Open AccessStructure of hydrated oligonucleotides studied by in situ scanning tunneling microscopy.
Author(s) -
T. W. Jing,
A.M. Jeffrey,
James DeRose,
Yuri L. Lyubchenko,
Luda S. Shlyakhtenko,
R. M. Harrington,
E. Appella,
Jan Larsen,
A. Vaught,
D. Rekesh
Publication year - 1993
Publication title -
proceedings of the national academy of sciences of the united states of america
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.011
H-Index - 771
eISSN - 1091-6490
pISSN - 0027-8424
DOI - 10.1073/pnas.90.19.8934
Subject(s) - scanning tunneling microscope , stacking , molecule , crystallography , chemistry , quantum tunnelling , substrate (aquarium) , oligonucleotide , microscopy , base (topology) , materials science , chemical physics , nanotechnology , optics , physics , optoelectronics , dna , mathematical analysis , biochemistry , oceanography , organic chemistry , mathematics , geology
We have used the scanning tunneling microscope (STM) to image several synthetic oligonucleotides adsorbed onto a positively charged Au(111) electrode. The molecules were deposited and imaged in aqueous electrolyte under potential control, a procedure that eliminated the problem of the substrate artifacts that had limited some previous STM studies. Experiments were carried out with two types of single-stranded molecules (11 and 20 bases long) and three types of double-stranded molecules (20 and 61 base pairs and 31 bases with 25 bases paired and 6-base "sticky" ends). The molecules lie along symmetry directions on the reconstructed (23 x square root of 3) gold surface, and length measurements indicate that they adopt simple base-stacked structures. The base stacking distances are, within experimental uncertainty, equal to the 0.33 nm measured for polymeric aggregates of stacked purines by direct imaging in identical conditions. The images show features consistent with helical structures. Double helices have a major-groove periodicity that is consistent with a 36 degrees twist. The single helices appear to be more tightly twisted. A simple tunneling model of STM contrast generates good agreement between measured and calculated images.