Sequence, packing and nanometer scale structure in stm images of nucleic acids under water

Stuart Lindsay, L. A. Nagahara, T. Thundat, P. Oden

Research output: Contribution to journalArticle

17 Scopus citations

Abstract

Scanning tunneling microscope (STM) images of random-sequence nucleic acid polymers under water show internal structure which depends strongly on the packing density of the polymer. Images of dense aggregates have a semicrystalline order with the individual polymers adopting simple periodic structures. Loose aggregates (or isolated molecules) show structural variability with considerable local bending and curving on a nanometer scale. It is not clear to what extent this structure is induced by the operation of the microscope. In order to investigate the possibility that the structure is sequence directed, we have imaged various DNA and RNA polymers at low packing densities. We present results here for random sequence DNA poly(dAT) · poly(dAT), poly(dA) · poly(dT), poly(dCG) · poly(dCG) and for random sequence RNA and poly(U)-In contrast to loose aggregates of the random sequence material, the homopolymers show few sharp bends. Furthermore, the homopolymers appear to yield characteristic backbone patterns, usually at resolutions in excess of that obtained with random sequence polymers. The random sequence polymers show much more evidence of image distortion due to tip-molecule interactions, suggesting that they are, on average, mechanically less stable in the STM tunnel-gap than the homopolymers. Thus, while some of the structure observed in STM images is a consequence of tip-molecule interactions, it is related to sequence-directed properties of the polymer.

Original languageEnglish (US)
Pages (from-to)289-299
Number of pages11
JournalJournal of Biomolecular Structure and Dynamics
Volume7
Issue number2
DOIs
StatePublished - Oct 1989

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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