Smectic-B phase and temperature-driven smectic-B to -A transition in concentrated solutions of “gapped” DNA

Gyawali, Prabesh; Saha, Rony; Kodikara, Sineth G.; Li, Ruipeng; Fukuto, Masafumi; Gleeson, J. T.; Smith, Gregory P.; Clark, Noel A.; Jákli, Antal; Balci, Hamza; Sprunt, Samuel

doi:10.1103/physrevresearch.4.033046

Cited by 6 publications

(18 citation statements)

References 20 publications

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“…This peak corresponds to a layer spacing of ∼17.5 nm, slightly larger than the length of a single duplex. Careful examination of the data in Figure reveals that this peak develops from a splitting of the first harmonic of the bilayer peak ( q ∼ 0.359 nm –1 ) at elevated temperature, consistent with the bilayer smectic-B to “monolayer” smectic-A structural transition that we previously identified in AT-terminated 48-10T-48 samples without divalent cations but at significantly higher (∼280 mg/mL) DNA concentration.…”

Section: Resultssupporting

confidence: 83%

“…For each sample, the fundamental order of diffraction observed at small angle is centered on wavenumber q 1 = 0.182 nm –1 (with ±0.002 nm –1 variation across different constructs) at the lowest temperature (5–7 °C), which gives a smectic layer spacing of d = 2π/ q 1 = 34.5 nm (±0.4). The layer spacing slightly exceeds the 32 nm length of two 48-bp duplexes and confirms a bilayer structure. ,, A weaker first harmonic appears at 2 q 1 . As previously established from SAXS studies, the sharp wider angle peak at q w = 2.15 nm –1 (with ±0.02 nm –1 variation across different constructs), observed in a significant subset of samples in Figure , represents the lowest order diffraction from hexagonal positional ordering of the duplexes within the layers that characterize the smectic-B phase.…”

Section: Resultsmentioning

confidence: 60%

“…Polyacrylamide gel electrophoresis (PAGE) purified oligomers (O1, O2, and O3) were purchased from ExonanoRNA (Columbus, OH) or Genescript (Piscataway, NJ). Details of the GDNA synthesis process, sample loading process into thin-walled borosilicate capillaries, and the details of the SAXS/WAXS measurements carried out are described in previous publications. ,, Briefly, the GDNA constructs, denoted as 48-20T-48, consist of two symmetric 48-base pair duplexes bridged by a single-strand gap of 20 Thymine bases (Figure A). These constructs are created by annealing a long strand (O1, 116 nt) with two short strands (O2 and O3, each 48 nt) that are complementary to the regions except the 20T sequence in the middle of O1.…”

Section: Methodsmentioning

confidence: 99%

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Impact of Divalent Cations on In-Layer Positional Order of DNA-Based Liquid Crystals: Implications for DNA Condensation

Kodikara,

Gyawali,

Gleeson

et al. 2024

Biomacromolecules

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The layered liquid crystalline phases formed by DNA molecules, which include rigid and flexible segments ("gapped DNA"), enable the study of both end-to-end stacking and side-to-side (helix-to-helix) lateral interactions, forming a model system to study such interactions at physiologically relevant DNA and ion concentrations. The observed layer structure exhibits long-range interlayer and in-layer positional correlations. In particular, the in-layer order has implications for DNA condensation, as it reflects whether these normally repulsive interactions become attractive under certain ionic conditions. Using synchrotron small-angle X-ray scattering measurements, we investigate the impact of divalent Mg 2+ cations (in addition to a constant 150 mM Na + ) on the stability of the interand in-layer DNA ordering as a function of temperature between 5 and 65 °C. DNA constructs with different terminal base pairings were created to mediate the strength of the attractive end-to-end stacking interactions between the blunt ends of the gapped DNA constructs. We demonstrate that the stabilities at a fixed DNA concentration of both interlayer and in-layer order are significantly enhanced even at a few mM Mg 2+ concentration. The stabilities are even higher at 30 mM Mg 2+ ; however, a marked decrease is observed at 100 mM Mg 2+ , suggesting a change in the nature of side-by-side interactions within this Mg 2+ concentration range. We discuss the implications of these results in terms of counterion-mediated DNA−DNA attraction and DNA condensation.

