Is the 5 end phosphate or hydroxyl?
Its 5′ end contains a free phosphate group. The 3′ end has a free hydroxyl group.
What is 5 and 3 when describing DNA?
The 5′ and 3′ specifically refer to the 5th and 3rd carbon atoms in the deoxyribose/ribose sugar ring. The phosphate group attached to the 5′ end of one nucleotide and the hydroxyl group at the 3′ end of another nucleotide have the potential to form phospodiester bonds, and hence link adjacent nucleotides.
Are phosphate groups or hydroxyl groups found at the 5 ends of DNA strands?
The 3ʹ end of each strand has a free hydroxyl group, while the 5ʹ end of each strand has a free phosphate group. The sugar and phosphate of the polymerized nucleotides form the backbone of the structure, whereas the nitrogenous bases are stacked inside.
Does 5′-phosphorylation enhance gap filling by DNA polymerase β?
With a substrate containing a nick bounded by 3′- and 5′-OH termini, the rate of gap filling by polymerase β was significantly enhanced in the presence of polynucleotide kinase and ATP, indicating the positive influence of 5′-phosphorylation. The reaction was further enhanced by addition of DNA ligase I to the reaction mixture.
Does PNK have a 3’-phosphatase activity?
Here we report an extension of these studies to examine the 3′-phosphatase activity of PNK and the use of this enzyme in conjunction with purified mammalian DNA polymerase β and DNA ligase I to repair nicks and gaps in duplex DNA with 5′-OH and 3′-phosphate termini.
Why are 3’ and 5’ terminals restored to hydroxyl groups?
Nonetheless, all 3′-termini have to be restored to hydroxyl groups, and 5′-termini to phosphate groups, in order to allow DNA polymerases and ligases to catalyze repair synthesis and strand rejoining.
What is the difference between 5′-phosphate and 45mer and p45?
The 5′-phosphate is radiolabelled. 45mer (comp) refers to the complementary 45mer as opposed to p45 used in the text and other figures to indicate the product of ligation of the 21mer and 24mer oligonucleotides. Composition of oligonucleotides and model substrates.