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Research Article

Quantum technology a tool for sequencing of the ratio DSS/DNA modifications for the development of new DNA-binding proteins

ORCID Icon &
Pages 308-323 | Received 11 Apr 2022, Accepted 23 May 2022, Published online: 27 Jun 2022

References

  • Heather JM, Chain B. The sequence of sequencers: the history of sequencing DNA. Genomics. 2016;107(1):1–8.
  • Minchin S, Lodge J. Understanding biochemistry: structure and function of nucleic acids. Essays Biochem. 2019;63(4):433–456.
  • Godbey WT. Chapter 15 - DNA fingerprinting. In: Godbey WT, editor. Biotechnology and its applications. Second ed. Cambridge, Massachusetts: Academic Press; 2022. p. 357–367.
  • Keni R, Alexander A, Nayak PG, et al. COVID-19: emergence, spread, possible treatments, and global burden. Frontiers in Public Health. 2020;8. DOI:10.3389/fpubh.2020.00216
  • Lander ES, Rubenfield M, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409(1):860–921.
  • Nadeem MA, Nawaz MA, Shahid MQ, et al. DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnol Biotechnol Equip. 2018;32(2):261–285.
  • Mitchelson KR. DNA SEQUENCING. In: Worsfold P, Townshend A, Poole C, editors. Encyclopedia of analytical science. Second ed. Oxford: Elsevier; 2005. p. 286–293.
  • Liao X, Li M, Zou Y, et al. Current challenges and solutions of de novo assembly. Quantitative Biology. 2019;7(2):90–109.
  • Park ST, Kim J. Trends in next-generation sequencing and a new era for whole genome sequencing. Int Neurourol J. 2016;20(Suppl 2):S76–83.
  • Chaisson MJ, Wilson RK, Eichler EE. Genetic variation and the de novo assembly of human genomes. Nat Rev Genet. 2015;16(11):627–640.
  • Myers EW. The fragment assembly string graph. Bioinformatics. 2005;21(Suppl 2):79–85.
  • Ladd TD, Jelezko F, Laflamme R, et al. Quantum computers. Nature. 2010;464(7285):45–53.
  • Harrow AW, Montanaro A. Quantum computational supremacy. Nature. 2017;549(7671):203–209.
  • Lloyd S. Universal quantum simulators. Science. 1996;273(5278):1073–1078.
  • Biamonte J, Wittek P, Pancotti N, et al. Quantum machine learning. Nature. 2017;549(7671):195–202.
  • Boev AS, Rakitko AS, Usmanov SR, et al. Genome assembly using quantum and quantum-inspired annealing. Sci Rep. 2021b;11(1):13183.
  • Emani PS, Warrell J, Anticevic A, et al. Quantum computing at the frontiers of biological sciences. Nat Methods. 2021;18(7):701–709.
  • Boev AS, Rakitko AS, Usmanov SR, et al. Genome assembly using quantum and quantum-inspired annealing. Sci Rep. 2021a;11(1):13183.
  • Prousalis K, Konofaos N. Α quantum pattern recognition method for improving pairwise sequence alignment. Sci Rep. 2019;9(1):7226.
  • Fedorov AK, Gelfand MS. Towards practical applications in quantum computational biology. Nature Computational Science. 2021;1(2):114–119.
  • Lin M, Guo J-T. New insights into protein-DNA binding specificity from hydrogen bond based comparative study. Nucleic Acids Res. 2019;47(21):11103–11113.
  • Rosano GL, Ceccarelli EA. Recombinant protein expression in Escherichia coli: advances and challenges Front. Microbiol. 5 (2014).
  • Latchman DS. Transcription factors: an overview. Int J Biochem Cell Biol. 1997;29(12):1305–1312.
  • Vaquerizas JM, Kummerfeld SK, Teichmann SA, et al. A census of human transcription factors: function, expression and evolution. Nat Rev Genet. 2009;10(4):252–263.
  • Cawley S, Bekiranov S, Ng HH, et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell. 2004;116(4):499–509.
