Nullomer

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A nullomer ( suitcase word made up of 'zero occurrence' and oligomer ) is a short DNA sequence that does not appear in the genome of a particular species , although it would theoretically be possible. The function of these “forbidden” sequences is still unknown, they may be toxic or serve to identify and eliminate pathogens .

properties

Nullomers are, based on the respective species, the shortest non-naturally occurring DNA sequences. In bacteria , some DNA sequences are toxic, e.g. B. the codon AGA, which codes for the amino acid arginine and is almost not used in bacteria (but CGA). There are species-specific differences in the codon usage . Furthermore, some GC-rich sequences can serve as sensors for oxidative stress , since there an oxidation leads to a single strand break and the activation of the DNA repair .

Sequence of human nullomers 11 base pairs in length in the human genome
No occurrence CGCTCGACGTA, GTCCGAGCGTA, CGACGAACGGT, CCGATACGTCG
Unique occurrence TACGCGCGACA, CGCGACGCATA, TCGGTACGCTA, TCGCGACCGTA, CGATCGTGCGA, CGCGTATCGGT
Double occurrence CGTCGCTCGAA, TCGCGCGAATA, TCGACGCGATA, ATCGTCGACGA, CTACGCGTCGA, CGTATACGCGA, CGATTACGCGA, CGATTCGGCGA, CGACGTACCGT, CGACGAACGAG, CGCGTAATACG, CGCGCTATACG
Triple occurrence CGCGCATAATA, CGACGGCAGTA, CGAATCGCGTA, CGGTCGTACGA, GCGCGTACCGA, CGCGTAATCGA, CGTCGTTCGAC, CCGTCGAACGC, ACGCGCGATAT, CGAACGGTCGT, CGCGTAACGCG, CCCGATCG
Table of the number and length of nullomers in different types
Art 10bp 11bp 12bp 13bp
Arabidopsis 107 23646 1167012 20237388
C elegans 2 7686 1152038 23339534
chicken 2 590 131515 4722702
chimpanzee 0 136 45938 2426474
cow 0 96 45060 2432554
dog 0 40 25217 1868964
Fruit fly 0 206 221616 12399300
human 0 80 39852 2232448
mouse 0 178 54383 2625646
rat 0 50 30708 1933220
Zebrafish 0 2 15561 2469558

Applications

Nullomers are used as markers and internal standards in forensic DNA analysis , as there is no cross-contamination from natural DNA .

Individual evidence

  1. ↑ C. Acquisti, G. Poste, D. Curtiss, S. Kumar: Nullomers: really a matter of natural selection? In: PloS one. Volume 2, number 10, 2007, p. E1022, ISSN  1932-6203 . doi : 10.1371 / journal.pone.0001022 . PMID 17925870 . PMC 1995752 (free full text).
  2. ↑ A. Alileche, J. Goswami, W. Bourland, M. Davis, G. Hampikian: nullomers derived anticancer peptides (NulloPs): differential lethal effects on normal and cancer cells in vitro. In: Peptides. Volume 38, Number 2, December 2012, pp. 302-311, ISSN  1873-5169 . doi : 10.1016 / j.peptides.2012.09.015 . PMID 23000474 .
  3. ↑ LR Cruz-Vera, MA Magos-Castro, E. Zamora-Romo, G. Guarneros: Ribosome stalling and peptidyl-tRNA drop-off during translational delay at AGA codons. In: Nucleic acids research. Volume 32, Number 15, 2004, pp. 4462-4468, ISSN  1362-4962 . doi : 10.1093 / nar / gkh784 . PMID 15317870 . PMC 516057 (free full text).
  4. ↑ M. dos Reis, R. Savva, L. Wernisch: Solving the riddle of codon usage preferences: a test for translational selection. In: Nucleic acids research. Volume 32, Number 17, 2004, pp. 5036-5044, ISSN  1362-4962 . doi : 10.1093 / nar / gkh834 . PMID 15448185 . PMC 521650 (free full text).
  5. ^ Keith A. Friedman, Adam Heller: On the Non-Uniform Distribution of Guanine in Introns of Human Genes: Possible Protection of Exons against Oxidation by Proximal Intron Poly-G Sequences. In: The Journal of Physical Chemistry B. 105, 2001, pp. 11859-11865, doi : 10.1021 / jp012043n .
  6. ↑ a b G. Hampikian, T. Andersen: Absent sequences: nullomers and primes. In: Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 2007, pp. 355-366, ISSN  2335-6936 . PMID 17990505 .
  7. Jump up ↑ J. Goswami, MC Davis, T. Andersen, A. Alileche, G. Hampikian: Safeguarding forensic DNA reference samples with nullomer barcodes. In: Journal of forensic and legal medicine. Volume 20, Number 5, July 2013, pp. 513-519, ISSN  1878-7487 . doi : 10.1016 / j.jflm.2013.02.003 . PMID 23756524 .