Differential stability of DNA based on salt concentration

Maity, Arghya; Singh, Awatar; Singh, Navin

doi:10.1007/s00249-016-1132-3

Cited by 22 publications

(19 citation statements)

References 60 publications

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“…The high-salt condition is also known to compromise the double helical structure and lead to partial denaturation of dsDNA. 59 This change of structural integrity was then reflected in the alkyne-HDX speed-up for both EdU-labeled dsDNA and cellular DNA. Collectively, our results for different DNA species under varied conditions establish the viability of employing alkyne-HDX to sense and study the local DNA environments.…”

Section: ■ Resultsmentioning

confidence: 85%

“…This result implies that our alkyne-HDX strategy is indeed sensitive to the change of DNA structures. To gain more insights into the causes of varying alkyne-HDX kinetics across different EdU-labeled DNA structures, we next investigated how the high-salt condition (DPBS-D 2 O buffer with 2 M NaCl), which could perturb the DNA electrostatic interactions, modulates the alkyne-HDX of EdU (Figure e, light blue bars). We confirmed that the high osmolarity would not alter the D 2 O diffusion rate across cells by both spontaneous Raman and SRS measurements (Figure S3d–f).…”

Section: Resultsmentioning

confidence: 99%

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Alkyne-Tagged Raman Probes for Local Environmental Sensing by Hydrogen–Deuterium Exchange

Miao

2022

J. Am. Chem. Soc.

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Alkyne-tagged Raman probes have shown high promise for noninvasive and sensitive visualization of small biomolecules to understand their functional roles in live cells. However, the potential for alkynes to sense cellular environments that goes beyond imaging remains to be further explored. Here, we report a general strategy for Raman imaging-based local environment sensing by hydrogen–deuterium exchange (HDX) of terminal alkynes (termed alkyne-HDX). We first demonstrate, in multiple Raman probes, that deuterations of the alkynyl hydrogens lead to remarkable shifts of alkyne Raman peaks for about 130 cm–1, providing resolvable signals suited for imaging-based analysis with high specificity. Both our analytical derivation and experimental characterizations subsequently establish that HDX kinetics are linearly proportional to both alkyne pK as and environmental pDs. After validating the quantitative nature of this strategy, we apply alkyne-HDX to sensing local chemical and cellular environments. We establish that alkyne-HDX exhibits high sensitivity to various DNA structures and demonstrates the capacity to detect DNA structural changes in situ from UV-induced damage. We further show that this strategy is also applicable to resolve subtle pD variations in live cells. Altogether, our work lays the foundation for utilizing alkyne-HDX strategy to quantitatively sense the local environments for a broad spectrum of applications in complex biological systems.

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Section: ■ Resultsmentioning

confidence: 85%

Section: Resultsmentioning

confidence: 99%

Alkyne-Tagged Raman Probes for Local Environmental Sensing by Hydrogen–Deuterium Exchange

Miao

2022

J. Am. Chem. Soc.

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“…By evaluating the partition function, we calculate free energy per base pair hence specific heat as a function of temperature. The melting temperature T m of chain at various angular separations(θ) for conical confined geometry and in different diameter of the cylinder for cylindrical confined geometry are calculated through the peak in specific heat as a function of temperature [2,57]. The results are plotted in Fig.…”

Section: Resultsmentioning

confidence: 99%

Melting of DNA in confined geometry

Maity,

Singh

2019

Preprint

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The stability of DNA molecule during the encapsulation process is a topic of intense research. We study the thermal stability of the double-stranded DNA molecule of different lengths in a confined space. Using a statistical model we evaluate the melting profile of DNA of different length in two geometries: conical and cylindrical. Our results show that not only the confinement but also the geometry of the confined space plays a prominent role in the stability and opening manner of the molecule.

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“…If the solutions are allowed to dry on the fused silica substrate upon which the bowtie antennas are mounted, then buffer solutions become concentrated, leading to DNA denaturation under high salt conditions (48)(49)(50). This occurs for both m-and n-types of DNA.…”

Section: Denaturationmentioning

confidence: 99%

DNA Methylation Detection Using Resonance and Nanobowtie-Antenna-Enhanced Raman Spectroscopy

Lim

Puretzky

et al. 2018

Biophysical Journal

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We show that DNA carrying 5-methylcytosine modifications or methylated DNA (m-DNA) can be distinguished from DNA with unmodified cytosine by Raman spectroscopy enhanced by both a bowtie nanoantenna and excitation resonance. In particular, m-DNA can be identified by a peak near 1000 cm and changes in the Raman peaks in the 1200-1700 cm band that are enhanced by the ring-absorption resonance. The identification is robust to the use of resonance Raman and nanoantenna excitation used to obtain significant signal improvement. The primary differences are three additional Raman peaks with methylation at 1014, 1239, and 1639 cm and spectral intensity inversion at 1324 (C=C) and 1473 cm (C=N) in m-DNA compared to that of DNA with unmodified cytosine. We attribute this to the proximity of the methyl group to the antenna, which brings the (C=C) mode closer to experiencing a stronger near-field enhancement. We also show distinct Raman spectral features attributed to the transition of DNA from a hydrated state, when dissolved, to a dried/denatured state. We observe a general broadening of the larger lines and a transfer of spectral weight from the ∼1470 cm vibration to the two higher-energy lines of the dried m-DNA solution. We attribute the new spectral characteristics to DNA softening under high salt conditions and find that the m-DNA is still distinguishable via the ∼1000 cm peak and distribution of the signal in the 1200-1700 cm band. The nanoantenna gain exceeds 20,000, whereas the real signal ratio is much less because of a low average enhanced region occupancy even with these relatively high DNA concentrations. It is improved when fixed DNA in a salt crystal lies near the nanoantenna. The Raman resonance gain profile is consistent with A-term expectations, and the resonance is found at ∼259 nm excitation wavelength.

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Differential stability of DNA based on salt concentration

Cited by 22 publications

References 60 publications

Alkyne-Tagged Raman Probes for Local Environmental Sensing by Hydrogen–Deuterium Exchange

Alkyne-Tagged Raman Probes for Local Environmental Sensing by Hydrogen–Deuterium Exchange

Melting of DNA in confined geometry

DNA Methylation Detection Using Resonance and Nanobowtie-Antenna-Enhanced Raman Spectroscopy

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