RNA double-helical fragments at atomic resolution

I. The crystal and molecular structure of sodium adenylyl-3′,5′-uridine hexahydrate

Nadrian Seeman, John M. Rosenberg, F. L. Suddath, Jung Ja Park Kim, Alexander Rich

Research output: Contribution to journalArticle

Abstract

The crystal structure of sodium adenylyl-3′,5′-uridine (ApU) hexahydrate has been determined by X-ray diffraction procedures and refined to an R factor of 0.057. ApU crystallizes with two molecules per asymmetric unit in a monoclinic unit cell, space group P21, with cell dimensions: a = 18.025, b = 17.501, c = 9.677 A ̊and β = 99.45 °. The two independent molecules of ApU form a small segment of right-handed antiparallel double-helical RNA in the crystal, with Watson-Crick base-pairing between adenine and uracil. This is the first time that this Watson-Crick base-pair has been seen unambiguously at atomic resolution and it is also the first time that a nucleic acid fragment with double-helical symmetry has been seen at atomic resolution. The distance between the C1′ atoma of the adenine-uracil base-pair is slightly shorter than the analogous distance seen in guanine-cytosine base-pairs. The bases in each strand are heavily stacked. One sodium cation binds to the phosphates, as expected; however, the other sodium cation binds on the dyad axis in the minor groove of the double helix. It is co-ordinated directly to the two uracil carbonyl groups which protrude into the minor groove and is shielded from the nearest phosphates by a shell of water. This binding appears to be sequence-specific for ApU. One of the adenines also forms a pair of hydrogen bonds to a nearby ribose, utilizing N6 and N7. The 12 water molecules per double-helical fragment are all part of the first co-ordination shell. The ions and the symmetry of the double-helical fragment are the major organizing elements of the solvent region.

Original languageEnglish (US)
Pages (from-to)109-144
Number of pages36
JournalJournal of Molecular Biology
Volume104
Issue number1
DOIs
StatePublished - Jun 14 1976

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Uridine
Molecular Structure
Base Pairing
Uracil
Adenine
Sodium
RNA
Cations
Pair Bond
Phosphates
Ribose
Water
R Factors
Cytosine
Guanine
X-Ray Diffraction
Nucleic Acids
Hydrogen
Ions

ASJC Scopus subject areas

  • Virology

Cite this

RNA double-helical fragments at atomic resolution : I. The crystal and molecular structure of sodium adenylyl-3′,5′-uridine hexahydrate. / Seeman, Nadrian; Rosenberg, John M.; Suddath, F. L.; Kim, Jung Ja Park; Rich, Alexander.

In: Journal of Molecular Biology, Vol. 104, No. 1, 14.06.1976, p. 109-144.

Research output: Contribution to journalArticle

Seeman, Nadrian ; Rosenberg, John M. ; Suddath, F. L. ; Kim, Jung Ja Park ; Rich, Alexander. / RNA double-helical fragments at atomic resolution : I. The crystal and molecular structure of sodium adenylyl-3′,5′-uridine hexahydrate. In: Journal of Molecular Biology. 1976 ; Vol. 104, No. 1. pp. 109-144.
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abstract = "The crystal structure of sodium adenylyl-3′,5′-uridine (ApU) hexahydrate has been determined by X-ray diffraction procedures and refined to an R factor of 0.057. ApU crystallizes with two molecules per asymmetric unit in a monoclinic unit cell, space group P21, with cell dimensions: a = 18.025, b = 17.501, c = 9.677 A ̊and β = 99.45 °. The two independent molecules of ApU form a small segment of right-handed antiparallel double-helical RNA in the crystal, with Watson-Crick base-pairing between adenine and uracil. This is the first time that this Watson-Crick base-pair has been seen unambiguously at atomic resolution and it is also the first time that a nucleic acid fragment with double-helical symmetry has been seen at atomic resolution. The distance between the C1′ atoma of the adenine-uracil base-pair is slightly shorter than the analogous distance seen in guanine-cytosine base-pairs. The bases in each strand are heavily stacked. One sodium cation binds to the phosphates, as expected; however, the other sodium cation binds on the dyad axis in the minor groove of the double helix. It is co-ordinated directly to the two uracil carbonyl groups which protrude into the minor groove and is shielded from the nearest phosphates by a shell of water. This binding appears to be sequence-specific for ApU. One of the adenines also forms a pair of hydrogen bonds to a nearby ribose, utilizing N6 and N7. The 12 water molecules per double-helical fragment are all part of the first co-ordination shell. The ions and the symmetry of the double-helical fragment are the major organizing elements of the solvent region.",
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