Skip to main content

Necessity of Quantum Coherence to Account for the Spectrum of Time-Dependent Mutations Exhibited by Bacteriophage T4

Biochemical Genetics volume 47, Article number: 892 (2009) Cite this article

Abstract

Transcriptase measurements of quantum expectations due to time-dependent coherent states populating informational DNA base-pair sites, designated by G–C → *G–*C, G–C → G′–C′, and A–T → *A–*T, provide a model for transcription and replication of time-dependent DNA lesions exhibited by bacteriophage T4. Coherent states are introduced as consequences of hydrogen bond arrangement, keto-amino → enol-imine, where product protons are shared between two sets of indistinguishable electron lone-pairs and thus participate in coupled quantum oscillations at frequencies of ~1013 s−1. The transcriptase deciphers and executes genetic specificity instructions by implementing measurements on superposition proton states at *G–*C, G′–C′, and *A–*T sites in an interval Δt ≪ 10−13 s. Decohered states participate in Topal–Fresco replication, which introduces substitutions *C → T, *G → A, G′ → T, and G′ → C, but superposition *A–*T states are deleted. These results imply an evolutionary shift favoring A–T richness.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

43,34 €

Price includes VAT (Finland)
Tax calculation will be finalised during checkout.

Fig. 1
Fig. 2
Fig. 3

References

  • Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002) Molecular biology of the cell, 4th edn. Garland, New York

    Google Scholar 

  • Antequera F, Bird A (1993) Number of CpG islands and genes in human and mouse. Proc Natl Acad Sci USA 90:11995–11999

    Article  CAS  PubMed  Google Scholar 

  • Auerbach C (1959) Spontaneous mutations in dry spores of Neurospora crassa. Z Vererbungslehre 90:335–346

    Article  CAS  Google Scholar 

  • Baltz RH, Bingham PM, Drake JW (1976) Heat mutagenesis in bacteriophage T4: The transition pathway. Proc Natl Acad Sci USA 73:1269–1273

    Article  CAS  PubMed  Google Scholar 

  • Bell NF, Sawyer RF, Volkas RR (2002) Entanglement and quantal coherence: study of two limiting cases of rapid systems-bath interactions. Phys Rev A65:052105-1–052105-12

    Google Scholar 

  • Benzer S (1961) On the topography of the genetic fine structure. Proc Natl Acad Sci USA 47:403–415

    Article  CAS  PubMed  Google Scholar 

  • Bingham PM, Baltz RH, Ripley LS, Drake JW (1976) Heat mutagenesis in bacteriophage T4: The transversion pathway. Proc Natl Acad Sci USA 73:4159–4163

    Article  CAS  PubMed  Google Scholar 

  • Bromham L, Penny D (2003) The modern molecular clock. Nat Rev Genet 4:216–224

    Article  CAS  PubMed  Google Scholar 

  • Bromham LD, Rambaut A, Hamdy MD, Penny D (2000) The power of relative rates tests depends on the data. J Mol Evol 50:296–301

    CAS  PubMed  Google Scholar 

  • Caldin EF (1968) Tunneling in proton transfer reactions in solution. Chem Rev 69:135–156

    Article  Google Scholar 

  • Cooper WG (1993) Roles of evolution, quantum mechanics and point mutations in origins of cancer. Cancer Biochem Biophys 13:147–170

    CAS  PubMed  Google Scholar 

  • Cooper WG (1994) T4 phage evolution data in terms of a time-dependent Topal-Fresco mechanism. Biochem Genet 32:383–395

    Article  CAS  PubMed  Google Scholar 

  • Cooper WG (1995) Evolutionary origin of expandable G-C rich triplet repeat DNA sequences. Biochem Genet 33:173–181

    Article  CAS  PubMed  Google Scholar 

  • Cooper WG (1996) Hypothesis on a causal link between EMF and an evolutionary class of cancer and spontaneous abortion. Cancer Biochem Biophys 15:151–170

    CAS  PubMed  Google Scholar 

  • Cooper WG (2009) Evidence for transcriptase quantum processing implies entanglement and decoherence of superposition proton states. Biosystems 97(2):73–89

    Article  CAS  PubMed  Google Scholar 

  • Cooper DN, Youssoufian H (1988) The CpG dinucleotide and human genetic diseases. Hum Genet 78:151–155

    Article  CAS  PubMed  Google Scholar 

  • Cortopassi G, Liu Y (1995) Genotypic selection of mitochondrial and oncogenic mutations in human tissue suggest mechanisms of age-related pathophysiology. Mutat Res 338:151–159

