### Abstract

Assignment of the^{1}H and^{31}P resonances of a decamer DNA duplex, d(CGCTTAAGCG)_{2} was determined by two-dimensional COSY, NOESY and^{1}H-^{31}P Aire Absorption phase Constant time (PAC) heteronuclear correlation spectroscopy. The solution structure of the decamer was calculated by an iterative hybrid relaxation matrix method combined with NOESY-distance restrained molecular dynamics. The distances from the 2D NOESY spectra were calculated from the relaxation rate matrix which were evaluated from a hybrid NOESY volume matrix comprising elements from the experiment and those calculated from an initial structure. The hybrid matrix-derived distances were then used in a restrained molecular dynamics procedure to obtain a new structure that better approximates the NOESY spectra. The resulting partially refined structure was then used to calculate an improved theoretical NOESY volume matrix which is once again merged with the experimental matrix until refinement is complete J_{H3’-P} coupling constants for each of the phosphates of the decamer were obtained from ‘H- P J-resolved selective proton flip 2D spectra. By using a modified Karplus relationship the C4’-C3’-03’-P torsional angles (ε) were obtained. Comparison of the^{31}P chemical shifts and J_{H3’-P} coupling constants of this sequence has allowed a greater insight into the various factors responsible for^{31}P chemical shift variations in oligonucleotides. It also provides an important probe of the sequence-dependent structural variation of the deoxyribose phosphate backbone of DNA in solution. These correlations are consistent with the hypothesis that changes in local helical structure perturb the deoxyribose phosphate backbone. The variation of the 3IP chemical shift, and the degree of this variation from one base step to the next is proposed as a potential probe of local helical conformation within the DNA double helix. The pattern of calculated ε and ζ torsional angles from the restrained molecular dynamics refinement agrees quite well with the measured J_{H3’-P} coupling constants. Thus, the local helical parameters determine the length of the phosphodiester backbone which in turn constrains the phosphate in various allowed conformations.

Original language | English (US) |
---|---|

Pages (from-to) | 253-294 |

Number of pages | 42 |

Journal | Journal of Biomolecular Structure and Dynamics |

Volume | 8 |

Issue number | 2 |

DOIs | |

State | Published - Oct 1990 |

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### ASJC Scopus subject areas

- Structural Biology
- Molecular Biology

### Cite this

^{1}H and

^{31}P NMR spectra and restrained molecular dynamics structure of an oligodeoxyribonucleotide duplex refined via a hybrid relaxation matrix procedure.

*Journal of Biomolecular Structure and Dynamics*,

*8*(2), 253-294. https://doi.org/10.1080/07391102.1990.10507805

**Two-dimensional ^{1}H and^{31}P NMR spectra and restrained molecular dynamics structure of an oligodeoxyribonucleotide duplex refined via a hybrid relaxation matrix procedure.** / Powers, Robert; Jones, Claude R.; Gorenstein, David G.

Research output: Contribution to journal › Article

^{1}H and

^{31}P NMR spectra and restrained molecular dynamics structure of an oligodeoxyribonucleotide duplex refined via a hybrid relaxation matrix procedure',

*Journal of Biomolecular Structure and Dynamics*, vol. 8, no. 2, pp. 253-294. https://doi.org/10.1080/07391102.1990.10507805

^{1}H and

^{31}P NMR spectra and restrained molecular dynamics structure of an oligodeoxyribonucleotide duplex refined via a hybrid relaxation matrix procedure. Journal of Biomolecular Structure and Dynamics. 1990 Oct;8(2):253-294. https://doi.org/10.1080/07391102.1990.10507805

}

TY - JOUR

T1 - Two-dimensional1H and31P NMR spectra and restrained molecular dynamics structure of an oligodeoxyribonucleotide duplex refined via a hybrid relaxation matrix procedure

AU - Powers, Robert

AU - Jones, Claude R.

AU - Gorenstein, David G.

