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Antibiotics Used in Molecular Biology

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 of 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)
Ampicillin
Beta-lactam (Penicillins)
Gm+, Gm-Inhibits transpepsidase required for cell wall synthesisBeta-lactamase: cleaves the beta-lactam ring of ampicillin100-200
Amphotericin BAntifungal (Polyenes)Ye, Fu, MyBinding to ergosterol at the membrane, inducing pore formation and ergosterol sequestration, induction of oxidative damagePleiotropic mechanisms: altered membrane composition, ATP-binding cassette transporters, and upregulated thiol metabolic pathway2.5
CarbenicillinBeta-lactam (Penicillins)Gm+, Gm-Similar to Ampicillin: inhibits transpeptidase required for cell wall synthesisAs for ampicillin: but carbenicillin is broken down more slowly by beta-lactamase100
CiprofloxacinSynthetic (Fluoroquinolones)Gm+, Gm-, MyInhibits bacterial DNA gyrase and topoisomerase IVPleiotropic mechanisms: genetic mutation of the A subunit of DNA gyrase, and by alteration of drug permeation through the outer membrane of the cell5-25
ChloramphenicolSemi-syntheticGm+, Gm-Binds to ribosomal 50S subunit, preventing peptidyl transferase required for translationChloramphenicol acetyltransferase: adds an acetyl group from ACoA to chloramphenicol, which inactivates it5-10
ErythomycinMacrolidesGm+, MySimilar to ChloramphenicolermC methyltransferase: methylates the 23S rRNA, preventing erythromycin binding to the ribosome100
KanamycinAminoglycosidesGm+, Gm-, MyBinds to the 30S ribosomal subunit, blocking the initiation complex and causing frame-shift mutations and inhibition of translationKanamycin phosphotransferase: affects the ATP dependent phosphorylation of hydroxyl residues on kanamycin100
GentamicinAminoglycosidesGm+, Gm-Similar to kanamycin: inhibits bacterial protein synthesis through irreversible binding to the 30S ribosomal subunitGentamicin acetyltransferase: mechanism similar to chloramphenicol acetyltransferase25-50
NeomycinAminoglycosidesGm+, Gm-Similar to kanamycin: inhibits bacterial protein synthesis through irreversible binding to the 30S ribosomal subunitNeomycin phosphotransferase: mechanism similar to kanamycin phosphotransferase25-50
NystatinAntifungal (Polyenes)Ye, FuSimilar to amphotericin B: formation of a membrane-spanning pore in the fungal plasma membraneGenetic mutation: resulting in changes in sterol spectrum specificity50
Rifampicin (rifampin)Semi-synthetic (Rifamycins)Gm+, Gm-Inhibits DNA dependent RNA polymerase, preventing transcriptionGenetic mutation: of the rpoB gene encoding the beta subunit of RNA polymerase that alter residues of the rifampicin binding site on RNA polymerase, resulting in decreased affinity for rifampicin50
StreptomycinAminoglycosidesGm+, Gm-Binds to 16S ribosomal subunit, preventing initiation of translationStreptomycin 3'-adenyltransferase: transfers the adenyl group from ATP onto streptomycin50
TetracyclineTetracyclinesGm+, Gm-Prevents aminoacyl tRNA from binding to 30S subunitPleiotropic mechanisms: Tetracycline efflux, ribosome protection, enzymatic inactivation of Tetracycline50
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 on 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?

Our downloadable wall chart aims to provide an easy reference to some of the main antibiotics used in molecular biology, their mechanisms, range, and working concentrations. Print it off and post it in your lab for some eye-catching yet educational decoration.

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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