  • McGuire AL, Gabriel S, Tishkoff SA, et al. The road ahead in genetics and genomics. Nat Rev Genet. 2020;21(10):581–596.
  • Arnold PR, Wells AD, Li XC. Diversity and emerging roles of enhancer RNA in regulation of gene expression and cell fate. Frontiers in Cell and Developmental Biology. 2020;7. DOI:10.3389/fcell.2019.00377
  • Gardner AF, Jackson KM, Boyle MM, et al. Therminator DNA polymerase: modified nucleotides and unnatural substrates Front. Mol. Biosci. 6 (2019).
  • Yang W. Nucleases: diversity of structure, function and mechanism. Q Rev Biophys. 2011;44(1):1–93.
  • Nishino T, Morikawa K. Structure and function of nucleases in DNA repair: shape, grip and blade of the DNA scissors. Oncogene. 2002;21(58):9022–9032.
  • Chatterjee N, Walker GC. Mechanisms of DNA damage, repair, and mutagenesis. Environ Mol Mutagen. 2017;58(5):235–263.
  • Krishna SS, Majumdar I, Grishin NV. Structural classification of zinc fingers: survey and summary. Nucleic Acids Res. 2003;31(2):532–550.
  • Grishin NV. Two tricks in one bundle: helix-turn-helix gains enzymatic activity. Nucleic Acids Res. 2000;28(11):2229–2233.
  • Pu WT, Struhl K. Dimerization of leucine zippers analyzed by random selection. Nucleic Acids Res. 1993;21(18):4348–4355.
  • Vinson C, Myakishev M, Acharya A, et al. Classification of human B-ZIP proteins based on dimerization properties. Mol Cell Biol. 2002;22(18):6321–6335.
  • Pogenberg V, Ogmundsdóttir MH, Bergsteinsdóttir K, et al. Restricted leucine zipper dimerization and specificity of DNA recognition of the melanocyte master regulator MITF. Genes Dev. 2012;26(23):2647–2658.
  • Rooman M, René W. Protein–DNA Interactions. In: eLS. John Wiley & Sons, Ltd: Chichester. DOI:10.1002/9780470015902.a0001348.pub3
  • Au - Routh ED, Au - Creacy SD, Au - Beerbower PE, et al. A G-quadruplex DNA-affinity approach for purification of enzymatically active G4 resolvase1. JoVE. 2017;18(121):55496.
  • Burge S, Parkinson GN, Hazel P, et al. Quadruplex DNA: sequence, topology and structure. Nucleic Acids Res. 2006;34(19):5402–5415.
  • Patel DJ, Phan AT, Kuryavyi V. Human telomere, oncogenic promoter and 5’-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics. Nucleic Acids Res. 2007;35(22):7429–7455.
  • Weisz K. A world beyond double-helical nucleic acids: the structural diversity of tetra-stranded G-quadruplexes. ChemTexts. 2021;7(4):25.
  • Bhattacharyya D, Mirihana Arachchilage G, Basu S. Metal cations in G-quadruplex folding and stability Front. Chem. 4 (2016).
  • Sagi J. G-quadruplexes incorporating modified constituents: a review. J Biomol Struct Dyn. 2014;32(3):477–511.
  • Wang Z, Chen R, Hou L, et al. Molecular dynamics and principal components of potassium binding with human telomeric intra-molecular G-quadruplex. Protein Cell. 2015;6(6):423–433.
  • Hänsel-Hertsch R, Beraldi D, Lensing SV, et al. G-quadruplex structures mark human regulatory chromatin. Nat Genet. 2016;48(10):1267–1272.
  • Poetsch AR. AP-Seq: a method to measure apurinic sites and small base adducts genome-wide. In: Hancock R, editor. The nucleus. New York NY: Springer US; 2020. p. 95–108.
  • Roychoudhury S, Pramanik S, Harris HL, et al 2020. Endogenous oxidized DNA bases and APE1 regulate the formation of G-quadruplex structures in the genome. Proceedings of the National Academy of Sciences USA 117:11409.
