Refinement of the structure of B-DNA and implications for the analysis of X-ray diffraction data from fibers of biopolymers

Arnott, Struther; Hukins, D.W.L.

doi:10.1016/0022-2836(73)90182-4

Cited by 325 publications

(127 citation statements)

References 42 publications

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“…The sample was sealed in a flat aluminum holder, effectively fixing the humidity level, as in other, recent neutron scattering experiments [19]. The sample has been used for diffraction studies and presents a well-defined B-DNA structure, as reported by Langridge et al [20] Arnott et al [21] and more recently Fuller et al [22]. In this concentrated form of DNA, fibres are aligned to within a few degrees which is a requirement of the scattering experiment.…”

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confidence: 99%

Direct Determination of the Base-Pair Force Constant of DNA from the Acoustic Phonon Dispersion of the Double Helix

et al. 2011

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Quantifying the molecular elasticity of DNA is fundamental to our understanding of its biological functions. Recently different groups, through experiments on tailored DNA samples and numerical models, have reported a range of stretching force constants (0.3 to 3 N=m). However, the most direct, microscopic measurement of DNA stiffness is obtained from the dispersion of its vibrations. A new neutron scattering spectrometer and aligned, wet spun samples have enabled such measurements, which provide the first data of collective excitations of DNA and yield a force constant of 83 N=m. Structural and dynamic order persists unchanged to within 15 K of the melting point of the sample, precluding the formation of bubbles. These findings are supported by large scale phonon and molecular dynamics calculations, which reconcile hard and soft force constants. DOI: 10.1103/PhysRevLett.107.088102 PACS numbers: 87.14.gk, 63.22.Àm, 78.70.Nx, 87.10.Tf DNA stores the genetic code of all living organisms. Its principle biological functions of DNA are therefore transcription and replication. These processes take place in cells where DNA undergoes protein-mediated, mechanical manipulation resulting in folding, coiling and denaturing of the DNA molecule. The elasticity of DNA also underpins cleavage by enzymes [1] and the formation of 'bubbles' of locally denatured zones along the helix [2,3]. Models describing biologically relevant processes depend on the mechanical properties of DNA expressed as parameters, such as the base-pair force constant, which is crucial in the process of denaturing of DNA [4,5]. All measurements of DNA elasticity are therefore important in understanding the biological function of DNA and here we focus on stretching elasticity and the underlying base-pair stacking interaction.Recently considerable progress has been made in measuring the flexibility of the DNA helix although one concern is the extent to which the experimental or theoretical approaches themselves influence the results [6]. From well-defined oligomers of DNA, the stretch-torsion coupling can be obtained via magnetic tweezers and measuring the consequent over-or under-winding of the helix by tracking an attached rotor bead. In the work of Gore et al.[7], a stretching elastic modulus is reported, which equates to an inter base-pair force constant of 3 N=m. Another example of a molecular sculpturing approach involves DNA oligomers capped with gold nanoparticles, which allow the end-to-end distance to be measured by small angle x-ray scattering [8]. This work reported corresponding values 10 times smaller: 0:3 N=m. Similarly, Wiggins et al.[9] extracted bending force constants from single DNA molecule conformations on a substrate. They too found that the corresponding force constants are much smaller on a local length scale than predicted by classical elasticity models. A more theoretical approach [10] uses the well-known melting temperatures of DNA to calculate the flexibility on a local length scale via the Peyrard-Bishop model [11], assuming ...

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Direct Determination of the Base-Pair Force Constant of DNA from the Acoustic Phonon Dispersion of the Double Helix

et al. 2011

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“…Figure 8a, shows a TX molecule with an even number of half turns between junctions. 31 In this case, all the helix axes are parallel, but the upper and lower domains form an angle of 163° about the middle domain. Figure 8 b shows a TX with odd numbers of half turns between domains.…”

Section: Approachmentioning

confidence: 99%

“…Figures 7 and 8 show precision SDN models including the 6° tilt of bases known to occur in B-DNA. 31 Figures 7 a and b are two DX molecules with antiparallel domains and an even number of half-turns between crossovers (DAE). Panel a shows a DAE molecule with exactly 2 helical turns (21 nucleotide pairs in each helix) between crossovers.…”

Section: Approachmentioning

confidence: 99%

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Architecture with GIDEON, a program for design in structural DNA nanotechnology

