Nullomers

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Nullomers are short sequences of DNA that do not occur in the genome of a species (for example, humans), even though they are theoretically possible. [1] [2] Nullomers must be under 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]

Contents

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] Moreover, it has been shown that statistically significant nullomers (i.e. absent short sequences which are highly expected to exist) in virus genomes are restriction recognition sites indicating that viruses have probably got rid of these motifs to facilitate invasion of bacterial hosts. [8] Nullomers Database provides a comprehensive collection of minimal absent sequences from hundreds of species and viruses as well as the human and mouse proteomes.

Sequence of Human nullomers of 11bp in length [4]
No occurrence in the Human GenomeCGCTCGACGTA, GTCCGAGCGTA, CGACGAACGGT, CCGATACGTCG
One occurrence in the Human GenomeTACGCGCGACA, CGCGACGCATA, TCGGTACGCTA, TCGCGACCGTA, CGATCGTGCGA, CGCGTATCGGT
Two occurrences in the Human GenomeCGTCGCTCGAA, TCGCGCGAATA, TCGACGCGATA, ATCGTCGACGA, CTACGCGTCGA, CGTATACGCGA, CGATTACGCGA, CGATTCGGCGA, CGACGTACCGT, CGACGAACGAG, CGCGTAATACG, CGCGCTATACG
Three occurrences in the Human GenomeCGCGCATAATA, 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]
Organism10bp11bp12bp13bp
Arabidopsis 10723646116701220237388
C Elegans 27686115203823339534
Chicken 25901315154722702
Chimpanzee 0136459382426474
Cow 096450602432554
Dog 040252171868964
Fruitfly 020622161612399300
Human 080398522232448
Mouse 0178543832625646
Rat 050307081933220
Zebrafish 02155612469558

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]

Related Research Articles

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In molecular biology, a stop codon is a codon that signals the termination of the translation process of the current protein. Most codons in messenger RNA correspond to the addition of an amino acid to a growing polypeptide chain, which may ultimately become a protein; stop codons signal the termination of this process by binding release factors, which cause the ribosomal subunits to disassociate, releasing the amino acid chain.

Central dogma of molecular biology Explanation of the flow of genetic information within a biological system

The central dogma of molecular biology is an explanation of the flow of genetic information within a biological system. It is often stated as "DNA makes RNA, and RNA makes protein", although this is not its original meaning. It was first stated by Francis Crick in 1957, then published in 1958:

The Central Dogma. This states that once "information" has passed into protein it cannot get out again. In more detail, the transfer of information from nucleic acid to nucleic acid, or from nucleic acid to protein may be possible, but transfer from protein to protein, or from protein to nucleic acid is impossible. Information means here the precise determination of sequence, either of bases in the nucleic acid or of amino acid residues in the protein.

Gene expression Conversion of a genes sequence into a mature gene product or products

Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, protein or non-coding RNA, and ultimately affect a phenotype, as the final effect. These products are often proteins, but in non-protein-coding genes such as transfer RNA (tRNA) and small nuclear RNA (snRNA), the product is a functional non-coding RNA. Gene expression is summarized in the central dogma of molecular biology first formulated by Francis Crick in 1958, further developed in his 1970 article, and expanded by the subsequent discoveries of reverse transcription and RNA replication.

The coding region of a gene, also known as the coding DNA sequence(CDS), is the portion of a gene's DNA or RNA that codes for protein. Studying the length, composition, regulation, splicing, structures, and functions of coding regions compared to non-coding regions over different species and time periods can provide a significant amount of important information regarding gene organization and evolution of prokaryotes and eukaryotes. This can further assist in mapping the human genome and developing gene therapy.

Translation (biology) Cellular process of protein synthesis

In molecular biology and genetics, translation is the process in which ribosomes in the cytoplasm or endoplasmic reticulum synthesize proteins after the process of transcription of DNA to RNA in the cell's nucleus. The entire process is called gene expression.

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Transfer RNA is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length, that serves as the physical link between the mRNA and the amino acid sequence of proteins. Transfer RNA (tRNA) does this by carrying an amino acid to the protein synthesizing machinery of a cell called the ribosome. Complementation of a 3-nucleotide codon in a messenger RNA (mRNA) by a 3-nucleotide anticodon of the tRNA results in protein synthesis based on the mRNA code. As such, tRNAs are a necessary component of translation, the biological synthesis of new proteins in accordance with the genetic code.

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Transfer-messenger RNA

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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. Bibcode:2007PLoSO...2.1022A. doi: 10.1371/journal.pone.0001022 . PMC   1995752 . PMID   17925870. Open Access logo PLoS transparent.svg
  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. S2CID   4207067.
  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. 20 (5): 513–519. doi:10.1016/j.jflm.2013.02.003. PMID   23756524.
  4. 1 2 3 Hampikian, Greg; Andersen, Tim (2007). "Absent Sequences: Nullomers and Primes". Pacific Symposium on Biocomputing: 355–66. doi:10.1142/9789812772435_0034. ISBN   978-981-270-417-7. 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.
  8. ↑ Koulouras, Grigorios; Frith, Martin C (2021-04-06). "Significant non-existence of sequences in genomes and proteomes". Nucleic Acids Research. 49 (6): 3139–3155. doi: 10.1093/nar/gkab139 . ISSN   0305-1048. PMC   8034619 . PMID   33693858.
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