  • Canugovi C, Shamanna RA, Croteau DL, et al. Base excision DNA repair levels in mitochondrial lysates of Alzheimer’s disease. Neurobiol Aging. 2014;35(6):1293–1300.
  • Sun D, Hurley LH. The importance of negative superhelicity in inducing the formation of G-quadruplex and i-motif structures in the c-Myc promoter: implications for drug targeting and control of gene expression. J Med Chem. 2009;52(9):2863–2874.
  • Ba X, Boldogh I. 8-Oxoguanine DNA glycosylase 1: beyond repair of the oxidatively modified base lesions. Redox Biol. 2018;14:669–678.
  • Schaffitzel C, Berger I, Postberg J, et al. 2001. In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei. Proceedings of the National Academy of Sciences USA 98:8572.
  • Kar A, Jones N, Arat NÖ, et al. Long repeating (TTAGGG)n single-stranded DNA self-condenses into compact beaded filaments stabilized by G-quadruplex formation. J Biol Chem. 2018;293(24):9473–9485.
  • Jafri MA, Ansari SA, Alqahtani MH, et al. Roles of telomeres and telomerase in cancer, and advances in telomerase-targeted therapies. Genome Med. 2016;8(1):69.
  • Frank-Kamenetskii MD, Mirkin SM. Triplex DNA structures. Annu Rev Biochem. 1995;64(1):65–95.
  • Ricciardi AS, McNeer NA, Anandalingam KK, et al. Targeted genome modification via triple helix formation. In: Wajapeyee N, ed. Cancer genomics and proteomics: methods and protocols. New York: Springer New York; 2014. p. 89–106.
  • Jain A, Wang G, Vasquez KM. DNA triple helices: biological consequences and therapeutic potential. Biochimie. 2008;90(8):1117–1130.
  • Rogers FA, Vasquez KM, Egholm M, et al. 2002. Site-directed recombination via bifunctional PNA–DNA conjugates. Proceedings of the National Academy of Sciences USA 99:16695.
  • McNeer NA, Schleifman EB, Cuthbert A, et al. Systemic delivery of triplex-forming PNA and donor DNA by nanoparticles mediates site-specific genome editing of human hematopoietic cells in vivo. Gene Ther. 2013;20(6):658–669.
  • Vasquez KM, Christensen J, Li L, et al. 2002. Human XPA and RPA DNA repair proteins participate in specific recognition of triplex-induced helical distortions. Proceedings of the National Academy of Sciences of the United States of America USA 99:5848–5853.
  • Hnedzko D, Cheruiyot SK, Rozners E. Using triple-helix-forming peptide nucleic acids for sequence-selective recognition of double-stranded RNA. Curr Protoc Nucleic Acid Chem. 2014;58(1):4.60.61–64.60.23.
  • Schleifman Erica B, Bindra R, Leif J, et al. Targeted disruption of the CCR5 gene in human hematopoietic stem cells stimulated by Peptide nucleic acids. Chem Biol. 2011;18(9):1189–1198.
  • Gupta A, Bahal R, Gupta M, et al. Nanotechnology for delivery of peptide nucleic acids (PNAs). J Control Release. 2016;240:302–311.
  • McNeer NA, Anandalingam K, Fields RJ, et al. Nanoparticles that deliver triplex-forming peptide nucleic acid molecules correct F508del CFTR in airway epithelium. Nat Commun. 2015;6(1):6952.
  • Svoboda P, Di Cara A. Hairpin RNA: a secondary structure of primary importance. Cell Mol Life Sci. 2006;63(7–8):901–908.
  • Stratton MR, Campbell PJ, Futreal PA. The cancer genome. Nature. 2009;458(7239):719–724.
  • Armaghany T, Wilson JD, Chu Q, et al. Genetic alterations in colorectal cancer. Gastrointest Cancer Res GCR. 2012;5(1):19–27.
  • Takeshima H, Ushijima T. Accumulation of genetic and epigenetic alterations in normal cells and cancer risk. NPJ Precis Oncol. 2019;3(1):7.
  • Yadav V, Sun S, Coelho MA, et al. 2020. Centromere scission drives chromosome shuffling and reproductive isolation. Proceedings of the National Academy of Sciences USA 117:7917.
