Back

Advancing Understanding of DNA-BfiI Restriction Endonuclease Cis and Trans Interactions through smFRET Technology

Tutkus, M.; Ivanovaite, S.; Paksaite, J.; Kopustas, A.; Karzaite, G.; Rutkauskas, D.; Silanskas, A.; Sasnauskas, G.; Zaremba, M.; Jones, S. K.

2023-04-01 biophysics
10.1101/2023.03.31.535070 bioRxiv
Show abstract

Monitoring of DNA-protein interactions is essential in understanding many biological processes. Proteins must find their target site on a DNA molecule to perform their function, and the mechanisms for target search differ across proteins. Revealing temporal interactions with two target sites, both in Cis and in Trans, is crucial in target search mechanisms studies. Here, we present two single-molecule Forster resonance energy transfer (smFRET)-based assays to study BfiI-DNA interactions. The first assay, smFRET-based DNA looping assay, detects both "Phi" and "U"-shaped DNA looping events. We modified it to only allow in Trans BfiI-target DNA interactions to improve specificity and reduce limitations in the observation time. Our TIRF microscopy measurements directly observe the on- and off-target binding events and characterize BfiI binding events. Our results show that BfiI binding events last longer on target sites and that the BfiI rarely changes conformations during binding. This newly developed assay could be useful for other two-targets-binding DNA-interacting proteins and could be employed for dsDNA substrate BfiI-PAINT, which is useful for DNA stretch-assays and other super-resolution fluorescence microscopy studies.

Matching journals

The top 10 journals account for 50% of the predicted probability mass.

1
Analytical Chemistry
● 218 papers in training set
Top 0.5%
7.0%
Similar papers in this journal
2
Biophysical Journal
○ 631 papers in training set
Top 1%
6.0%
Similar papers in this journal
3
The Journal of Physical Chemistry B
● 167 papers in training set
Top 0.4%
6.0%
Similar papers in this journal
4
Chemical Communications
● 25 papers in training set
Top 0.1%
5.3%
Similar papers in this journal
5
Scientific Reports
○ 3612 papers in training set
Top 20%
4.7%
6
ACS Sensors
● 49 papers in training set
Top 0.2%
4.7%
Similar papers in this journal
7
Nano Letters
● 71 papers in training set
Top 0.2%
4.7%
8
Nature Communications
○ 5641 papers in training set
Top 31%
4.2%
9
Biophysical Reports
○ 37 papers in training set
Top 0.1%
4.2%
10
Nucleic Acids Research
◐ 1281 papers in training set
Top 5%
3.9%
50% of probability mass above
11
Biochemistry
● 148 papers in training set
Top 0.8%
3.1%
12
ChemBioChem
○ 55 papers in training set
Top 0.4%
3.1%
13
Methods
○ 34 papers in training set
Top 0.1%
3.1%
14
Protein Science
○ 246 papers in training set
Top 2%
2.3%
15
JACS Au
● 43 papers in training set
Top 0.3%
2.3%
16
Langmuir
● 36 papers in training set
Top 0.3%
2.0%
17
Journal of Biological Chemistry
○ 690 papers in training set
Top 5%
2.0%
18
eLife
● 5828 papers in training set
Top 52%
1.7%
19
Nanoscale
● 42 papers in training set
Top 0.4%
1.7%
20
Journal of the American Chemical Society
● 217 papers in training set
Top 2%
1.6%
21
Biosensors and Bioelectronics
○ 57 papers in training set
Top 0.5%
1.4%
22
iScience
○ 1154 papers in training set
Top 24%
1.3%
23
ACS Omega
● 105 papers in training set
Top 2%
1.3%
24
ACS Chemical Biology
● 167 papers in training set
Top 2%
1.1%
25
Biochimica et Biophysica Acta (BBA) - General Subjects
○ 18 papers in training set
Top 0.2%
1.1%
26
Proceedings of the National Academy of Sciences
● 2444 papers in training set
Top 38%
1.0%
27
International Journal of Molecular Sciences
○ 494 papers in training set
Top 13%
1.0%
28
SLAS Discovery
○ 25 papers in training set
Top 0.3%
1.0%
29
RSC Chemical Biology
● 39 papers in training set
Top 0.6%
1.0%
30
Molecular Therapy Nucleic Acids
○ 39 papers in training set
Top 0.8%
1.0%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.