    CAS  PubMed  Google Scholar 

  • Drake JW (1966) Spontaneous mutations accumulating in bacteriophage T4 in the complete absence of DNA replication. Proc Natl Acad Sci USA 55:738–743

    Article  CAS  PubMed  Google Scholar 

  • Drake JW, Baltz RH (1976) The biochemistry of mutagenesis. Ann Rev Biochem 45:11–37

    Article  CAS  PubMed  Google Scholar 

  • Drake JW, McGuire J (1967) Characteristics of mutations appearing spontaneously in extracellular particles of bacteriophage T4. Genetics 55:387–398

    CAS  PubMed  Google Scholar 

  • Drake JW, Ripley LS (1994) Mutagenesis. In: Karam JD (ed) Molecular biology of bacteriophage T4. American Society for Microbiology, Washington, DC, pp 98–124

    Google Scholar 

  • Drake JW, Charlesworth B, Charlesworth D, Crow JF (1998) Rates of spontaneous mutation. Genetics 148:1667–1686 (see p. 1671)

    CAS  PubMed  Google Scholar 

  • Drummond A, Pybus OG, Rambaut A (2003) Inference of viral evolutionary rates from molecular sequences. Adv Parasitol 54:331–358

    Article  PubMed  Google Scholar 

  • Elango N, Kim S-H, NICS Program, Vigoda E, Yi SV (2008) Mutations of different molecular origins exhibit contrasting patterns of regional substitution rate variation. PLoS Comput Biol 4:e1000015. doi:10.1371/journal.pcbi.1000015

    Article  PubMed  Google Scholar 

  • Evans D, Burbach J, van Leeuwen F (1995) Somatic mutations in the brain: relationship to aging? Mutat Res 338:173–182

    CAS  PubMed  Google Scholar 

  • Fitch WM, Leiter JM, Li XQ, Palese P (1991) Positive Darwinian evolution in human influenza A viruses. Proc Natl Acad Sci USA 88:4270–4274

    Article  CAS  PubMed  Google Scholar 

  • Fu YH, Kuhl DAP, Pizzuti A, Pieretti M, Sutcliffe J, Richards S, Verkerk A, Holden J, Fenwick R Jr, Warren ST, Oostra BA, Nelson DL, Caskey CT (1991) Variation of the CGG repeat at the fragile X site results in genetic instability: Resolution of the Sherman paradox. Cell 67:1047–1058

    Article  CAS  PubMed  Google Scholar 

  • Garcia-Viloca M, Gao J, Karplus M, Truhlar DG (2004) How enzymes work: analysis by modern rate theory and computer simulations. Science 303:186–195

    Article  CAS  PubMed  Google Scholar 

  • Ghosh S, Rosenbaum TF, Aeppll G, Coppersmith SN (2003) Entangled quantum states of magnetic dipoles. Nature 425:48–51

    Article  CAS  PubMed  Google Scholar 

  • Gillispie JH (1991) The causes of molecular evolution. Oxford University Press, Oxford, UK

    Google Scholar 

  • Grace M, Brif C, Rabitz H, Walmsley IA, Kosut RL, Lidar DA (2007) Optimal control of quantum gates and suppression of decoherence in a system of interacting two-level particles. J Phys B At Mol Opt Phys 40:S103–S125

    Article  CAS  Google Scholar 

  • Hwang DG, Green P (2004) Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proc Natl Acad Sci USA 101:13994–14001

    Article  CAS  PubMed  Google Scholar 

  • Kadenbach B, Munscher C, Frank V, Muller-Hocker J, Napiwotzki J (1995) Human aging is associated with stochastic somatic mutations of mitochondrial DNA. Mutat Res 338:161–172

    CAS  PubMed  Google Scholar 

  • Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge, UK

    Google Scholar 

  • Korber B, Muldoon M, Theiler J, Gao F, Gupta R, Lapedes A, Hahn BH, Wolinsky S, Bhattacharya T (2000) Timing the ancestor of the HIV-1 pandemic strains. Science 288:1789–1796

    Article  CAS  PubMed  Google Scholar 

  • Kricker M, Drake JW (1990) Heat mutagenesis in bacteriophage T4: another walk down the transversion pathway. J Bacteriol 172:3037–3039

    CAS  PubMed  Google Scholar 

  • Löwdin PO (1965) Quantum genetics and the aperiodic solid: some aspects on the biological problems of heredity, mutations, aging and tumors in view of the quantum theory of the DNA molecule. Adv Quantum Chem 2:213–359

    Article  Google Scholar 

  • Matsuura T, Fang P, Pearson CE, Jayakar P, Ashizawa T, Roa BB, Nelson DL (2006) Interruptions in the expanded ATTCT repeat of spinocerebellar ataxia type 10: repeat purity as a disease modifier. Am J Hum Genet 78:125–129