  • Kang Z-J, Liu Y-F, Xu L-Z, et al. The Philadelphia chromosome in leukemogenesis. Chin J Cancer. 2016;35(1):48.
  • Quintás-Cardama A, Cortes J. Molecular biology of bcr-abl1-positive chronic myeloid leukemia. Blood. 2009;113(8):1619–1630.
  • Goswami R, Subramanian G, Silayeva L, et al. Gene therapy leaves a vicious cycle Front. Oncol. 9 (2019).
  • Kastan MB. DNA damage responses: mechanisms and roles in human disease. Mol Cancer Res. 2008;6(4):517.
  • Cunningham FH, Fiebelkorn S, Johnson M, et al. A novel application of the margin of exposure approach: segregation of tobacco smoke toxicants. Food Chem Toxicol. 2011;49(11):2921–2933.
  • Anna B, Blazej Z, Jacqueline G, et al. Mechanism of UV-related carcinogenesis and its contribution to nevi/melanoma. Exp Rev Dermatol. 2007;2(4):451–469.
  • Bhattacharyya A, Chattopadhyay R, Mitra S, et al. Oxidative stress: an essential factor in the pathogenesis of gastrointestinal mucosal diseases. Physiol Rev. 2014;94(2):329–354.
  • Maynard S, Schurman SH, Harboe C, et al. Base excision repair of oxidative DNA damage and association with cancer and aging. Carcinogenesis. 2009;30(1):2–10.
  • Hodgson S. Mechanisms of inherited cancer susceptibility. J Zhejiang Univ Sci B. 2008;9(1):1–4.
  • Jasperson KW, Tuohy TM, Neklason DW, et al. Hereditary and familial colon cancer. Gastroenterology. 2010;138(6):2044–2058.
  • Lahtz C, Pfeifer GP. Epigenetic changes of DNA repair genes in cancer. J Mol Cell Biol. 2011;3(1):51–58.
  • Fayyad N, Kobaisi F, Beal D, et al. Xeroderma pigmentosum C (XPC) mutations in primary fibroblasts impair base excision repair pathway and increase oxidative DNA damage. Frontiers in Genetics. 2020;11. DOI:10.3389/fgene.2020.561687.
  • Forrester HB, Li J, Hovan D, et al. DNA repair genes: alternative transcription and gene expression at the exon level in response to the DNA damaging agent, ionizing radiation. PloS one. 2012;7(12):e53358.
  • Bernstein C, Nfonsam V, Prasad AR, et al. Epigenetic field defects in progression to cancer. World J Gastrointest Oncol. 2013;5(3):43–49.
  • Guo M, Peng Y, Gao A, et al. Epigenetic heterogeneity in cancer. Biomark Res. 2019;7:23.
  • Han M, Jia L, Lv W, et al. Epigenetic enzyme mutations: role in tumorigenesis and molecular inhibitors Front. Oncol. 9 (2019).
  • Zhang Q, Xu F, Li L, et al. Quantum information research in China. Quantum Sci Technol. 2019;4(4):040503.
  • Saleem M. The failure of classical physics and the advent of quantum mechanics. Quantum Mechanics: IOP Publishing; 2015. p. 1-1-1–34.
  • Pauli W. Über das Wasserstoffspektrum vom standpunkt der neuen quantenmechanik. Zeitschrift für Physik A Hadrons Nuclei. 1926;36(5):336–363.
  • Mensing L. Die Rotations-Schwingungsbanden nach der Quantenmechanik. Zeitschrift für Physik. 1926;36(11–12):814–823.
  • Knight P, Walmsley I. UK national quantum technology programme. Quantum Sci Technol. 2019;4(4):040502.
  • Riedel MF, Binosi D, Thew R, et al. The European quantum technologies flagship programme. Quantum Sci Technol. 2017;2(3):030501.
  • Riedel M, Kovacs M, Zoller P, et al. Europe’s Quantum Flagship initiative. Quantum Sci Technol. 2019;4(2):020501.