From:   glenna@uchicago.edu
Subject: multi-state RNA trajectories? data
Date: September 11, 2007 5:47:54 PM PDT
To:   jchodera@gmail.com, nsinghal@stanford.edu
Cc:   nfschere@uchicago.edu

Hi John and Nina,

The equilibrium RNA trajectories for what we call the high [Mg2+] condition (0.1-10 mM Mg2+) are here:

http://craterellus.uchicago.edu/~bolete/
user: smdata
passwd: p0rc1n1

Each element in the traj structure contains the full raw donor  and acceptor trajectories, the active component of the raw trajectory, and the filtered active trajectory.

I included a matlab script to plot each filtered trajectory in a separate window. By filtered I mean that the raw data was passed through Gilad Haran's adaptation of the Chung and Kennedy filter (Haran (2004) Chem Phys v307 p137 Noise reduction in single-molecule fluorescence trajectories of folding proteins).

Compared to the low [Mg2+] data (any concentration below 0.1 mM), high [Mg2+] data always engages in more frequent pathological behaviors, which have made data collection difficult. Pathological-ness can be sorted out with a sufficiently large data set, and I didn't yet optimize signal-to noise and trajectory length, so I wouldn't worry too much about these things at this point.

High [Mg2+] pathologies include 
-faster photobleaching
-wierd photophysics activity after photobleaching events
-FRET states are noisier (maybe because of increased underlying dynamics, which warrants a closer look)
-there is always more fluorescent junk (floater RNA or unidentified aggregates), this is observable in the worst data sets as incessant burst noise.

In spite of these difficulties, there are some clear interesting behavioral trends on the interval [0.1mM 10mM].

I'll send an email when I upload the two manuscripts.

Thanks again for taking a look at the data, I look forward to talking with you soon!

:)

Glenna