Thank you, Edwin! I don't think I knew about Erez Lieberman Aiden's work directly, but had seen other people refer to it. The first 20 minutes of this 31-minute video shows really nice graphics of (human-like) DNA in chromosonal "fractal globules", which have the "locality" properties I described, and are _not_ knotted. This video also describes how this data was gathered & processed. http://www.youtube.com/watch?v=7hT0_tQVjzA Erez Lieberman Aiden: Things You Can't Browse at UCSC broadinstitutebroadinstitute·114 videos Published on Oct 2, 2012 This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (http://www.vizbi.org) funded by NIH & EMBO. At 10:46 AM 12/28/2012, W. Edwin Clark wrote:
Henry is perhaps thinking of the work of Harvard Fellow Erez Lieberman. He claims that human nuclear DNA folds into something he calls a fractal globule which has few if any knots. http://www.aaas.org/news/releases/2011/1201sp_ge_prize.shtml I hear him speak on this in April, but I don't recall the details --only that he had some beautify simulations of DNA folding and unfolding.
On Fri, Dec 28, 2012 at 1:07 PM, Henry Baker <hbaker1@pipeline.com> wrote:
From the article in the nih.gov link below:
"The *** E. coli *** strains used in this study and their relevant genotype are detailed in Supplementary Table S1."
http://en.wikipedia.org/wiki/Escherichia_coli
"The first complete DNA sequence of an E. coli genome ... was published in 1997. It was found to be a *** circular *** DNA molecule 4.6 million base pairs in length, containing 4288 annotated protein-coding genes (organized into 2584 operons), seven ribosomal RNA (rRNA) operons, and 86 transfer RNA (tRNA) genes."
E. coli has *** circular *** DNA. Human nuclear (non-mitochondrial) DNA isn't circular.
At 09:41 AM 12/28/2012, Michael Kleber wrote:
On Fri, Dec 28, 2012 at 11:56 AM, Henry Baker <hbaker1@pipeline.com> wrote:
I don't know what % of the time (human nuclear--i.e., non-mitochondrial)
DNA spends doing recombination, but I would guess/hope very small. During the rest of the time, it is my understanding that there aren't any knots in this DNA.
I'm sorry, I didn't realize we were still arguing about this question of fact. Let me re-post the link from up-thread, along with the beginning of the article this time.
http://www.ncbi.nlm.nih.gov/pubmed/22187153 "Topo IV is the topoisomerase that knots and unknots sister duplexes during DNA replication"