Back

Paranemic cohesion of DNA molecules in different counter ions at room and physiological temperatures

Anderson, L.; Talbot, H.; Chandrasekaran, A. R.

2025-08-22 synthetic biology
10.1101/2025.08.21.671517 bioRxiv
Show abstract

Isothermal assembly allows the construction of DNA nanostructures at constant moderate temperatures. Further, assembly of DNA nanostructures in different counter ions expands their utility in various applications. In this work, we demonstrate the isothermal assembly of paranemic crossover (PX) DNA motifs in magnesium (Mg2+), calcium (Ca2+) and strontium (Sr2+) at 20 {degrees}C and 37 {degrees}C. Further, we study how differences in design affect the assembly of 4-stranded and 2-stranded PX molecules.

Matching journals

The top 6 journals account for 50% of the predicted probability mass.

1
ChemBioChem
○ 55 papers in training set
Top 0.1%
14.7%
Similar papers in this journal
2
Nano Letters
● 71 papers in training set
Top 0.1%
9.4%
Similar papers in this journal
3
ACS Synthetic Biology
● 287 papers in training set
Top 0.5%
7.1%
Similar papers in this journal
4
Chemical Communications
● 25 papers in training set
Top 0.1%
6.6%
Similar papers in this journal
5
Nanoscale
● 42 papers in training set
Top 0.1%
6.6%
Similar papers in this journal
6
Nature Communications
○ 5641 papers in training set
Top 26%
6.1%
50% of probability mass above
7
Journal of the American Chemical Society
● 217 papers in training set
Top 0.6%
6.1%
8
Nucleic Acids Research
◐ 1281 papers in training set
Top 4%
5.3%
9
ACS Nano
● 113 papers in training set
Top 0.5%
4.2%
10
ACS Omega
● 105 papers in training set
Top 0.6%
3.1%
11
Small
○ 78 papers in training set
Top 0.8%
1.9%
12
Biochemistry
● 148 papers in training set
Top 1%
1.7%
13
Biomacromolecules
● 29 papers in training set
Top 0.3%
1.6%
14
Biophysical Journal
○ 631 papers in training set
Top 3%
1.5%
15
Scientific Reports
○ 3612 papers in training set
Top 59%
1.4%
16
ACS Biomaterials Science & Engineering
● 37 papers in training set
Top 0.7%
1.1%
17
Nature Nanotechnology
○ 32 papers in training set
Top 0.5%
1.1%
18
Angewandte Chemie International Edition
○ 93 papers in training set
Top 1%
1.1%
19
Communications Chemistry
○ 48 papers in training set
Top 1.0%
1.0%
20
Analytical Chemistry
● 218 papers in training set
Top 2%
1.0%
21
ACS Applied Bio Materials
● 24 papers in training set
Top 0.6%
1.0%
22
Journal of Molecular Biology
○ 232 papers in training set
Top 4%
0.8%
23
Communications Biology
○ 993 papers in training set
Top 32%
0.8%
24
Langmuir
● 36 papers in training set
Top 0.6%
0.8%
25
International Journal of Molecular Sciences
○ 494 papers in training set
Top 16%
0.8%
26
Cell Reports Physical Science
○ 19 papers in training set
Top 0.3%
0.6%
27
Science Advances
● 1243 papers in training set
Top 34%
0.6%
28
Sensors
○ 43 papers in training set
Top 2%
0.6%
29
iScience
○ 1154 papers in training set
Top 43%
0.6%

"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.