Back

Directionality bias in T/A cloning

Dountcheva, V.; Bubulya, A.; Rouhana, L.

2026-02-12 molecular biology
10.64898/2026.02.11.705383 bioRxiv
Show abstract

T/A cloning is a popular method for generating recombinant DNA plasmids. This method relies on single A:T nucleotide base pairs between PCR product ends and vector. Theoretically, the directionality of insert ligation with relation to the vector is random. However, we have continuously observed directionality bias using the pGEM-T Vector System for T/A cloning in a Course-based Undergraduate Research Experience (CURE). Cloning of over 400 inserts has shown directional bias higher than 74% (p-value < 0.0005) "sense" to the T7 promoter of the vector. Awareness of biased insertion in our applications reduces time and cost in cloning and downstream analyses.

Matching journals

The top 2 journals account for 50% of the predicted probability mass.

1
PLOS ONE
● 4510 papers in training set
Top 0.8%
41.4%
2
Scientific Reports
○ 3102 papers in training set
Top 5%
10.6%
50% of probability mass above
3
Current Protocols
○ 13 papers in training set
Top 0.1%
3.9%
4
FEBS Open Bio
○ 29 papers in training set
Top 0.1%
2.9%
5
Molecular Biology Reports
○ 19 papers in training set
Top 0.1%
2.0%
6
Frontiers in Public Health
○ 140 papers in training set
Top 4%
1.8%
7
Biology
○ 43 papers in training set
Top 0.6%
1.7%
8
Biology Methods and Protocols
◐ 53 papers in training set
Top 1%
1.6%
9
PeerJ
◐ 261 papers in training set
Top 8%
1.6%
10
BMC Genomics
○ 328 papers in training set
Top 3%
1.4%
11
F1000Research
○ 79 papers in training set
Top 3%
1.0%
12
Diagnostics
○ 48 papers in training set
Top 2%
1.0%
13
Genes
○ 126 papers in training set
Top 2%
0.9%
14
International Journal of Molecular Sciences
○ 453 papers in training set
Top 12%
0.9%
15
Bioengineering
○ 24 papers in training set
Top 1%
0.8%
16
BioTechniques
○ 24 papers in training set
Top 0.2%
0.8%
17
BMC Bioinformatics
○ 383 papers in training set
Top 7%
0.8%
18
BMC Biotechnology
○ 10 papers in training set
Top 0.1%
0.8%
19
Journal of Bioinformatics and Systems Biology
○ 14 papers in training set
Top 0.6%
0.8%
20
Plant Methods
○ 39 papers in training set
Top 0.7%
0.8%
21
Frontiers in Bioengineering and Biotechnology
○ 88 papers in training set
Top 3%
0.8%
22
Antibiotics
○ 32 papers in training set
Top 1%
0.7%
23
Biochemistry and Biophysics Reports
○ 28 papers in training set
Top 2%
0.7%
24
Nucleic Acids Research
◐ 1128 papers in training set
Top 19%
0.7%
25
FEBS Letters
○ 42 papers in training set
Top 0.4%
0.7%
26
eLife
● 5422 papers in training set
Top 62%
0.5%
27
ACS Omega
● 90 papers in training set
Top 5%
0.5%
28
Frontiers in Microbiology
○ 375 papers in training set
Top 10%
0.5%
29
Frontiers in Cellular and Infection Microbiology
○ 98 papers in training set
Top 7%
0.5%