TY - JOUR
T1 - Sequence, packing and nanometer scale structure in stm images of nucleic acids under water
AU - Lindsay, Stuart
AU - Nagahara, L. A.
AU - Thundat, T.
AU - Oden, P.
N1 - Funding Information:
We thank Manfred Philipp for giving us the RNA samples and the Facility for High Resolution Electron Microscopy at ASU for assistance with preparation of substrates. We are grateful to Randy Rill for supplying us with nucleosomal DNA. Uwe Knipping wrote all the operating and image processing code used in this work. This work was supported by the National Science Foundation (BBS861 5653) and the vice president for research at ASU.
Copyright:
Copyright 2015 Elsevier B.V., All rights reserved.
PY - 1989/10
Y1 - 1989/10
N2 - 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.
AB - 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.
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U2 - 10.1080/07391102.1989.10507772
DO - 10.1080/07391102.1989.10507772
M3 - Article
C2 - 2481464
AN - SCOPUS:0024471922
SN - 0739-1102
VL - 7
SP - 289
EP - 299
JO - Journal of Biomolecular Structure and Dynamics
JF - Journal of Biomolecular Structure and Dynamics
IS - 2
ER -