Solution structure of [d(ATGAGCGAATA)]2. Adjacent G:A mismatches stabilized by cross-strand base-stacking and BII phosphate groups.

The solution structure of a rather unusual B-form duplex [d(ATGAGCGAATA)]2 has been determined using two-dimensional nuclear magnetic resonance (2D-NMR) and distance geometry methods. This sequence forms a stable ten base-pair B-form duplex with 3' overhangs and two pairs of adjacent G:A mismatches paired via a sheared hydrogen-bonding scheme. All non-exchangeable protons, including the stereo-specific H-5'S/H-5'R of the 3G and 7G residues, were assigned by 2D-NMR. The phosphorus spectrum was assigned using heteronuclear correlation with H-3' and H-4' reasonances. The complete assignments reveal several unusual nuclear Overhauser enhancements (NOEs) and unusual chemical shifts for the neighboring G:A mismatch pairs and their adjacent nucleotides. Inter-proton distances were derived from time-dependent NOEs and used to generate initial structures, which were further refined by iterative back-calculation of the two-dimensional nuclear Overhauser enhancement spectra; 22 final structures were calculated from the refined distance bounds. All these final structures exhibit fully wound helical structures with small penalty values against the refined distance bounds and small pair-wise root-mean-square deviation values (typically 0.5 A to 0.9 A). The two helical strands exchange base stacking at both of the two G:A mismatch sites, resulting in base stacking down each side rather than down each strand of the twisted duplex. Very large twist angles (77 degrees) were found at the G:A mismatch steps. All the final structures were found to have BII phosphate conformations at the adjacent G:A mismatch sites, consistent with observed downfield 31P chemical shifts and Monte-Carlo conformational search results. Our results support the hypothesis that 31P chemical shifts are related to backbone torsion angles. These BII phosphate conformations in the adjacent G:A mismatch step suggest that hydrogen bonding of the G:A pair G-NH2 to a nearby phosphate oxygen atom is unlikely. The unusual structure of the duplex may be stabilized by strong interstrand base stacking as well as intrastrand stacking, as indicated by excellent base overlap within the mismatch stacks.

[1]  B. Reid,et al.  Solution structure of the EcoRI DNA sequence: refinement of NMR-derived distance geometry structures by NOESY spectrum back-calculations. , 1989, Biochemistry.

[2]  W. Hunter,et al.  Molecular structure of the G.A base pair in DNA and its implications for the mechanism of transversion mutations. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[3]  D. Gorenstein,et al.  Two-dimensional 1H and 31P NMR spectra and restrained molecular dynamics structure of a mismatched GA decamer oligodeoxyribonucleotide duplex. , 1990, Biochemistry.

[4]  K. Wüthrich,et al.  Application of phase sensitive two-dimensional correlated spectroscopy (COSY) for measurements of 1H-1H spin-spin coupling constants in proteins. , 1983, Biochemical and biophysical research communications.

[5]  B. Reid,et al.  Three-dimensional solution structure of a DNA duplex containing the BclI restriction sequence: two-dimensional NMR studies, distance geometry calculations, and refinement by back-calculation of the NOESY spectrum. , 1989, Biochemistry.

[6]  T. Alam,et al.  Deuterium NMR investigation of backbone dynamics in the synthetic oligonucleotide [d(CGCGAATTCGCG)]2. , 1991, Biochemistry.

[7]  S. Chou,et al.  High-resolution NMR studies of chimeric DNA-RNA-DNA duplexes, heteronomous base pairing, and continuous base stacking at junctions. , 1991, Biochemistry.

[8]  V. Zhurkin,et al.  Different families of double‐stranded conformations of DNA as revealed by computer calculations , 1978 .

[9]  B. Reid,et al.  Determination of nucleic acid backbone conformation by proton nmr , 1992 .

[10]  D. States,et al.  A two-dimensional nuclear overhauser experiment with pure absorption phase in four quadrants☆ , 1982 .

[11]  U Heinemann,et al.  Helix geometry, hydration, and G.A mismatch in a B-DNA decamer. , 1987, Science.

[12]  B. Reid,et al.  Automated NMR structure refinement via NOE peak volumes. Application to a dodecamer DNA duplex , 1992 .

[13]  D S Goodsell,et al.  The effect of crystal packing on oligonucleotide double helix structure. , 1987, Journal of biomolecular structure & dynamics.

[14]  R. Hosur,et al.  Application of two‐dimensional NMR spectroscopy in the determination of solution conformation of nucleic acids , 1988 .

[15]  G. Zon,et al.  Deoxyribose conformation in [d(GTATATAC)]2: evaluation of sugar pucker by simulation of double-quantum-filtered COSY cross-peaks. , 1990, Biochemistry.

[16]  N. Go,et al.  Ring Closure and Local Conformational Deformations of Chain Molecules , 1970 .

[17]  S. Chou,et al.  Solution structure of [d(GCGTATACGC)]2. , 1992, Journal of molecular biology.

