Source data for "Recycling of Bacterial RNA Polymerase by the Swi2/Snf2 ATPase RapA"

Source data for:

Recycling of Bacterial RNA Polymerase by the Swi2/Snf2 ATPase RapA

In press, PNAS 2023

Koe Inlow^a, Debora Tenenbaum^b, Larry J. Friedman^a, Jane Kondev^b,*, and Jeff Gelles^a,*

^aDepartment of Biochemistry and ^bDepartment of Physics, Brandeis University, Waltham, MA 02453, USA.
*To whom correspondence may be addressed. Email: gelles@brandeis.edu (J.G.) or kondev@brandeis.edu (J.K.).

Source data for the single-molecule experiments is provided as “intervals” files that can be read and manipulated by the Matlab program “Imscroll”, which is publicly available at:

https://github.com/gelles-brandeis/CoSMoS_Analysis

The files are identified in Source data index.docx, the contents of which are also reproduced below.

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Fig 1B, 1E (top):

• ki00447_core_intervals.dat; ki00446_oligo_intervals.dat
• ki00174_core_intervals.dat; ki00175_oligo_intervals.dat
• ki00586_core_intervals.dat; ki00587_oligo_intervals.dat

 

Fig 1C, 1D, 1E (bottom):

• ki00411_core_intervals.dat; ki00411_RapA_intervals.dat; ki00412_oligo_intervals.dat
• ki00416_core_intervals.dat; ki00416_RapA_intervals.dat; ki00417_oligo_intervals.dat
• ki00590_core_intervals.dat; ki00592_RapA_intervals.dat; ki00591_oligo_intervals.dat

 

Fig 2B:

•  

 

Fig 2C, premix (orange data):

• 0 nM RapA, no ATP: ki00038_intervals.dat
• 5 nM RapA, no ATP: ki00022_intervals.dat; ki00007_intervals.dat
• 10 nM RapA, no ATP: ki00083_intervals.dat; ki00031_intervals.dat
• 0 nM RapA + 1 mM ATP: ki00026_intervals.dat; ki00117_intervals.dat
• 1 nM RapA + 1 mM ATP: ki00140_core_intervals.dat; ki00010_intervals.dat
• 5 nM RapA + 1 mM ATP: ki00136_intervals.dat; ki00164_core_intervals.dat; ki00044_intervals.dat
• 10 nM RapA + 1 mM ATP: ki00016_intervals.dat; ki00034_intervals.dat; ki00123_intervals.dat; ki000444_intervals.dat
• 25 nM RapA + 1 mM ATP: ki00218_core_intervals.dat
• 50 nM RapA + 1 mM ATP: ki00225_core_intervals.dat
• 100 nM RapA + 1 mM ATP: ki00047_intervals.dat
• 500 nM RapA + 1 mM ATP: ki000381_intervals.dat; ki00042_intervals.dat; ki00050_intervals.dat

 

Fig 2C, washout (green data):

• 0 nM RapA, no ATP: ki00092_intervals.dat; ki00254_intervals.dat; ki00075_intervals.dat
• 2 nM RapA, no ATP: ki00058_intervals.dat
• 4 nM RapA, no ATP: ki00355_core_intervals.dat
• 5 nM RapA, no ATP: ki00287_intervals.dat; ki00294_intervals.dat; ki00313_intervals.dat; ki00327_core_intervals.dat; ki00381_core_intervals.dat
• 50 nM RapA, no ATP: ki00474_core_intervals.dat
• 75 nM RapA, no ATP: ki00246_intervals.dat; ki00304_intervals.dat; ki00081_intervals.dat
• 100 nM RapA, no ATP: ki00290_intervals.dat; ki00065_intervals.dat
• 0 nM RapA + 1 mM ATP: ki00344_core_intervals.dat; ki00236_intervals.dat
• 1 nM RapA + 1 mM ATP: ki00015_intervals.dat; ki00263_intervals.dat; ki00279_intervals.dat; ki00331_core_intervals.dat; ki00378_core_intervals.dat; ki00429_core_intervals.dat
• 2 nM RapA + 1 mM ATP: ki00478_core_intervals; ki00267_intervals.dat
• 2.5 nM RapA + 1 mM ATP: ki00335_core_intervals.dat; ki00482_core_intervals.dat; ki00318_intervals.dat
• 3 nM RapA + 1 mM ATP: ki00283_core_intervals.dat; ki00341_core_intervals.dat; ki00465_core_intervals.dat
• 5 nM RapA + 1 mM ATP: ki00017_intervals.dat; ki00298_core_intervals.dat; ki00301_core_intervals.dat; ki00271_intervals.dat; ki00288_core_intervals.dat; ki00323_core_intervals.dat
• 10 nM RapA + 1 mM ATP: ki00084_intervals.dat; ki00240_core_intervals.dat

