Base inclinations in natural and synthetic DNAs

Chou, Ping-Jung; Johnson, W. Curtis

doi:10.1021/ja00057a001

Cited by 72 publications

(65 citation statements)

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“…10,11,14,[19][20][21] Due to the aforementioned difficulties, some reports do not agree on the orientation of the basepairing plane of dsDNA, assessed using LD r spectroscopy in the UV, where nucleic acids strongly absorb. Inclination angles of up to 25 • have been reported, 11,14,19,20 whereas structural studies reported the base-pairing plane to make only a small (<10 • ) angle with respect to the B-form helix. 14,22,23 A similar disagreement exists about the orientation of fluorescent dyes intercalated in dsDNA.…”

Section: Introductionmentioning

confidence: 99%

A polarized view on DNA under tension

Mameren

Vermeulen

Wuite

2017

The Journal of Chemical Physics

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In the past decades, sensitive fluorescence microscopy techniques have contributed significantly to our understanding of the dynamics of DNA. The specific labeling of DNA using intercalating dyes has allowed for quantitative measurement of the thermal fluctuations the polymers undergo. On the other hand, recent advances in single-molecule manipulation techniques have unraveled the mechanical and elastic properties of this intricate polymer. Here, we have combined these two approaches to study the conformational dynamics of DNA under a wide range of tensions. Using polarized fluorescence microscopy in conjunction with optical-tweezers-based manipulation of YOYO-intercalated DNA, we controllably align the YOYO dyes using DNA tension, enabling us to disentangle the rapid dynamics of the dyes from that of the DNA itself. With unprecedented control of the DNA alignment, we resolve an inconsistency in reports about the tilted orientation of intercalated dyes. We find that intercalated dyes are on average oriented perpendicular to the long axis of the DNA, yet undergo fast dynamics on the time scale of absorption and fluorescence emission. In the overstretching transition of doublestranded DNA, we do not observe changes in orientation or orientational dynamics of the dyes. Only beyond the overstretching transition, a considerable depolarization is observed, presumably caused by an average tilting of the DNA base pairs. Our combined approach thus contributes to the elucidation of unique features of the molecular dynamics of DNA.

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Section: Introductionmentioning

confidence: 99%

A polarized view on DNA under tension

Mameren

Vermeulen

Wuite

2017

The Journal of Chemical Physics

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“…Thus the stacked dimer structure has less absorbance than the sum of its two isolated components, leading to hypochromicity. 8 Hypochromicity is often observed in dsDNA where DNA's UV absorption is due to in-plane π-π* transitions in the bases, 15 with contributions from the sugars and phosphates occurring mainly below 190 nm. Because these dipole transitions occur in all four of DNA's bases, all of these transitions are affected by hypochroism in the DNA, where the π-stacking between adjacent base pairs is the dominant energy term stabilizing the double helix.…”

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confidence: 99%

“…Poly(dC)'s absorbance curve is due to three major transitions in cytosine occurring at 212, 228, and 269 nm 15 (Figure 2b). While the transition at 269 nm appears to be unaffected by poly(dC)'s hybridization with SWNT, the 228 and 212 nm transitions are obviously attenuated when poly(dC) is bound to SWNT.…”

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confidence: 99%

Optical Absorption of DNA−Carbon Nanotube Structures

2007

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We measured the UV optical absorption of single-stranded DNA bound to single-walled carbon nanotubes (DNA/SWNT). The nucleotide absorbance from DNA/SWNT provides the first experimental confirmation that DNA binds to nanotubes through π-stacking. Because the hypochromic absorbance typical of π-stacked structures are expected to occur primarily for DNA dipole transitions that lie along the axis of the optically anisotropic SWNTs, the absorbance changes following binding of DNA to nanotubes reveal the preferred orientation assumed by each of the four bound nucleotides with respect to the nanotube's long axis.Zheng et al. reported that bundles of SWNTs in water can be effectively dispersed by sonication in the presence of single-stranded DNA (ssDNA). 1,2 Molecular modeling by that group suggested that DNA molecules hybridize with individual nanotubes by wrapping around them, with the interaction strength being provided by π-stacking, with the plane of the aromatic nucleotide bases oriented parallel to the surface of the nanotube. 1 The novel properties of this hybrid structure make it possible to separate a motley collection of nanotubes by electronic type, 1 an essential step toward nanotube electronic devices. The electrical properties of the hybrid may also be of special interest in the development of molecular-based electronic devices. Finally, nanotubes offer the potential of providing a scaffold on which DNA molecules can be oriented, manipulated, and studied without the need for chemical functionalization.Although DNA/SWNT structures have been studied using optical absorption spectroscopy in the past, 1-7 little attention has been paid to the range of wavelengths of most interest for examining DNA, namely the UV region. DNA's UV absorbance has been studied extensively and has been central in understanding conformational changes of nucleic acids, such as the transition from double-stranded to single-stranded DNA. 8 Absorbance studies of DNA/SWNT samples have largely ignored the UV because, until not long ago, there was very little known about the absorbance properties of SWNT in this region. Some authors argue that the UV absorbance is entirely due to amorphous carbon material, 7 while others find the two absorbance peaks in the UV to be intrinsic to the nanotubes and, furthermore, to display a strong polarization dependence. 9 By the methods described here, we have found the UV absorbance peak locations and intensities to be repeatable under a variety of SWNT sample preparation conditions, and we demonstrate that the UV region provides important information about DNA/SWNT structure.We used optical absorption spectroscopy from λ) 190900 nm to explore the DNA-SWNT interaction of SWNT dispersed with DNA homopolymers of poly d(A30), poly d(C30), poly

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“…22 The method uses stability of the parameters, rather than a perfect fit to imperfect data, as the criterion for analysis. This method was used successfully to analyze the LD data of both synthetic polynucleotides and natural nucleic acids as a function of wavelength for individual base inclinations and axes of inclination.…”

Section: Discussionmentioning

confidence: 99%

Comparison of base inclination in ribo‐AU and deoxyribo‐AT polymers

Jin

Johnson

1995

Biopolymers

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The inclination angle between the base normal and the helix axis is measured for ribo-AU polymers by using flow linear dichroism (LD), and compared to measurements for deoxyribo-AT polymers under dehydrating conditions. The CD of the DNA polymers under the dehydrating conditions is not the same as the corresponding RNA polymers, which are presumed to be in the A form. However, the LD indicates that poly(dAdT)-poly(dAdT) can assume the A form in 80% 2,2,2-trifluoroethanol, although poly(dA)-poly(dT) retains B form structure in this dehydrating solvent. The inclination angles are similar for B form poly(dAdT)-poly(dAdT) and poly(dA)-poly(dT), and these parameters are also similar for A form poly(rArU)-poly(rArU) and poly(rA)-poly(rU). All inclination axes are similar.

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Base inclinations in natural and synthetic DNAs

Cited by 72 publications

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A polarized view on DNA under tension

A polarized view on DNA under tension

Optical Absorption of DNA−Carbon Nanotube Structures

Comparison of base inclination in ribo‐AU and deoxyribo‐AT polymers

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