Sequencing Technologies 



Scanning Tunneling Microscopy of DNA 



Rodney L. Balhurn and Wigbert Siekhaus 



Biomedical Sciences Division. Lawrence Livennore National Laboratory. 



Livemiore, CA 94550 



(415) 422-6284. FTS 532-6284 



Researchers at Lawrence Livermore National Laboratory, and at other institutions, have 

 recently shown that scanning tunneling microscopy (STM) can be performed on the 

 DNA molecule with angstrom resolution. In addition, STM in the spectroscopic mode 

 (scanning tunneling spectroscopy or STS) has been used to characterize the electronic 

 structure of semiconductor substrates and their interaction with molecules adsorbed on 

 such substrates. The goals of this project are ( 1 ) to develop the instrumentation and 

 techniques required for imaging naked double- and single-stranded DNA at or near 

 atomic resolution using STM and (2) to devise methods for obtaining spectroscopic 

 information with STM that allow us to distinguish between the four bases and to 

 sequence DNA. To accomplish these goals, the four nucleotides and various single- and 

 double-stranded DNAs will be imaged, after electrophoresis, onto graphite and other 

 substrates. Experiments will be performed to determine how specific counterions and 

 the hydration state of the deposited DNA affect imaging. To identify individual bases 

 and specific molecular tags, measurements of synthetic and tagged sequences of known 

 length will be made so that various types of spectroscopy (work function, laser- 

 enhanced vibration, and photon emission) can be performed on the molecules. Our 

 application of STM and STS to the analysis and sequencing of DNA should directly 

 impact the progress of the human genome effort by eventually providing a new, 

 electronic method for sequencing DNA at three orders of magnitude faster than existing 

 methods. The techniques and instrumentation developed during the course of this 

 project will also be directly applicable to the analysis of biological samples in general. 



85 



