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Lambda phage DNA

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From Molecupedia, the encyclopedia of very small things
Double-stranded DNA genome of a bacteriophage, the standard long test molecule of nanopore laboratories

Lambda phage DNA (λ DNA) is the genome of bacteriophage lambda, a virus of Escherichia coli. It is a linear double helix of 48,502 base pairs, 16.5 µm long if stretched out, with a mass of about 31.5 million daltons. Suppliers sell it by the microgram as a size standard, and a microgram holds about 19 billion molecules.[a] A 2019 paper that made nanopores with a hand-held Tesla-coil lighter tested them on what it called "the canonical test molecule, λ-DNA".[1]

A laboratory with a new pore needs to know whether it works. Lambda DNA answers the question with a molecule that is long enough to take milliseconds to pass, has a sequence that has been known since 1982, and arrives in a tube from any supplier.

Genome

Frederick Sanger and colleagues published the complete sequence in 1982: 48,502 base pairs, of which 49.9% are guanine or cytosine.[2][3] Inside the virus particle the molecule is linear. Each 5' end carries a single-stranded extension of 12 nucleotides, and the two extensions are complementary: the left end reads 5'-GGGCGGCGACCT-3'. When the DNA enters a cell the ends anneal and the molecule closes into a ring, and the site where they meet is called cos, for cohesive end.[4]

Restriction enzymes cut it into fragments of known size, which is the other reason it is in every laboratory freezer. Digested with EcoRI, the sequence above gives six fragments, from 21,226 to 3,530 base pairs.[b]

Discovery and host

Esther Lederberg found the phage in 1950 in the laboratory strain E. coli K-12, which carries it as a dormant prophage, and she and Joshua Lederberg described its genetics in 1953.[5] To infect a cell the particle binds LamB, an outer-membrane channel that admits maltose, a receptor first isolated in 1973.[6]

In the nanopore laboratory

A solid-state nanopore about 10 nm wide passes double-stranded DNA, which is about 2.2 nm across, and it passes either straight or folded. In 2003 a Harvard group recorded single molecules going through in both forms, a straight molecule blocking the ionic current to one level and a molecule that enters as a hairpin to twice that.[7] The pore in the lighter paper gave the same pattern, with the deeper level about 2.03 times the shallower. See Current blockade.

Duration depends on length in a way that is not linear. Storm and colleagues drove molecules of 6,500 to 97,000 base pairs through a 10 nm pore in silicon oxide and found that the time to cross grew as length to the power 1.27, which they attributed to the hydrodynamic drag of the part of the chain still outside the pore.[8] At the speeds of a bare solid-state pore, a lambda molecule crosses in 0.5 to 50 ms (see Translocation (nanopore)), which is slow enough to see in a recording at kilohertz bandwidth. Read base by base through a protein pore at the 250 bases a second announced for the R9 pore in 2016, the same molecule would take more than three minutes.[9]

As a control

Oxford Nanopore Technologies puts lambda in its sequencing kits. Its DNA control strand is "a 3.6 kb standard amplicon mapping to the 3' end of the Lambda genome", supplied at 10 ng/µL, and a user whose run fails can sequence the control to learn whether the sample or the library preparation was at fault.[10] A separate lambda DNA reagent is sold in its Control Expansion pack.[11] The benchmark study of the MinION on the International Space Station ran equal mixtures of lambda, E. coli and mouse DNA.[12]

At Molecular Reality

Molecular Reality Corporation has met lambda DNA in two places. A 2013 paper on Molecular Threading, a method of pulling single DNA molecules out of a droplet and laying them on a surface, drew M13mp18 single-stranded DNA and the genome of phage T4 GT7 out to 40 µm. Lambda, about 16 µm long, did not thread at that distance and could be drawn out only to less than 20 µm.[13]

In June 2026 the company's essay on The Nanopore World Model proposed, as its "Step 0", training a model on public nanopore recordings, such as Oxford Nanopore's files of lambda DNA, before building any rig, and it called the alternative of "building a 200 µm pore and collecting 100 hours of slurry" a misallocation of startup capital.[14]

See also

Notes

  1. ^ 1 µg ÷ (48,502 × 650 g/mol per base pair) × 6.022 × 1023 per mole = 1.9 × 1010.
  2. ^ Calculated from the reference sequence NC_001416.1 by searching for the site GAATTC. The standard commercial preparation is of a laboratory strain that carries a few mutations, so a digest of it can differ from a digest of the reference at some sites.

References

  1. ^ Bandara, Y. M. N. D. Y.; Karawdeniya, B. I.; Dwyer, J. R. (2019). "Push-button method to create nanopores using a Tesla-coil lighter". ACS Omega 4 (1): 226-230. doi:10.1021/acsomega.8b02660.
  2. ^ Sanger, F.; Coulson, A. R.; Hong, G. F.; Hill, D. F.; Petersen, G. B. (1982). "Nucleotide sequence of bacteriophage λ DNA". Journal of Molecular Biology 162 (4): 729-773. doi:10.1016/0022-2836(82)90546-0.
  3. ^ "Enterobacteria phage lambda, complete genome (NC_001416.1)". National Center for Biotechnology Information. Retrieved October 25, 2026.
  4. ^ Wu, R.; Kaiser, A. D. (1968). "Structure and base sequence in the cohesive ends of bacteriophage lambda DNA". Journal of Molecular Biology 35 (3): 523-537. doi:10.1016/S0022-2836(68)80012-9.
  5. ^ Lederberg, E. M.; Lederberg, J. (1953). "Genetic studies of lysogenicity in Escherichia coli". Genetics 38 (1): 51-64. doi:10.1093/genetics/38.1.51.
  6. ^ Randall-Hazelbauer, L.; Schwartz, M. (1973). "Isolation of the bacteriophage lambda receptor from Escherichia coli". Journal of Bacteriology 116 (3): 1436-1446. doi:10.1128/jb.116.3.1436-1446.1973.
  7. ^ Li, J.; Gershow, M.; Stein, D.; Brandin, E.; Golovchenko, J. A. (2003). "DNA molecules and configurations in a solid-state nanopore microscope". Nature Materials 2 (9): 611-615. doi:10.1038/nmat965.
  8. ^ Storm, A. J.; Storm, C.; Chen, J.; Zandbergen, H.; Joanny, J.-F.; Dekker, C. (2005). "Fast DNA translocation through a solid-state nanopore". Nano Letters 5 (7): 1193-1197. doi:10.1021/nl048030d.
  9. ^ "Update: New "R9" nanopore for faster, more accurate sequencing, and new ten minute preparation kit". Oxford Nanopore Technologies. May 26, 2016. Retrieved October 25, 2026.
  10. ^ "What is DNA CS (DCS)?" Oxford Nanopore Technologies. Retrieved October 25, 2026.
  11. ^ "Control Expansion". Oxford Nanopore Technologies. Retrieved October 25, 2026.
  12. ^ Castro-Wallace, S. L. et al. (2017). "Nanopore DNA sequencing and genome assembly on the International Space Station". Scientific Reports 7: 18022. doi:10.1038/s41598-017-18364-0.
  13. ^ "Molecular Threading: Mechanical Extraction, Stretching and Placement of DNA Molecules from a Liquid-Air Interface". PLoS ONE 8 (7): e69058. 2013. doi:10.1371/journal.pone.0069058.
  14. ^ "Keltar's Critique v2: The Nanopore World Model (Hardened)". Molecular Reality Corporation. June 2026.
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