Home Forums Deep Time Journey Forum Is the universe a "living system"? Reply To: Is the universe a "living system"?

#4042
Ursula Goodenough
Participant

Here’s the abstract of the article:

 

“DNA Double Helices Recognize Mutual Sequence Homology in a Protein Free Environment

Geoff S. Baldwin,*,† Nicholas J. Brooks,‡ Rebecca E. Robson,†,‡ Aaron Wynveen,‡

Arach Goldar,‡,§ Sergey Leikin,*,| John M. Seddon,*,‡ and Alexei A. Kornyshev*,‡

DiVision of Molecular Biosciences, Imperial College London, SW7 2AZ London, U.K., Department of

Chemistry, Imperial College London, SW7 2AZ London, U.K., and Section on Physical Biochemistry,

National Institute of Child Health and Human DeVelopment, National Institutes of Health, DHHS,

Bethesda, Maryland 20892

ReceiVed: NoVember 27, 2007

The structure and biological function of the DNA double helix are based on interactions recognizing sequence

complementarity between two single strands of DNA. A single DNA strand can also recognize the double

helix sequence by binding in its groove and forming a triplex. We now find that sequence recognition occurs

between intact DNA duplexes without any single-stranded elements as well. We have imaged a mixture of

two fluorescently tagged, double helical DNA molecules that have identical nucleotide composition and length

(50% GC; 294 base pairs) but different sequences. In electrolytic solution at minor osmotic stress, these

DNAs form discrete liquid-crystalline aggregates (spherulites). We have observed spontaneous segregation

of the two kinds of DNA within each spherulite, which reveals that nucleotide sequence recognition occurs

between double helices separated by water in the absence of proteins, consistent with our earlier theoretical

hypothesis. We thus report experimental evidence and discuss possible mechanisms for the recognition of

homologous DNAs from a distance.”

 

The Daily Galaxy’s report on this has been fun to follow on Google — became all sorts of “action from a distance.” The distances referred to in this paper, however, are several nanometers. 

 

Follow-up studies of this phenomenon, e.g. PNAS 106:19824 (2009)

Single molecule detection of direct, homologous, DNA/DNA pairing

  1. C. Danilowicza,
  2. C. H. Leea,
  3. K. Kimb,
  4. K. Hatcha,
  5. V. W. Coljeea,
  6. N. Klecknerb,1 and
  7. M. Prentissa,1

  1. aDepartment of Physics and

  2. bDepartment of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
  1. Contributed by Nancy Kleckner, September 30, 2009 (received for review August 10, 2009)

Abstract

Using a parallel single molecule magnetic tweezers assay we demonstrate homologous pairing of two double-stranded (ds) DNA molecules in the absence of proteins, divalent metal ions, crowding agents, or free DNA ends. Pairing is accurate and rapid under physiological conditions of temperature and monovalent salt, even at DNA molecule concentrations orders of magnitude below those found in vivo, and in the presence of a large excess of nonspecific competitor DNA. Crowding agents further increase the reaction rate. Pairing is readily detected between regions of homology of 5 kb or more. Detected pairs are stable against thermal forces and shear forces up to 10 pN. These results strongly suggest that direct recognition of homology between chemically intact B-DNA molecules should be possible in vivo. The robustness of the observed signal raises the possibility that pairing might even be the “default” option, limited to desired situations by specific features. Protein-independent homologous pairing of intact dsDNA has been predicted theoretically, but further studies are needed to determine whether existing theories fit sequence length, temperature, and salt dependencies described here.

 

The homology recognition well as an innate property of DNA structure

  1. Alexei A. Kornysheva,b,1 and
  2. Aaron Wynveena,c,1

  1. aDepartment of Chemistry, Imperial College London, Faculty of Natural Sciences, London SW7 2AZ, United Kingdom;

  2. bMax-Planck-Institut für Mathematik in den Naturwissenschaften, D-04103 Leipzig, Germany; and

  3. cInstitut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, D-40225 Düsseldorf, Germany
  1. Edited by Nicholas J. Turro, Columbia University, New York, NY, and approved January 30, 2009 (received for review November 6, 2008)

Abstract

Mutual recognition of homologous sequences of DNA before strand exchange is considered to be the most puzzling stage of recombination of genes. In 2001, a mechanism was suggested for a double-stranded DNA molecule to recognize from a distance its homologous match in electrolytic solution without unzipping [Kornyshev AA, Leikin S (2001) Phys Rev Lett 86:3666–3669]. Based on a theory of electrostatic interactions between helical molecules, the difference in the electrostatic interaction energy between homologous duplexes and between nonhomologous duplexes, called the recognition energy, was calculated. Here, we report a theoretical investigation of the form of the potential well that DNA molecules may feel sliding along each other. This well, the bottom of which is determined by the recognition energy, leads to trapping of the molecular tracks of the same homology in direct juxtaposition. A simple formula for the shape of the well is obtained. The well is quasi-exponential. Its half-width is determined by the helical coherence length, introduced first in the same 2001 article, the value of which, as the latest study shows, is ≈10 nm.

 

Double-stranded DNA homology produces a physical signature

  1. Xing Wanga,2,
  2. Xiaoping Zhanga,
  3. Chengde Maob, and
  4. Nadrian C. Seemana,1

  1. aDepartment of Chemistry, New York University, New York, NY 10003; and

  2. bDepartment of Chemistry, Purdue University, West Lafayette, IN 47907
  • 2Present address: Department of Molecular Biology, Princeton University, Princeton, NJ 08544.

  1. Edited* by Alexander Rich, Massachusetts Institute of Technology, Cambridge, MA, and approved June 7, 2010 (received for review January 7, 2010)

Abstract

DNA is found in the cell largely as a negatively supercoiled molecule. This high-energy form of the genetic material can engender sequence-dependent structures, such as cruciforms, Z-DNA, or H-DNA, even though they are not favored by conventional conditions in relaxed DNA. A key feature of DNA in living systems is the presence of homology. We have sought homology-dependent structural phenomena based on topological relaxation. Using two-dimensional electrophoresis, we demonstrate a structural transition in supercoiled plasmid molecules containing homologous segments. Atomic force microscopy (AFM) reveals a dumbbell structure in molecules whose linking difference is beyond the transition point. The position of the dumbbell shaft is a function of the site of homology, and its extent is proportional to the linking difference. Second-site-reversion electrophoresis data support the notion that the shaft contains PX-DNA. Predicted cross-linking patterns generated in vivo suggest that homology-dependent structures can occur within the cell.

 

All of these are bona-fide chemistry papers documenting that identical DNA helices can recognize each other without unwinding, indicating that they have previously unexpected surface recognition signatures. It has zero to do with telepathy.

 

As for the spontaneous part, please read the reference I offered earlier by Goodenough and Deacon — it’s written for lay audience — and then we can see where we are.