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Nucleic Acids Research, 1984, Vol. 12, No. 1Part1 347-366
© 1984

MINICOMPUTERS

Computer-aided nucleic acid secondary structure modeling incorporating enzymatic digestion data

Gary J. Quigley*, Lee Gehrke+,§, David A. Roth+ and Philip E. Auron*,+,{ddagger}

*Biology Department, Massachusetts Institute of Technology Cambridge, MA 02139, USA +Harvard-M.I.T. Division of Health Sciences and Technology Cambridge, MA 02139, USA §Department of Anatomy, Harvard Medical School Boston, MA 02115, USA {ddagger}Department of Experimental Medicine, Tufts University Medical School Boston, MA 02111, USA

Received August 15, 1983. We present a computer-aided method for determining nucleic acid secondary structure. The method utilizes a program which has the capability to filter matrix diagonal data on the basis of diagonal length, stabilization energy, and chemical and enzymatic data. The program also allows the user to assign selected regions of the structure as uniquely single-stranded or paired, and to filter out "trade-off" structures on the basis of such pairing.

In order to demonstrate the utility of the program we present a preliminary secondary structure for the 3' end of alfalfa mosaic virus RNA 4 (ANV-4 RNA). This structure is based on an analysis which includes the use of in vitro partial enzymatic digestion of the RNA.


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