Nullomers

Nullomers are short sequences of DNA base pairs that do not occur in the genome of a species (commonly humans), even though they are theoretically possible.[1][2] Nullomers must be under a selective pressure - for example, they may be toxic to the cell.[2] Some nullomers have been shown to be useful to treat leukemia, breast, and prostate cancer. They are not useful in healthy cells because normal cells adapt and become immune to them.[2] Nullomers are also being developed for use as DNA tags to prevent cross contamination when analyzing crime scene material.[3]

Background

Nullomers are naturally available but potentially unused sequences of DNA. Determining these "forbidden" sequences can improve the understanding of the basic rules that govern sequence evolution.[4] Sequencing the entire genome has shown that there is a high level of non-uniformity in genomic sequences. When a codon is artificially substituted for a synonymous codon, it often results in a lethal change and cell death. This is believed to be due to ribosomal stalling and early termination of protein synthesis. For example, both AGA and CGA code for arginine in bacteria; however, bacteria almost never use AGA, and when substituted it proves lethal.[5] Such codon biases have been seen in all species,[6] and are examples of constraints on sequence evolution. Other sequences may have selective pressure; for example, GG-rich sequences are used as sacrificial sinks for oxidative damage because oxidizing agents are attracted to regions with GG-rich sequences and then induce strand breakage.[7]

Sequence of Human nullomers of 11bp in length[4]
No occurrence in the Human Genome CGCTCGACGTA, GTCCGAGCGTA, CGACGAACGGT, CCGATACGTCG
One occurrence in the Human Genome TACGCGCGACA, CGCGACGCATA, TCGGTACGCTA, TCGCGACCGTA, CGATCGTGCGA, CGCGTATCGGT
Two occurrences in the Human Genome CGTCGCTCGAA, TCGCGCGAATA, TCGACGCGATA, ATCGTCGACGA, CTACGCGTCGA, CGTATACGCGA, CGATTACGCGA, CGATTCGGCGA, CGACGTACCGT, CGACGAACGAG, CGCGTAATACG, CGCGCTATACG
Three occurrences in the Human Genome CGCGCATAATA, CGACGGCAGTA, CGAATCGCGTA, CGGTCGTACGA, GCGCGTACCGA, CGCGTAATCGA, CGTCGTTCGAC, CCGTCGAACGC, ACGCGCGATAT, CGAACGGTCGT, CGCGTAACGCG, CCGAATACGCG, CATATCGCGCG
Table of the number of nullomers present in different organisms and the nullomer length[4]
Organism 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
Fruitfly 0 206 221616 12399300
Human 0 80 39852 2232448
Mouse 0 178 54383 2625646
Rat 0 50 30708 1933220
Zebrafish 0 2 15561 2469558

Cancer Treatment

Nullomers have been used as an approach to drug discovery and development. Nullomer peptides were screened for anti-cancer action. Absent sequences have short polyarginine tails added to increase solubility and uptake into the cell, producing peptides called PolyArgNulloPs. One successful sequence, RRRRRNWMWC, was demonstrated to have lethal effects in breast and prostate cancer. It damaged mitochondria by increasing ROS production, which reduced ATP production, leading to cell growth inhibition and cell death. Normal cells show a decreased sensitivity to PolyArgNulloPs over time.[2]

Forensics

Accidental transfer of biological material containing DNA can produce misleading results. This is a particularly important consideration in forensic and crime labs, where mistakes can cause an innocent person to be convicted of a crime. There was no way to detect if a reference sample was mislabeled as evidence or if a forensic sample is contaminated, but a nullomer barcode can be added to reference samples to distinguish them from evidence on analysis. Tagging can be carried out during sample collection without affecting genotype or quantification results. Impregnated filter paper with various nullomers can be used to soak up and store DNA samples from a crime scene, making the technology simple and effective.[3] Tagging with nullomers can be detected—even when diluted to a million-fold and spilled on evidence, these tags are still clearly detected.[3] Tagging in this way supports National Research Council's recommendations on quality control to reduce fraud and mistakes.[3]

References

  1. ↑ Acquisti, Claudia; Poste, George; Curtiss, David; Kumar, Sudhir (2007). Salzberg, Steven, ed. "Nullomers: Really a Matter of Natural Selection?". PLoS ONE 2 (10): e1022. doi:10.1371/journal.pone.0001022. PMC 1995752. PMID 17925870.
  2. 1 2 3 4 Alileche, Abdelkrim; Goswami, Jayita; Bourland, William; Davis, Michael; Hampikian, Greg (2012). "Nullomer derived anticancer peptides (NulloPs): Differential lethal effects on normal and cancer cells in vitro". Peptides 38 (2): 302–11. doi:10.1016/j.peptides.2012.09.015. PMID 23000474. Lay summary – New Scientist (October 25, 2012).
  3. 1 2 3 4 Goswami, Jayita; Davis, Michael C.; Andersen, Tim; Alileche, Abdelkrim; Hampikian, Greg (2013). "Safeguarding forensic DNA reference samples with nullomer barcodes". Journal of Forensic and Legal Medicine. doi:10.1016/j.jflm.2013.02.003. Lay summary – New Scientist (May 3, 2013).
  4. 1 2 3 Hampikian, Greg; Andersen, Tim (2007). "Absent Sequences: Nullomers and Primes". Pacific Symposium on Biocomputing: 355–66. PMID 17990505.
  5. ↑ Cruz-Vera, Luis Rogelio; Magos-Castro, Marco Antonio; Zamora-Romo, Efraín; Guarneros, Gabriel (2004). "Ribosome stalling and peptidyl-tRNA drop-off during translational delay at AGA codons". Nucleic Acids Research 32 (15): 4462–8. doi:10.1093/nar/gkh784. PMC 516057. PMID 15317870.
  6. ↑ dos Reis, Mario; Savva, Renos; Wernisch, Lorenz (2004). "Solving the riddle of codon usage preferences: A test for translational selection". Nucleic Acids Research 32 (17): 5036–44. doi:10.1093/nar/gkh834. PMC 521650. PMID 15448185.
  7. ↑ Friedman, Keith A.; Heller, Adam (2001). "On the Non-Uniform Distribution of Guanine in Introns of Human Genes:  Possible Protection of Exons against Oxidation by Proximal Intron Poly-G Sequences". The Journal of Physical Chemistry B 105 (47): 11859–65. doi:10.1021/jp012043n.
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