Thermodynamic investigation of kissing-loop interactions

Carr, Carolyn E.; Marky, Luis A.

doi:10.1016/j.biochi.2018.11.012

Cited by 4 publications

(2 citation statements)

References 47 publications

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“…It is common to imagine hairpin-kissing as in Figure 1D , where base pairing occurs somewhere in the central portion of the loops. Such hairpin interactions with five complementary bases have been shown to have melting temperatures ∼29°C, which makes them difficult to use as structural components in DNA origami ( Carr and Marky, 2019 ). Having longer stretches of complementary bases in each loop may seem like it would increase stability; however, there is an upper limit to the number of base pairs that can form between even fully complementary loops.…”

Section: The Secondary Structural Building Blocks In Ssorigamimentioning

confidence: 99%

A single strand: A simplified approach to DNA origami

et al. 2023

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Just as a single polypeptide strand can self-fold into a complex 3D structure, a single strand of DNA can self-fold into DNA origami. Most DNA origami structures (i.e., the scaffold-staple and DNA tiling systems) utilize hundreds of short single-stranded DNA. As such, these structures come with challenges inherent to intermolecular construction. Many assembly challenges involving intermolecular interactions can be resolved if the origami structure is constructed from one DNA strand, where folding is not concentration dependent, the folded structure is more resistant to nuclease degradation, and the synthesis can be achieved at an industrial scale at a thousandth of the cost. This review discusses the design principles and considerations employed in single-stranded DNA origami and its potential benefits and drawbacks.

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Section: The Secondary Structural Building Blocks In Ssorigamimentioning

confidence: 99%

A single strand: A simplified approach to DNA origami

et al. 2023

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“…Single-stranded RNA fold rigid secondary structures dependent on the sequence. For example, tmRNA, [1,2] pseudoknot, [3,4] and kissing complex [5,6] are RNA motifs with characteristic secondary structures that play important roles in the decomposition of unnecessary RNA, [7,8] the activation of telomerase, [9,10] and the recognition of protein interactions. [11][12][13] Recently, gene expression control using proteins that immobilize RNA and research using higher-order structures such as light up aptamer [14][15][16][17] are also being conducted.…”

Section: Introductionmentioning

confidence: 99%

Fluorescence In Situ Hybridization of 16S rRNA in Escherichia coli Using Multiple Photo‐Cross‐Linkable Probes

Fujimoto

Watanabe

2020

ChemistrySelect

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RNA forms various secondary structures depending on its sequence in cells; the influence of secondary structures must be considered when detecting, regulating, or manipulating RNA. In this study, we utilized the cooperativity of multiple photo‐cross‐linkable assistant probes to evaluate photo‐cross‐linking for RNAs with complex secondary structures. We succeeded in increasing the fluorescence intensity 39.9 times in the region where detection was difficult owing to the formation of a complex secondary structure in the conventional fluorescence in situ hybridization method. This method enables the detection, regulation, and manipulation of RNA that forms various structures depending on the sequence.

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