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Antibiotics Used in Molecular Biology

Content sponsored by New England Biolabs

antibiotics

Antibiotics are used in a wide range of techniques in molecular biology including molecular cloning and are important for treating pesky mycoplasma contamination in cell cultures. They can also be used to maximize your plasmid yields by reducing protein synthesis, in certain circumstances.

The aim with this post is to provide an easy reference to some of the main antibiotics that are used in molecular biology, their mechanisms, range, and working concentrations. I hope you will find it useful.

Your Personal Antibiotics Reference Guide

AntibioticClassRangeMechanismResistance conferred byConc. (μg/ml)
AmpicillinBeta-lactamGm+, Gm-Inhibits transpepsidase required for cell wall synthesisBeta-lactamase. Cleaves the beta-lactam ring of ampicillin100-200
Amphotericin BYe, Fu, MyComplexes with cholesterol, forming a pore that allows leakage of glucose2.5
CarbenicillinBeta-lactamGm+, Gm-Inhibits transpepsidase required for cell wall synthesisAs for ampicillin, but carbenicillin in broken down more slowly by beta-lactamase100
CiprofloxacinSyntheticGm+, Gm-, MyInhibits bacterial DNA gyrase and topoisomerase IV5-25
ChloramphenicolGm+, Gm-Binds to ribosomal 50S subunit, preventing peptidyl transferase required for translationChloramphenicol acetyltransferase adds an aceytl group from ACoA to chloramphenicol, which inactivates it5-10
ErythomycinMacrolideGm+, MySimilar to ChloramphenicolermC methyltransferase methylates the 23S rRNA, preventing erythromycin binding to the ribosome100
KanamycinAminoglycosideGm+, Gm-, MyBinds to the 30S ribosomal subunit, blocking the initiation complex and causing frame-shift mutations and inhibition od translationKanamycin phosphotransferase effect the ATP dependent phosphorylation of hydroxyl residues on kanamycin100
GentamycinAminoglycosideGm+, Gm-Similar to kanamycinGentamycin acetyltransferase: mechanism similar to chloramphenicol acetyltransferase25-50
NeomycinAminoglycosideGm+, Gm-Similar to kanamycinNeomycin phosphotransferase: mechanism similar to kanamycin phosphotransferase25-50
NystatinYe, FuSimilar to amphotericin B50
Rifampicin (rifampin)Semi-syntheticGm+, Gm-Inhibits DNA dependent RNA polymerase, preventing transcription50
StreptomycinAminoglycosideGm+, Gm-Binds to 16S ribosomal subunit, preventing initiation of translationStreptomycin 3'-adenyltransferase transfers the adenyl group from ATP onto streptomycin50
TetracyclineTetracylinGm+, Gm-Prevetns aminoacyl tRNA from binding to 30S subunitTerR-TN10 gene encodes an inner membrane protein that pumps tetracycline out of the cell.50
Abbreviations: Fu = fungus; Gm(+/-) = Gram positive/negative; My= mycoplasma; Ye = yeast.

This is by no means an exhaustive list of all antibiotics used in molecular biology, so if I have missed out an antibiotic that you use routinely in your work, please leave a comment and I will add it to the table.

It’s important that you store your antibiotics appropriately, so you can ensure that they are working correctly when you come to use them. For a guide on proper storage and use of antibiotics, check out our related article Antibiotic Stability: Keep Your (Gun)powder Dry. This article also provides information on the best solvent to use for your stock and whether the antibiotic is light-sensitive or not.

When using antibiotics in plates, do you know how long in advance you can prepare them, or if the plates that have been in your cold rooms for the past few weeks are still usable? You might be surprised when you find the answers in our article: Ye Olde Antibiotic Plates.

If you are planning to use ampicillin for selection (for example when cloning or performing protein purification in E. coli), there are several limitations you need to be aware of that might affect how you use this antibiotic. We go into the details of these limitations as well as precautions you can take in our article What’s The Problem With Ampicillin Selection?

Originally published on October 2, 2007.  Updated and revised on 10 December 2019.

Image Credit: yothinsanchai

2 Comments

  1. Luke on August 16, 2016 at 1:12 am

    Thank you for this table! We use Ciprofloxacin a lot in our lab, would you be able to add this when you have a chance please? Thank you!

  2. Anon on August 4, 2016 at 2:33 pm

    Small correction, amphotericin is now thought to be fungicidal independent of its ability to form a pore by instead “sponging” up ergosterol from the membrane (see Martin Burke lab for details)

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