Initiation Elongation of DNA Synthesis

The initiation of DNA synthesis (Figure 36-14) requires priming by a short length of RNA, about 10-200 nucleotides long. This priming process involves the nucleophilic attack by the 3'-hydroxyl group of the RNA primer on the a phosphate of the first entering deoxynucleoside triphosphate (N in Figure 36-14) with the splitting off of pyrophosphate. The 3'-hy-droxyl group of the recently attached deoxyribonu-cleoside monophosphate is then free to carry out a nucleophilic attack on the next entering deoxyribonu-cleoside triphosphate (N + 1 in Figure 36-14), again at its a phosphate moiety, with the splitting off of pyrophosphate. Of course, selection of the proper de-oxyribonucleotide whose terminal 3'-hydroxyl group is to be attacked is dependent upon proper base pairing

Table36-6. A comparison of prokaryotic and eukaryotic DNA polymerases.

E coli

Mammalian

Function

I

a

Gap filling and synthesis of lagging strand

II

£

DNA proofreading and repair

ß

DNA repair

Y

Mitochondrial DNA synthesis

III

8

Processive, leading strand synthesis

RNA primer

RNA primer

First entering dNTP Ov O N o'

OH H

OH p

Second entering dNTP O^ o \ NoP

OH H

Figure 36-14. The initiation of DNA synthesis upon a primer of RNA and the subsequent attachment of the second deoxyribonucleoside triphosphate.

with the other strand of the DNA molecule according to the rules proposed originally by Watson and Crick (Figure 36-15). When an adenine deoxyribonucleoside monophosphoryl moiety is in the template position, a thymidine triphosphate will enter and its a phosphate will be attacked by the 3'-hydroxyl group of the deoxyribonucleoside monophosphoryl most recently added to the polymer. By this stepwise process, the template dictates which deoxyribonucleoside triphos-phate is complementary and by hydrogen bonding holds it in place while the 3'-hydroxyl group of the growing strand attacks and incorporates the new nu-cleotide into the polymer. These segments of DNA attached to an RNA initiator component are the Okazaki fragments (Figure 36-16). In mammals, after many Okazaki fragments are generated, the replication complex begins to remove the RNA primers, to fill in the gaps left by their removal with the proper base-paired deoxynucleotide, and then to seal the fragments of newly synthesized DNA by enzymes referred to as DNA ligases.

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