[18]  R. R. Ernst,et al.  Practical aspects of the E.COSY technique. Measurement of scalar spin-spin coupling constants in peptides , 1987 .

[19]  C. W. Hilbers,et al.  Nucleic acids and nuclear magnetic resonance. , 1988, European journal of biochemistry.

[20]  B. Reid,et al.  Three-dimensional structure of a DNA hairpin in solution: two-dimensional NMR studies and distance geometry calculations on d(CGCGTTTTCGCG). , 1986, Biochemistry.

[21]  J. Sussman,et al.  Adenine-guanine base pairing ribosomal RNA. , 1982, Nucleic acids research.

[22]  G. Drobny,et al.  Fourier transform multiple quantum nuclear magnetic resonance , 1978 .

[23]  G. A. van der Marel,et al.  Discrimination between A-type and B-type conformations of double helical nucleic acid fragments in solution by means of two-dimensional nuclear Overhauser experiments. , 1984, Journal of biomolecular structure & dynamics.

[24]  C. Altona,et al.  Conformational analysis of the deoxyribofuranose ring in DNA by means of sums of proton-proton coupling constants: a graphical method. , 1987, Journal of biomolecular structure & dynamics.

[25]  R. Symons,et al.  A catalytic 13-mer ribozyme. , 1989, Nucleic acids research.

[26]  Resolution-enhanced correlation of 1H and 31P chemical shifts , 1988 .

[27]  O. Uhlenbeck.  A small catalytic oligoribonucleotide , 1987, Nature.

[28]  K. J. Miller.  Interactions of molecules with nucleic acids. I. An algorithm to generate nucleic acid structures with an application to the B‐DNA structure and a counterclockwise helix , 1979, Biopolymers.

[29]  D. Patel,et al.  G(syn).cntdot.A(anti) mismatch formation in DNA dodecamers at acidic pH: pH-dependent conformational transition of G.cntdot.A mispairs detected by proton NMR , 1988 .

[30]  G. Drobny,et al.  Assignment of the non-exchangeable proton resonances of d(C-G-C-G-A-A-T-T-C-G-C-G) using two-dimensional nuclear magnetic resonance methods. , 1983, Journal of molecular biology.

[31]  B. Sykes,et al.  Solution conformation of purine-pyrimidine DNA octamers using nuclear magnetic resonance, restrained molecular dynamics and NOE-based refinement. , 1990, Journal of molecular biology.

[32]  W D Wilson,et al.  Unusual duplex formation in purine rich oligodeoxyribonucleotides. , 1988, Nucleic acids research.

[33]  G. Drobny,et al.  A solid-state deuterium NMR study of furanose ring dynamics in [d(CGCGAATTCGCG)]2 , 1990 .

[34]  M. L. Remerowski,et al.  Complete assignment of the deoxyribose 5'/5" proton resonances of the EcoRI DNA sequence using isotropic mixing. , 1989, Biochemistry.

[35]  A. Bax,et al.  Measurement of proton phosphorus 31 nmr coupling constants in double stranded dna fragments , 1987 .

[36]  V. P. Chuprina,et al.  Adjacent G : a mismatch base pairs contain BII phosphodiesters in solution , 1992 .

[37]  H. Heus,et al.  Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops. , 1991, Science.

[38]  G. Zon,et al.  NMR and molecular modeling evidence for a G.A mismatch base pair in a purine-rich DNA duplex. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[39]  D. Gorenstein,et al.  Assignments of 31P NMR resonances in oligodeoxyribonucleotides: origin of sequence-specific variations in the deoxyribose phosphate backbone conformation and the 31P chemical shifts of double-helical nucleic acids. , 1988, Biochemistry.

[40]  G. Drobny,et al.  Dynamics of bases in hydrated [d(CGCGAATTCGCG)]2. , 1989, Biochemistry.

[41]  B. Sykes,et al.  Solution structure of phage lambda half-operator DNA by use of NMR, restrained molecular dynamics, and NOE-based refinement. , 1990, Biochemistry.

[42]  R. Dickerson,et al.  Definitions and nomenclature of nucleic acid structure components. , 1989, Nucleic acids research.

[43]  S. Chou,et al.  Solid-phase synthesis and high-resolution NMR studies of two synthetic double-helical RNA dodecamers: r(CGCGAAUUCGCG) and r(CGCGUAUACGCG). , 1989, Biochemistry.

[44]  Z. Shakked,et al.  Proton nuclear Overhauser effect study of the structure of a deoxyoligonucleotide duplex in aqueous solution. , 1983, Biochemistry.

[45]  G. Leonard,et al.  Crystal structure and stability of a DNA duplex containing A(anti).G(syn) base-pairs. , 1989, Journal of molecular biology.

[46]  G. Zon,et al.  Two-dimensional COSY and two-dimensional NOE spectroscopy of d(AC)4.d(GT)4: extraction of structural constraints. , 1990, Biochemistry.

[47]  H R Drew,et al.  Structure of a B-DNA dodecamer: conformation and dynamics. , 1981, Proceedings of the National Academy of Sciences of the United States of America.