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PMID: 6320093 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

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

Nucleic acids research ·Vol. 12 ·No. 1 Pt 1 ·1984-01-11 ·Pages 347-66

Quigley GJ, Gehrke L, Roth DA, Auron PE

Abstract

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 (AMV-4 RNA). This structure is based on an analysis which includes the use of in vitro partial enzymatic digestion of the RNA.

MeSH Terms

Base Sequence Endonucleases Hydrogen Bonding Mosaic Viruses/genetics Nucleic Acid Conformation Nucleic Acids RNA, Viral Single-Strand Specific DNA and RNA Endonucleases Thermodynamics

Chemicals

Nucleic Acids RNA, Viral Endonucleases Single-Strand Specific DNA and RNA Endonucleases

Authors & Affiliations

4 authors, click to expand affiliations / ORCID

Quigley G J

Gehrke L

Roth D A

Auron P E

References (24)

24 references, click to expand

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Article Info

Journal

Nucleic acids research

Abbr.

Nucleic Acids Res

ISSN

0305-1048

DOI

10.1093/nar/12.1part1.347

Published

1984-01-11

Pages

347-66

Language

English

Region

England

NLM ID

0411011

PMCID

PMC321009

Subset

Grants

NCRR NIH HHS · 2-S07-RR7047-18 · United States

NCI NIH HHS · CAO-4186-25 · United States

External Links

PubMed source DOI: 10.1093/nar/12.1part1.347 PMC Full Text View journal details

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

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