 

 

Fig 3A:

• ki00491_RapA_intervals.dat (ki00491_RapA_intervals_new_all_spots_high_frmavg2_frames1to3005_newmap_rad2point4_up2.dat)
• ki00491_core_intervals.dat (ki00491_core_intervals_frmavg2_frames1_to_3005_newmap_rad2_up2point1.dat)
• ki00507_RapA_intervals.dat (ki00507_RapA_intervals_bg_corrected_frmavg2_newmap_rad2point5_up1point5.dat)
• ki00507_core_intervals.dat (ki00507_core_intervals_newmapfile_rad2_up1point5.dat)

 

Fig 3B:

• RapA binding npDNA (orange): ki00573_RapA_intervals.dat
• RapA binding off-target npDNA (grey): ki00573_RapA_off_target_intervals.dat
• RapA binding rPTCs (blue): ki00491_RapA_intervals.dat
• RapA binding off-target rPTCs (black): ki00491_RapA_off_target_intervals.dat (ki00491_RapA_off_target_intervals_up1point2_rad1.dat)

 

Fig 3C:

• ki00513_core_intervals.dat (ki00513_core_intervals_bg_corrected_uprad2.dat)
• ki00513_RapA_intervals.dat (ki00513_RapA_intervals_bg_corrected_uprad2.dat)
• ki00510_core_intervals.dat (ki00510_core_intervals_bg_corrected_rad2point5_up2point1.dat)
• ki00510_RapA_intervals.dat (ki00510_RapA_intervals_bg_corrected_rad3_up1point5.dat)

 

Fig 3D:

• ki00510_core_intervals.dat (ki00510_core_intervals_bg_corrected_rad2point5_up2point1.dat)
• ki00510_RapA_intervals.dat (ki00510_RapA_intervals_bg_corrected_rad3_up1point5.dat)

 

Fig 4A, S6:

• No nucleotide, green: ki00551_core_intervals.dat (ki00551_core_intervals_uprad2.dat)
• No nucleotide, red: ki00551_RapA_intervals.dat (ki00551_RapA_intervals_rad2_up1point5.dat)
• No nucleotide, blue: ki00552_RapA_intervals.dat (ki00552_RapA_intervals_rad2_up1point5.dat)
• + 1 mM AMPPNP, green: ki00555_core_intervals.dat (ki00555_core_intervals_uprad2_frmavg2.dat)
• + 1 mM AMPPNP, red: ki00555_RapA_intervals.dat (ki00555_RapA_intervals_uprad2_frmavg2.dat)
• + 1 mM AMPPNP, blue: ki00556_RapA_intervals.dat (ki00556_RapA_intervals_rad2_up2point5_frmavg2.dat)
• + 1 mM ATP, green: ki00559_core_intervals.dat (ki00559_core_intervals_uprad2.dat)
• + 1 mM ATP, red: ki00559_RapA_intervals.dat (ki00559_RapA_intervals_up1point5_rad2point5.dat)
• + 1 mM ATP, blue: ki00560_RapA_intervals.dat (ki00560_RapA_intervals_uprad2.dat)

 

Fig 4B-C, 5A:

• + 1 mM AMPPNP (purple): ki00555_RapA_intervals.dat; ki00555_RapA_off_target_intervals.dat (ki00555_RapA_off_target_intervals_uprad2.dat)
• + 1 mM ATP (blue): ki00559_RapA_intervals.dat; ki00559_RapA_off_target_intervals.dat ki00559_RapA_off_target_intervals_up1point5_rad2point5.dat
• No nucleotide (grey): ki00551_RapA_intervals.dat; ki00551_RapA_off_target_intervals.dat (ki00551_RapA_off_target_intervals_rad2_up1point5.dat)

 

Fig S1:

• Black: ki00295_intervals.dat (ki00236_intervals_rad2point5_thres6.dat)
• Blue: ki00298_intervals.dat
• Purple: ki00301_intervals.dat

 

Fig S3:

• 250 uW: ki00236_intervals.dat
• 350 uW: ki00254_intervals.dat
• 500 uW: ki00344_core_intervals.dat
• 1500 uW: ki00597_intervals.dat

 

Fig S4:

• 1080 uW: ki00516_RapA_intervals.dat (ki00516_RapA_intervals_frmavg2_bg_corrected_uprad2point5.dat)
• 5250 uW: ki00494_RapA_intervals.dat (ki00494_RapA_intervals_rad2point5_up1point5.dat)
• 321 uW: ki00556_RapA_intervals.dat