DNA replication occurs during the S phase of the cell cycle. Before DNA replication, the cell performs a check to ensure that there are no damages to the DNA molecules. One important molecule in this process is the cyclin-CDK complex. CDKs, or cyclin dependent kinases, are important kinases that facilitate the progression of cell through the cell cycle. Presence of CDK inhibitors will halt the progression of cell cycle and, subsequently, will halt DNA replication.

UV light is very damaging to DNA molecules. It changes the conformation of DNA molecules and prevents the activity of DNA replication enzymes; therefore, excessive UV light exposure will halt DNA replication.

Adenosine triphosphate, or ATP, is the main energy currency of the cell. It is used to power numerous energy consuming cellular processes. DNA replication requires lots of energy. Lack of energy, or ATP, will slow down DNA replication.

DNA methylation is an epigenetic process that involves the addition of a methyl group on DNA molecules. This makes the DNA molecule unavailable for and halts transcription. It does not stop DNA replication, however. Note that the methyl group added to the DNA here is different from the methyl cap added to RNA molecules during post-transcriptional processing.

The other epigenetic change that prevents transcription is the deacetylation of histones. Histones are proteins that facilitate the packaging and ordering of DNA molecules. Deacetylation of histones makes them more positive, strengthening the interaction between histones and negatively charged DNA molecules. This makes it harder for DNA molecules to open and be available for transcription.

CDKs are enzymes that facilitate the progression of a cell through the cell cycle. This involves the replication of DNA during the S phase. DNA polymerase is an important enzyme in DNA replication. It’s main function is to add complementary nucleotides to the growing daughter DNA strand. RNA polymerase serves a similar function as DNA polymerase; however, it is utilized only during transcription. All of the enzymes listed either enhance or have no effect on DNA replication.

The phases of cell cycle in order are as follows: G1 phase, S phase, G2 phase, and Mitosis. DNA replication occurs during the S phase; therefore, a checkpoint to ensure proper replication must occur before this phase, between the G1 and S phase. During this checkpoint, the cell checks for DNA damages that might have occurred. If the DNA is damaged, then the cell activates DNA repair enzymes. Upon repair, the cell undergoes the checkpoint one more time. If proper repairs have been made, the cell progresses into the S phase and undergoes DNA replication.

The nucleotide cytidine under certain chemical or heat conditions can be deaminated to form uracil. DNA repair mechanisms intervene at this point. Uracil is found only in RNA, so it needs to be removed and replaced with another cytosine molecule. The answers above are all steps in removing an uracil nucleotide from the DNA molecule.