User:Magladem96/sandbox-baseflipping

Definition

 * 1) "The ability of a base to protrude from the double helix in an extrahelical configuration. When extruded from the helix, the base can sit in the catalytic cavity of enzymes that methylate bases or remove damaged bases." Source: Molecular Biology of the Gene, 7th ed definition, eBook Glossary
 * 2) "Base flipping is the phenomenon whereby a base in normal B-DNA is swung completely out of the helix into an extrahelical position. It was discovered in 1994 when the first co-crystal structure was reported for a cytosine-5 DNA methyltransferase binding to DNA."  Base flipping.  www.ncbi.nlm.nih.gov/pubmed/9759487

Discovery
In 1994: Hhal methyltransferase flips its target base out of the DNA helix: http://ac.els-cdn.com.proxy1.library.jhu.edu/0092867494903425/1-s2.0-0092867494903425-main.pdf?_tid=6b3ba224-a40e-11e3-80a2-00000aacb35f&acdnat=1393986938_484c802af28f2ede25db086acd1b87b4  (Downloaded)

Experimental approaches
https://www.landesbioscience.com/pdf/04GrosjeanKlimasauskas.pdf (downloaded)

Good background

 * 1) http://www.atdbio.com/content/54/Base-flipping#Further-reading
 * 2) http://www.annualreviews.org.proxy1.library.jhu.edu/doi/pdf/10.1146/annurev.biochem.67.1.181

Molecular dynamics of base flipping
http://www.mpibpc.mpg.de/276493/paper_moleculare_dynamics_study.pdf

Recognition of Damaged DNA by Repair Enzymes

 * 1) http://www.enzim.hu/data/pdf/12417196.pdf

Images
pg 83 fig 4-8 in book which is from original paper fig 4

Draft Outline

 * Lead/Define
 * Discovery
 * Mechanism
 * 1. biochem: large energetic cost breaking H-bonds & base-stacking disruptions (atdbio.com)
 * 2. dynamics
 * 3. Active (bind & flip at same time) vs. Passive (flip, then bind) (atdbio.com & google books)


 * Biological Processes
 * 1. DNA modification and repair
 * 2. Replication, Transcription, & Recombination
 * 3. DNA Methylation
 * 4. Sequence Specific target recognition by restriction endonucleases


 * Experimental Approaches
 * 1. X-ray crystallography
 * 2. NMR spectroscopy
 * 3. Fluorescent spectroscopy
 * 4. Chemical probing


 * Systems?
 * 1. Hha1 DNA Methyltransferase
 * 2. Uracil-DNA glycosylase