PY - 1990/10

Y1 - 1990/10

N2 - Assignment of the1H and31P resonances of a decamer DNA duplex, d(CGCTTAAGCG)2 was determined by two-dimensional COSY, NOESY and1H-31P Aire Absorption phase Constant time (PAC) heteronuclear correlation spectroscopy. The solution structure of the decamer was calculated by an iterative hybrid relaxation matrix method combined with NOESY-distance restrained molecular dynamics. The distances from the 2D NOESY spectra were calculated from the relaxation rate matrix which were evaluated from a hybrid NOESY volume matrix comprising elements from the experiment and those calculated from an initial structure. The hybrid matrix-derived distances were then used in a restrained molecular dynamics procedure to obtain a new structure that better approximates the NOESY spectra. The resulting partially refined structure was then used to calculate an improved theoretical NOESY volume matrix which is once again merged with the experimental matrix until refinement is complete JH3’-P coupling constants for each of the phosphates of the decamer were obtained from ‘H- P J-resolved selective proton flip 2D spectra. By using a modified Karplus relationship the C4’-C3’-03’-P torsional angles (ε) were obtained. Comparison of the31P chemical shifts and JH3’-P coupling constants of this sequence has allowed a greater insight into the various factors responsible for31P chemical shift variations in oligonucleotides. It also provides an important probe of the sequence-dependent structural variation of the deoxyribose phosphate backbone of DNA in solution. These correlations are consistent with the hypothesis that changes in local helical structure perturb the deoxyribose phosphate backbone. The variation of the 3IP chemical shift, and the degree of this variation from one base step to the next is proposed as a potential probe of local helical conformation within the DNA double helix. The pattern of calculated ε and ζ torsional angles from the restrained molecular dynamics refinement agrees quite well with the measured JH3’-P coupling constants. Thus, the local helical parameters determine the length of the phosphodiester backbone which in turn constrains the phosphate in various allowed conformations.

AB - Assignment of the1H and31P resonances of a decamer DNA duplex, d(CGCTTAAGCG)2 was determined by two-dimensional COSY, NOESY and1H-31P Aire Absorption phase Constant time (PAC) heteronuclear correlation spectroscopy. The solution structure of the decamer was calculated by an iterative hybrid relaxation matrix method combined with NOESY-distance restrained molecular dynamics. The distances from the 2D NOESY spectra were calculated from the relaxation rate matrix which were evaluated from a hybrid NOESY volume matrix comprising elements from the experiment and those calculated from an initial structure. The hybrid matrix-derived distances were then used in a restrained molecular dynamics procedure to obtain a new structure that better approximates the NOESY spectra. The resulting partially refined structure was then used to calculate an improved theoretical NOESY volume matrix which is once again merged with the experimental matrix until refinement is complete JH3’-P coupling constants for each of the phosphates of the decamer were obtained from ‘H- P J-resolved selective proton flip 2D spectra. By using a modified Karplus relationship the C4’-C3’-03’-P torsional angles (ε) were obtained. Comparison of the31P chemical shifts and JH3’-P coupling constants of this sequence has allowed a greater insight into the various factors responsible for31P chemical shift variations in oligonucleotides. It also provides an important probe of the sequence-dependent structural variation of the deoxyribose phosphate backbone of DNA in solution. These correlations are consistent with the hypothesis that changes in local helical structure perturb the deoxyribose phosphate backbone. The variation of the 3IP chemical shift, and the degree of this variation from one base step to the next is proposed as a potential probe of local helical conformation within the DNA double helix. The pattern of calculated ε and ζ torsional angles from the restrained molecular dynamics refinement agrees quite well with the measured JH3’-P coupling constants. Thus, the local helical parameters determine the length of the phosphodiester backbone which in turn constrains the phosphate in various allowed conformations.

UR - http://www.scopus.com/inward/record.url?scp=0025197395&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0025197395&partnerID=8YFLogxK

U2 - 10.1080/07391102.1990.10507805

DO - 10.1080/07391102.1990.10507805

M3 - Article

C2 - 2268403

AN - SCOPUS:0025197395

VL - 8

SP - 253

EP - 294

JO - Journal of Biomolecular Structure and Dynamics

JF - Journal of Biomolecular Structure and Dynamics

SN - 0739-1102

IS - 2

ER -