The sequence d(CGGCGGCCGC) self-assembles into a two dimensional rhombic DNA lattice

Venkadesh, S.; Mandal, Pradeep K.; Gautham, N.

doi:10.1016/j.bbrc.2011.03.056

Cited by 4 publications

(10 citation statements)

References 19 publications

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“…Moreover, the effects of acidic and alkaline solvents or environment have been found to impart enormous significant information on the biochemical fluctuations in the DNA functionality and stability [ 14 , 15 ]. The crystal structure of the Holliday junction which have been taken for the study comprises of the sequence d(CGGCGGCCGC) 4 [ 16 ], possess the potential application in nanotechnology. It has a rhombus structure with twenty base-pairs which form large cavities in the crystal lattice [ 16 ].…”

Section: Introductionmentioning

confidence: 99%

“…The crystal structure of the Holliday junction which have been taken for the study comprises of the sequence d(CGGCGGCCGC) 4 [ 16 ], possess the potential application in nanotechnology. It has a rhombus structure with twenty base-pairs which form large cavities in the crystal lattice [ 16 ]. Its motif consists of double helical arms whose strands end in a single DNA, commonly called as sticky ends [ 17 ].…”

Section: Introductionmentioning

confidence: 99%

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Understanding the self-assembly dynamics of A/T absent ‘four-way DNA junctions with sticky ends’ at altered physiological conditions through molecular dynamics simulations

Singh

Yadav²,

Shati

et al. 2023

PLoS ONE

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Elucidation of structure and dynamics of alternative higher-order structures of DNA such as in branched form could be targeted for therapeutics designing. Herein, we are reporting the intrinsically dynamic and folds transitions of an unusual DNA junction with sequence d(CGGCGGCCGC)4 which self-assembles into a four-way DNA junction form with sticky ends using long interval molecular simulations under various artificial physiological conditions. The original crystal structure coordinates (PDB ID: 3Q5C) for the selected DNA junction was considered for a total of 1.1 μs molecular dynamics simulation interval, including different temperature and pH, under OPLS-2005 force field using DESMOND suite. Following, post-dynamics structure parameters for the DNA junction were calculated and analyzed by comparison to the crystal structure. We show here that the self-assembly dynamics of DNA junction is mitigated by the temperature and pH sensitivities, and discloses peculiar structural properties as function of time. From this study it can be concluded on account of temperature sensitive and pH dependent behaviours, DNA junction periodic arrangements can willingly be synthesized and redeveloped for multiple uses like genetic biomarkers, DNA biosensor, DNA nanotechnology, DNA Zipper, etc. Furthermore, the pH dis-regulation behaviour may be used to trigger the functionality of DNA made drug–releasing nanomachines.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Understanding the self-assembly dynamics of A/T absent ‘four-way DNA junctions with sticky ends’ at altered physiological conditions through molecular dynamics simulations

Singh

Yadav²,

Shati

et al. 2023

PLoS ONE

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“…Despite the success in the duplex crystal, another crystal designed from DNA Holliday junctions didn′t crystallize well after phosphorylation, even in the same buffer (Figure S11). 15 Likely, the crystal contacts were altered in the presence of 5′phosphate. From this perspective, the DNA tensegrity triangle crystals represent the best crystal model system to study stickyend cohesion, where all the crystal contacts are predictable, specific, robust, and resistant to change after chemical modifications.…”

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confidence: 98%

5′-Phosphorylation Strengthens Sticky-End Cohesions

Zheng

Liu

et al. 2021

J. Am. Chem. Soc.

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Sticky-end cohesion plays a critical role in molecular biology and nucleic acid nanotechnology. Although free energy calculations and molecular mechanics can predict these interactions, chemical modification would compromise such predictions. Herein, we have used rationally designed 3D DNA crystals as a tool to experimentally investigate the modulation of 5′-phosphorylation on sticky-end cohesions. We have found that 5′-phosphorylation strengthens the sticky-end cohesion: in a DNA crystal self-assembled exclusively via sticky-end cohesions, 5′-phosphorylation not only promotes the crystallization process, in general, but also accelerates the crystal growth along designed directions. Such a finding allows the fine-tuning of DNA crystallization kinetics and the control of DNA crystal morphology. It also suggests a potential difference in self-assembly kinetics between natural DNA (with 5′-phosphorylation) and synthetic DNA (without 5′-phosphorylation).

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“…Two-and three-dimensional structures have been constructed by this approach. [25][26][27][28][29] Combining the natural nucleotides with chemically modified building blocks [30][31][32][33][34][35][36][37][38][39][40][41][42] extends the range of structural and functional features of such nano-objects. Linking hydrophobic molecules onto DNA can lead to the formation of supramolecular polymers in aqueous medium.…”

mentioning

confidence: 99%

“…DNA origami allows the preparation of well-defined nanometer-sized objects by the folding of long DNAs with the help of guiding oligonucleotide strands. − Alternatively, large DNA constructs can be assembled from duplexes with nucleotide overhangs at their ends (sticky ends approach). Two- and three-dimensional structures have been constructed by this approach. − Combining the natural nucleotides with chemically modified building blocks − extends the range of structural and functional features of such nano-objects. Linking hydrophobic molecules to DNA can lead to the formation of supramolecular polymers in aqueous medium .…”

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confidence: 99%

Supramolecular Assembly of DNA-Phenanthrene Conjugates into Vesicles with Light-Harvesting Properties

et al. 2018

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Vesicle-shaped supramolecular polymers are formed by self-assembly of a DNA duplex containing phenanthrene overhangs at both ends. In the presence of spermine, the phenanthrene overhangs act as sticky ends linking the DNA duplexes together. In aqueous solution, the assembly leads to vesicles with a diameter in the range of 50-200 nm. Fluorescence measurements show that the assembled phenanthrene units act as light-harvesting complexes and transfer absorbed energy to an acceptor, such as pyrene or Cy3, which can either be directly added to the polymer or attached via a complementary DNA strand. The presence of DNA in the nanostructures allows the construction of light-harvesting vesicles that are amenable to derivatization with different functional groups.

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The sequence d(CGGCGGCCGC) self-assembles into a two dimensional rhombic DNA lattice

Cited by 4 publications

References 19 publications

Understanding the self-assembly dynamics of A/T absent ‘four-way DNA junctions with sticky ends’ at altered physiological conditions through molecular dynamics simulations

Understanding the self-assembly dynamics of A/T absent ‘four-way DNA junctions with sticky ends’ at altered physiological conditions through molecular dynamics simulations

5′-Phosphorylation Strengthens Sticky-End Cohesions

Supramolecular Assembly of DNA-Phenanthrene Conjugates into Vesicles with Light-Harvesting Properties

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