X-ray holography for sequencing DNA

T. Yorkey, J. Brase, J. Trebes, S. Lane, J. Gray

Research output: Contribution to journalConference article

2 Scopus citations

Abstract

In this paper we discuss the potential for application of X-ray holographic imaging techniques to thesequencing of DNA. We formulate an approximate model for the scattering of partially coherent X-raysfrom an oriented DNA fiber and show the feasibility of reconstruction of heavy atom label positionsfrom the X-ray scattering data. A series of simulations has been done to demonstrate the requiredreconstruction algorithms. An X-ray experiment is currently in progress to demonstrate the real feasibilityof the technique.The potential of X-ray imaging techniques for the sequencing of DNA is attractive because of theirinherently parallel nature. Hundreds or thousands of base pairs could be sequenced in a single set of X-rayimages. The fundamental idea is to attach heavy atom labels to a selected base type on the DNA fragmentto be sequenced. A large number (> 1012) of identical fragments can be constructed as an oriented fiberand illuminated with partially coherent X-rays. The heavy label positions can then be determined from therecorded pattern of scattered X-rays. If this operation is repeated for each of the four bases, the sequencecan be reconstructed.The phase determination problem is solved by attaching to each DNA fragment a reference label in aknown position. The scattered field then forms a Fourier transform hologram of the averaged DNA fragment.Because of the high photoelectric absorption of DNA relative to its coherent scattering cross-section, a singlemolecule would be damaged before an image could be formed. We solve this problem by distributing thedamage over a large number of identical copies of the DNA fragment.In this paper we model a relatively simple experiment whose objective is to form a Fourier transformhologram of a labelled DNA fiber using 1.54 A X-rays. We will first describe the hologram formation processand then the method for reconstructing the label positions.

Original languageEnglish (US)
Pages (from-to)474-478
Number of pages5
JournalProceedings of SPIE - The International Society for Optical Engineering
Volume1347
DOIs
StatePublished - Dec 27 1990
EventOptical Information Processing Systems and Architectures II 1990 - San Diego, United States
Duration: Jul 8 1990Jul 13 1990

ASJC Scopus subject areas

  • Electronic, Optical and Magnetic Materials
  • Condensed Matter Physics
  • Computer Science Applications
  • Applied Mathematics
  • Electrical and Electronic Engineering

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