Article Summaries

Question 1

Article 1: Transient Hoogsteen Base Pairs in Canonical Duplex DNA

Answer 1

Hypothesis: conformations that stray from traditional Watson-Crick model could be observed using nuclear magnetic resonance relaxation dispersion spectroscopy and molecular dynamics simulations

AKA wanted to identify alternative forms of DNA

Found other forms of base pairing exist called excited states. Used spectroscopy to distinguish between excited states and also tested if these states were thermodynamically stable

Conclusion: excited state of DNA is coded in DNA double helix

Question 2

Article 2: Watching DNA polymerase n make a phosphodiester bond

Answer 2

Hypothesis that the chemical reaction process of DNA synthesis has structural changes (phosphodiester bond formation) that can be seen via X ray crystallography

method: take advantage of the slow reaction created by human DNA polymerase to observe structural changes and formation of phosphodiester bond

x-crystallography allowed them to vieww and record DNA synthesis in real time.

Observed: different reaction rates between bonds formed on the 3’-OH and alpha phosphorous

Question 3

Article 3: E. Coli Lagging strand polymerase is triggered exclusively by the ability of a new primer at the replication fork

Answer 3

Want to know: what triggers cycling and the release of the lagging strand polymerase during okazaki frag. synthesis and what is the specific signal that causes trigger.

method: studied collision model and signaling model to come up with different triggers. WHich one is the model ?

Hypothesized that the signaling model leads to the trigger

Method: purified rolling circle reaction, used asymmetry between nucleotides of two strands

Conclusion: signaling model is the model for this

Question 4

Article 4: ATM and ATR signaling regulate the recruitment of Human telomerase to telomeres

Answer 4

investigate the role of ATM and ATR signaling in recruitment of telomerase to telomeres

Hypothesis: that there is evidence that ATM and ATR facilitate telomere lengthening by telomerase

Method: looked at human cells to confirm role of ATM and ATR. Diminished levels of ATM and ATR to see how that would affect telomerase. Used small interfering RNA for this. also used FISH to make observations.

Observed: telomerase recruitment decreases when ATM/ATR levels decrease and also affect telomerase complex assembly and replication fork stalling activities

Question 5

Article 5: Double Holliday junctions are intermediates of DNA break repair

Answer 5

Investigate intermediates involved during DSB repair in mitosis

Hypothesis: there are other intermediates outside the Holliday junction that are involved in DSB repair

Method: performed DSB assay to help single out intermediate

Observed inter-homologue joint molecule intermediates (JM) via 2 electrophoresis (appear as branched structures)

Conclusion: JMs are a minor pathway to the DSB repair in mitotic cells