    Article  CAS  PubMed  Google Scholar 

  • McFadden J, Al-Khalili J (1999) A quantum mechanical model of adaptive mutations. Biosystems 50:203–211

    Article  CAS  PubMed  Google Scholar 

  • Merzbacher E (1997) Quantum mechanics, 3rd edn. Wiley, New York

    Google Scholar 

  • Metzler R, Ambjörnsson T (2005) Dynamic approach to DNA breathing. J Biol Phys 31:339–350

    Article  CAS  Google Scholar 

  • Modrich P (1997) Strand-specific mismatch repair in mammalian cells. J Biol Chem 272:24727–24730

    Article  CAS  PubMed  Google Scholar 

  • Nei M, Glazko GV (2002) Estimation of divergence times for a few mammalian and several primate species. J Hered 93:157–164

    Article  CAS  PubMed  Google Scholar 

  • Nielson MA, Chuang IL (2000) Quantum computation and quantum information. Cambridge University Press, Cambridge, UK

    Google Scholar 

  • Ohta T (2002) Near-neutrality in evolution of genes and gene regulation. Proc Natl Acad Sci USA 99:16134–16137

    Article  CAS  PubMed  Google Scholar 

  • Ono T, Miyamura Y, Ikehata H (1995) Spontaneous mutant frequency of lacZ gene in spleen of transgenic mouse increases with age. Mutat Res 338:183–188

    CAS  PubMed  Google Scholar 

  • Pollard E, Lemke M (1965) Rate of mutation to phage resistance in 2H2O medium. Mutat Res 2:213–217

    CAS  PubMed  Google Scholar 

  • Reif F (1965) Fundamentals of statistical and thermal physics. McGraw Hill, New York

    Google Scholar 

  • Ripley LS (1988) Estimation of in vivo miscoding rates. Quantitative behavior of two classes of heat-induced DNA lesions. J Mol Biol 202:17–34

    Article  CAS  PubMed  Google Scholar 

  • Smith AB, Peterson KJ (2002) Dating the time of origin of major clades: molecular clocks and the fossil record. Annu Rev Earth Planet Sci 30:65–88

    Article  CAS  Google Scholar 

  • Sueoka N (2002) Wide intra-genomic G + C heterogeneity in human and chicken is mainly due to strand-symmetric directional mutation pressures: dGTP-oxidation and symmetric cytosine-deamination hypothesis. Gene 30:141–154

    Article  Google Scholar 

  • Topal MD, Fresco JR (1976) Complementary base pairing and the origin of base substitutions. Nature 263:285–289

    Article  CAS  PubMed  Google Scholar 

  • Twiddy SS, Holmes EC, Rambuat A (2003) Inferring the rate and time-scale of dengue virus evolution. Mol Biol Evol 20:122–129

    Article  CAS  PubMed  Google Scholar 

  • Vedral V (2003) Entanglements hit the big time. Nature 425:28–29

    Article  CAS  PubMed  Google Scholar 

  • Zhang XB, Urlando C, Tao KS, Heddle JA (1995) Factors affecting somatic mutation frequencies in vivo. Mutat Res 338:189–201

    CAS  PubMed  Google Scholar 

  • Zurek WH (1991) Decoherence and the transition from quantum to classical. Phys Today 44:36–44

    Article  Google Scholar 

  • Zurek WH (2003) Decoherence, einselection and the quantum origins of the classical. Rev Mod Phys 75:715–775

    Article  Google Scholar 

Download references

Acknowledgments

Insightful questions and discussions by Altonie Barber and Nikolay Sarychev are sincerely appreciated. I am grateful to an anonymous reviewer for calling my attention to an important reference and for identifying quantum coherence and decoherence as central issues in this report.

Author information

Affiliations

  1. International Physics Health and Energy, Inc., 5109 82nd Street, Suite 7, Lubbock, TX, 79424, USA

    W. Grant Cooper

Authors
  1. W. Grant Cooper
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to W. Grant Cooper.

Electronic Supplementary Material

Below is the link to the electronic supplementary material.

(DOC 33 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Cooper, W.G. Necessity of Quantum Coherence to Account for the Spectrum of Time-Dependent Mutations Exhibited by Bacteriophage T4. Biochem Genet 47, 892 (2009). https://doi.org/10.1007/s10528-009-9293-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s10528-009-9293-8

Keywords

  • Molecular evolution mechanism
  • Transcription enhancement of mutation
  • Transcriptase quantum processing
  • Coherent states in DNA
  • Entanglement
  • Replication
  • T4 phage genetics