Structural polymorphism and Raman conformation markers of cyclic deoxytriadenylic acid

Yifu Guan; James M. Benevides; Y. G. Gao; Andrew H.J. Wang; George J. Thomas

doi:10.1093/nar/26.17.3892

Structural polymorphism and Raman conformation markers of cyclic deoxytriadenylic acid

Yifu Guan, James M. Benevides, Y. G. Gao, Andrew H.J. Wang, George J. Thomas

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

6 Citations (Scopus)

Abstract

X-ray analysis of two different trigonal crystal forms (space groups R32 and P3) of cyclic deoxytriadenylic acid [c(dAp)₃] indicates for each an asymmetric unit consisting of two conformationally similar c(dAp)₃ molecules. Raman spectroscopy supports the X-ray interpretation for the R32 crystal, but identifies another c(dAp)₃ conformation not revealed in the P3 X-ray structure. The results for the P3 crystal can be explained if an additional c(dAp)₃ conformer is present but not sufficiently ordered within the lattice to contribute to X-ray diffraction. The Raman signature of aqueous c(dAp)₃, which differs from signatures of both the R32 and P3 crystals, exhibits backbone markers similar to those of thermally denatured DNA and indicates that c(dAp)₃ molecules in solution populate a wider range of phosphoester ring conformations than in R32 and P3 crystals. Thus, polymorphism is observed for both crystal and solution structures of c(dAp)₃. The results imply a highly flexible phosphoester ring that may be relevant to the function of cyclic oligonucleotides as biological effecters. A novel Raman marker at 821 cm^-1 is demonstrated as diagnostic of phosphoester torsions α and ζ in the gauche⁺ range. Specific Raman markers are also identified for the S type (C2'-endo) deoxyadenosine conformations that occur in R32 and P3 crystal structures of c(dAp)₃.

Original language	English
Pages (from-to)	3892-3899
Number of pages	8
Journal	Nucleic Acids Research
Volume	26
Issue number	17
DOIs	https://doi.org/10.1093/nar/26.17.3892
Publication status	Published - Sept 1 1998
Externally published	Yes

ASJC Scopus subject areas

Genetics

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title = "Structural polymorphism and Raman conformation markers of cyclic deoxytriadenylic acid",

abstract = "X-ray analysis of two different trigonal crystal forms (space groups R32 and P3) of cyclic deoxytriadenylic acid [c(dAp)3] indicates for each an asymmetric unit consisting of two conformationally similar c(dAp)3 molecules. Raman spectroscopy supports the X-ray interpretation for the R32 crystal, but identifies another c(dAp)3 conformation not revealed in the P3 X-ray structure. The results for the P3 crystal can be explained if an additional c(dAp)3 conformer is present but not sufficiently ordered within the lattice to contribute to X-ray diffraction. The Raman signature of aqueous c(dAp)3, which differs from signatures of both the R32 and P3 crystals, exhibits backbone markers similar to those of thermally denatured DNA and indicates that c(dAp)3 molecules in solution populate a wider range of phosphoester ring conformations than in R32 and P3 crystals. Thus, polymorphism is observed for both crystal and solution structures of c(dAp)3. The results imply a highly flexible phosphoester ring that may be relevant to the function of cyclic oligonucleotides as biological effecters. A novel Raman marker at 821 cm-1 is demonstrated as diagnostic of phosphoester torsions α and ζ in the gauche+ range. Specific Raman markers are also identified for the S type (C2'-endo) deoxyadenosine conformations that occur in R32 and P3 crystal structures of c(dAp)3.",

author = "Yifu Guan and Benevides, {James M.} and Gao, {Y. G.} and Wang, {Andrew H.J.} and Thomas, {George J.}",

note = "Funding Information: This paper is Part LXX in the series Raman Spectral Studies of Nucleic Acids. Support of this research by grants GM54378 (G.J.T.) and GM41612 (A.H.J.W.) from the National Institutes of Health is gratefully acknowledged.",

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doi = "10.1093/nar/26.17.3892",

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T1 - Structural polymorphism and Raman conformation markers of cyclic deoxytriadenylic acid

AU - Guan, Yifu

AU - Benevides, James M.

AU - Gao, Y. G.

AU - Wang, Andrew H.J.

AU - Thomas, George J.

N1 - Funding Information: This paper is Part LXX in the series Raman Spectral Studies of Nucleic Acids. Support of this research by grants GM54378 (G.J.T.) and GM41612 (A.H.J.W.) from the National Institutes of Health is gratefully acknowledged.

PY - 1998/9/1

Y1 - 1998/9/1

N2 - X-ray analysis of two different trigonal crystal forms (space groups R32 and P3) of cyclic deoxytriadenylic acid [c(dAp)3] indicates for each an asymmetric unit consisting of two conformationally similar c(dAp)3 molecules. Raman spectroscopy supports the X-ray interpretation for the R32 crystal, but identifies another c(dAp)3 conformation not revealed in the P3 X-ray structure. The results for the P3 crystal can be explained if an additional c(dAp)3 conformer is present but not sufficiently ordered within the lattice to contribute to X-ray diffraction. The Raman signature of aqueous c(dAp)3, which differs from signatures of both the R32 and P3 crystals, exhibits backbone markers similar to those of thermally denatured DNA and indicates that c(dAp)3 molecules in solution populate a wider range of phosphoester ring conformations than in R32 and P3 crystals. Thus, polymorphism is observed for both crystal and solution structures of c(dAp)3. The results imply a highly flexible phosphoester ring that may be relevant to the function of cyclic oligonucleotides as biological effecters. A novel Raman marker at 821 cm-1 is demonstrated as diagnostic of phosphoester torsions α and ζ in the gauche+ range. Specific Raman markers are also identified for the S type (C2'-endo) deoxyadenosine conformations that occur in R32 and P3 crystal structures of c(dAp)3.

AB - X-ray analysis of two different trigonal crystal forms (space groups R32 and P3) of cyclic deoxytriadenylic acid [c(dAp)3] indicates for each an asymmetric unit consisting of two conformationally similar c(dAp)3 molecules. Raman spectroscopy supports the X-ray interpretation for the R32 crystal, but identifies another c(dAp)3 conformation not revealed in the P3 X-ray structure. The results for the P3 crystal can be explained if an additional c(dAp)3 conformer is present but not sufficiently ordered within the lattice to contribute to X-ray diffraction. The Raman signature of aqueous c(dAp)3, which differs from signatures of both the R32 and P3 crystals, exhibits backbone markers similar to those of thermally denatured DNA and indicates that c(dAp)3 molecules in solution populate a wider range of phosphoester ring conformations than in R32 and P3 crystals. Thus, polymorphism is observed for both crystal and solution structures of c(dAp)3. The results imply a highly flexible phosphoester ring that may be relevant to the function of cyclic oligonucleotides as biological effecters. A novel Raman marker at 821 cm-1 is demonstrated as diagnostic of phosphoester torsions α and ζ in the gauche+ range. Specific Raman markers are also identified for the S type (C2'-endo) deoxyadenosine conformations that occur in R32 and P3 crystal structures of c(dAp)3.

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Structural polymorphism and Raman conformation markers of cyclic deoxytriadenylic acid

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