyl group with free 3′-hydroxyl groups. Such nucleotides can be utilized only for 5′-to-
The rate of strand separation is low owing to the hydrogen bonds of the helix and the stacking forces between bases. Although individually weak, the thousands or millions of such bonds that hold a helix together make spontaneous separation of the strands unlikely.
Replication would take twice as long.
Eventually, the DNA would become so tightly wound that movement of the replication complex would be energetically impossible.
A hallmark of most cancer cells is prolific cell division, which requires DNA replication. If the telomerase were not activated, the chromosomes would shorten until they became nonfunctional, leading to cell death. Interestingly, telomerase is often, but not always, found to be activated in cancer cells.
C36
The free energy of ATP hydrolysis under standard conditions is −30.5 kJ mol−1 (−7.3 kcal mol−1). In principle, it could be used to break three base pairs.
The nucleotide ddATP is virtually identical in structure with dATP except that it lacks a 3′-OH. Thus, it will be incorporated into a newly synthesized DNA by DNA polymerase when the polymerase first encounters a T in the template strand. However, because the incorporated ddAMP has no 3′-OH, synthesis stops.
Because the ddATP is only 10% of the concentration of dATP, there is a 10% chance that it will be incorporated into the newly synthesized DNA when a T is encountered in the template strand. Consequently, a population of fragments of DNA will be synthesized, all ending in ddAMP. The inability to extend a dideoxy nucleotide is the basis of the strand-
Positive supercoiling resists the unwinding of DNA. The melting temperature of DNA increases in proceeding from negatively supercoiled to relaxed to positively supercoiled DNA. Positive supercoiling is probably an adaptation to high temperature to prevent unregulated DNA unwinding.
Size; the top is relaxed and the bottom is supercoiled DNA.
Topoisomers
The DNA is becoming progressively more unwound, or relaxed, and thus slower moving.
The high concentration of nucleotides will have the effect of speeding up the polymerization reaction. Consequently, a misformed product may exit the polymerase active site before it has time to wander into the exonuclease activity site. The reverse is true if the next nucleotide is scarce. The polymerase pauses for a longer time, increasing the likelihood that a misformed product will visit the exonuclease site.
96.2 revolutions per second (1000 nucleotides per second divided by 10.4 nucleotides per turn for B-
0.34 μm s−1 (1000 nucleotides per second corresponds to 3400 Å s−1 because the axial distance between nucleotides in B-
Treat the DNA briefly with endonuclease to occasionally nick each strand. Add the polymerase with the radioactive dNTPs. At the broken bond, or nick, the polymerase will degrade the existing strand with its 5′ → 3′ exonuclease activity and replace it with a radioactive complementary copy by using its polymerase activity. This reaction scheme is referred to as nick translation because the nick is moved, or translated, along the DNA molecule without ever becoming sealed.