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Section: Resultssupporting

confidence: 83%

Section: Resultsmentioning

confidence: 60%

Section: Methodsmentioning

confidence: 99%

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Impact of Divalent Cations on In-Layer Positional Order of DNA-Based Liquid Crystals: Implications for DNA Condensation

Kodikara,

Gyawali,

Gleeson

et al. 2024

Biomacromolecules

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“…Careful examination of the data in Fig. 2 reveals that this peak develops from a splitting of the first harmonic of the bilayer peak ( q ∼ 0.359 nm -1 ) at elevated temperature, consistent with the bilayer smectic-B to “monolayer” smectic-A structural transition that we previously identified (32) in AT-terminated 48-10T-48 samples without divalent cations but at significantly higher (∼280 mg/ml) DNA concentration.…”

Section: Resultssupporting

confidence: 83%

“…The layer spacing slightly exceeds the 32 nm length of two 48-bp duplexes and confirms a bilayer structure(29, 30, 32). As previously established from SAXS studies (32), the sharp wider angle peak at q w = 2.15 nm -1 (with ±0.02 nm -1 variation across different constructs), observed in a significant subset of samples in Fig. 2, represents the lowest order diffraction from hexagonal positional ordering of the duplexes within the layers that characterizes the smectic-B phase.…”

Section: Resultsmentioning

confidence: 58%

Liquid Crystalline Layering and Divalent Cations Cooperatively Enhance DNA Condensation

Kodikara,

Gyawali,

Gleeson

et al. 2023

Preprint

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The layered liquid crystalline (LC) phases formed by DNA molecules which include rigid and flexible segments (‘gapped DNA’) enable the study of both end-to-end stacking and side-to-side lateral interactions that drive the condensation of DNA molecules. The resulting layer structure exhibits long-range inter-layer and intra-layer positional correlations. Using synchrotron small-angle x-ray scattering (SAXS) measurements, we investigate the impact of divalent Mg2+cations on the stability of the inter- and intra-layer DNA ordering as a function of temperature between 5-65 °C and for different terminal base pairings at the blunt ends of the gapped DNA constructs, which mediate the strength of the attractive end-to-end interaction. We demonstrate that the stabilities at a fixed DNA concentration of both inter-layer and intra-layer order are significantly enhanced even at a few mM Mg2+concentration. The stability continues to increase up to ∼30 mM Mg2+concentration, but at higher (∼100 mM) Mg2+content repulsion between positive ions counteracts and reverses the increase. On the other hand, sufficiently strong base-stacking interactions promote intra-layer order even in the absence of multivalent cations, which demonstrates the impact of liquid crystal layering on the DNA condensation process. We discuss the implications of these results in terms cation-mediated DNA-DNA attraction.

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Stability of End-to-End Base Stacking Interactions in Highly Concentrated DNA Solutions

et al. 2023

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Positionally ordered bilayer liquid crystalline nanostructures formed by gapped DNA (GDNA) constructs provide a practical window into DNA–DNA interactions at physiologically relevant DNA concentrations; concentrations several orders of magnitude greater than those in commonly used biophysical assays. The bilayer structure of these states of matter is stabilized by end-to-end base stacking interactions; moreover, such interactions also promote in-plane positional ordering of duplexes that are separated from each other by less than twice the duplex diameter. The end-to-end stacked as well as in-plane ordered duplexes exhibit distinct signatures when studied via small-angle X-ray scattering (SAXS). This enables analysis of the thermal stability of both the end-to-end and side-by-side interactions. We performed synchrotron SAXS experiments over a temperature range of 5–65 °C on GDNA constructs that differ only by the terminal base-pairs at the blunt duplex ends, resulting in identical side-by-side interactions, while end-to-end base stacking interactions are varied. Our key finding is that bilayers formed by constructs with GC termination transition into the monolayer state at temperatures as much as 30 °C higher than for those with AT termination, while mixed (AT/GC) terminations have intermediate stability. By modeling the bilayer melting in terms of a temperature-dependent reduction in the average fraction of end-to-end paired duplexes, we estimate the stacking free energies in DNA solutions of physiologically relevant concentrations. The free-energies thereby determined are generally smaller than those reported in single-molecule studies, which might reflect the elevated DNA concentrations in our studies.

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Smectic-B phase and temperature-driven smectic-B to -A transition in concentrated solutions of “gapped” DNA

Cited by 6 publications

References 20 publications

Impact of Divalent Cations on In-Layer Positional Order of DNA-Based Liquid Crystals: Implications for DNA Condensation

Impact of Divalent Cations on In-Layer Positional Order of DNA-Based Liquid Crystals: Implications for DNA Condensation

Liquid Crystalline Layering and Divalent Cations Cooperatively Enhance DNA Condensation

Stability of End-to-End Base Stacking Interactions in Highly Concentrated DNA Solutions

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