Structural and combinatorial constraints on base pairing in large nucleotide sequences

Ruth Nussinov; George Pieczenik

doi:10.1016/0022-5193(84)90029-8

Structural and combinatorial constraints on base pairing in large nucleotide sequences

Ruth Nussinov^*, George Pieczenik

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

Abstract

In this paper we discuss the constraints and combinatorial problems of folding long RNA and single stranded DNA molecules into base paired structures. A computer code FOLD-A was designed to perform base pairing foldings of very long sequence chains and search for low energy configurations. The logic of the FOLD-A algorithm is described in some detail. The applications of FOLD-A to the A-protein gene of MS2 and the whole genome of the φX 174 phage with over 5300 bases are discussed in the accompanying paper.

Original language	English
Pages (from-to)	245-259
Number of pages	15
Journal	Journal of Theoretical Biology
Volume	106
Issue number	3
DOIs	https://doi.org/10.1016/0022-5193(84)90029-8
State	Published - 7 Feb 1984
Externally published	Yes

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10.1016/0022-5193(84)90029-8

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title = "Structural and combinatorial constraints on base pairing in large nucleotide sequences",

abstract = "In this paper we discuss the constraints and combinatorial problems of folding long RNA and single stranded DNA molecules into base paired structures. A computer code FOLD-A was designed to perform base pairing foldings of very long sequence chains and search for low energy configurations. The logic of the FOLD-A algorithm is described in some detail. The applications of FOLD-A to the A-protein gene of MS2 and the whole genome of the φX 174 phage with over 5300 bases are discussed in the accompanying paper.",

author = "Ruth Nussinov and George Pieczenik",

note = "Funding Information: To Dr Barbara Brodsky of the Rutger{\textquoteright}s Medical School, we express our thanks for her continuing interest encouragement during the course of our work. We would also like to thank C.C.I.S. Hill Center at Rutger{\textquoteright}s University for computer facilities. This work was supported in part by grant NIH-GM.",

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AU - Pieczenik, George

N1 - Funding Information: To Dr Barbara Brodsky of the Rutger’s Medical School, we express our thanks for her continuing interest encouragement during the course of our work. We would also like to thank C.C.I.S. Hill Center at Rutger’s University for computer facilities. This work was supported in part by grant NIH-GM.

PY - 1984/2/7

Y1 - 1984/2/7

N2 - In this paper we discuss the constraints and combinatorial problems of folding long RNA and single stranded DNA molecules into base paired structures. A computer code FOLD-A was designed to perform base pairing foldings of very long sequence chains and search for low energy configurations. The logic of the FOLD-A algorithm is described in some detail. The applications of FOLD-A to the A-protein gene of MS2 and the whole genome of the φX 174 phage with over 5300 bases are discussed in the accompanying paper.

AB - In this paper we discuss the constraints and combinatorial problems of folding long RNA and single stranded DNA molecules into base paired structures. A computer code FOLD-A was designed to perform base pairing foldings of very long sequence chains and search for low energy configurations. The logic of the FOLD-A algorithm is described in some detail. The applications of FOLD-A to the A-protein gene of MS2 and the whole genome of the φX 174 phage with over 5300 bases are discussed in the accompanying paper.

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Structural and combinatorial constraints on base pairing in large nucleotide sequences

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