Birac

Sherman

Kopatsch

et al. 2006

Journal of Molecular Graphics and Modelling

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We present geometry based design strategies for DNA nanostructures. The strategies have been implemented with GIDEON -a Graphical Integrated Development Environment for OligoNucleotides. GIDEON has a highly flexible graphical user interface that facilitates the development of simple yet precise models, and the evaluation of strains therein. Models are built on a simple model of undistorted B-DNA double-helical domains. Simple point and click manipulations of the model allow the minimization of strain in the phosphate-backbone linkages between these domains and the identification of any steric clashes that might occur as a result. Detailed analysis of 3D triangles yields clear predictions of the strains associated with triangles of different sizes. We have carried out experiments that confirm that 3D triangles form well only when their geometrical strain is less than 4% deviation from the estimated relaxed structure. Thus geometry-based techniques alone, without energetic considerations, can be used to explain general trends in DNA structure formation. We have used GIDEON to build detailed models of double crossover and triple crossover molecules, evaluating the non-planarity associated with base tilt and junction mis-alignments. Computer modeling using a graphical user interface overcomes the limited precision of physical models for larger systems, and the limited interaction rate associated with earlier, command-line driven software.

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“…The molecular mechanics/dynamics program AMBER (51) was used to initially generate an idealized Arnott B-DNA decamer duplex structure (52). NOESY distance constraints were incorporated into the AMBER potential energy function through addition of a flat well potential (see Results).…”

Section: Noesy Distance Constrained Molecular Mechanics Calculations mentioning

confidence: 99%

Two-Dimensional¹H and³¹P NMR Spectra of a Decamer Oligodeoxyribonucleotide Duplex and a Quinoxaline ([MeCys³, MeCys⁷]TANDEM) Drug Duplex Complex

Powers

Olsen

Gorenstein

1989

Journal of Biomolecular Structure and Dynamics

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Assignment of the 1 H and 31 P NMR spectra of a decamer oligodeoxyribonucleotide duplex, d(CCCGATCGGG), and its quinoxaline ([MeCys 3 , MeCys 7 ]TANDEM) drug duplex complex has been made by two-dimensional 1 H-1 H and heteronuclear 31 P-1 H correlated spectroscopy. The 31 P chemical shifts of this 10 base pair oligonucleotide follow the general observation that the more internal the phosphate is located within the oligonucleotide sequence, the more upfield the 31 P resonance occurs. While the 31 P chemical shifts show sequence-specific variations, they also do not generally follow the Calladine "rules" previously demonstrated. 31 P NMR also provides a convenient monitor of the phosphate ester backbone conformational changes upon binding of the drug to the duplex. Although the quinoxaline drug, [MeCys 3 , MeCys 7 ]TANDEM, is generally expected to bind to duplex DNA by bis-intercalation, only small 31 P chemical shift changes are observed upon binding the drug to duplex d(CCCGATCGGG). Additionally, only small perturbations in the 1 H NMR and UV spectra are observed upon binding the drug to the decamer, although association of the drug stabilizes the duplex form relative to the other states. These results are consistent with a nonintercalative mode of association of the drug. Modeling and molecular mechanics energy minimization demonstrate that a novel structure in which the two quinoxaline rings of the drug binds in the minor groove of the duplex is possible.

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Refinement of the structure of B-DNA and implications for the analysis of X-ray diffraction data from fibers of biopolymers

Cited by 325 publications

References 42 publications

Direct Determination of the Base-Pair Force Constant of DNA from the Acoustic Phonon Dispersion of the Double Helix

Direct Determination of the Base-Pair Force Constant of DNA from the Acoustic Phonon Dispersion of the Double Helix

Architecture with GIDEON, a program for design in structural DNA nanotechnology

Two-Dimensional¹H and³¹P NMR Spectra of a Decamer Oligodeoxyribonucleotide Duplex and a Quinoxaline ([MeCys³, MeCys⁷]TANDEM) Drug Duplex Complex

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Refinement of the structure of B-DNA and implications for the analysis of X-ray diffraction data from fibers of biopolymers

Cited by 325 publications

References 42 publications

Direct Determination of the Base-Pair Force Constant of DNA from the Acoustic Phonon Dispersion of the Double Helix

Direct Determination of the Base-Pair Force Constant of DNA from the Acoustic Phonon Dispersion of the Double Helix

Architecture with GIDEON, a program for design in structural DNA nanotechnology

Two-Dimensional1H and31P NMR Spectra of a Decamer Oligodeoxyribonucleotide Duplex and a Quinoxaline ([MeCys3, MeCys7]TANDEM) Drug Duplex Complex

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Two-Dimensional¹H and³¹P NMR Spectra of a Decamer Oligodeoxyribonucleotide Duplex and a Quinoxaline ([MeCys³, MeCys⁷]TANDEM) Drug Duplex Complex