Dna I-motif
Dna I-motif - Related Videos
09:32
Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules
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Cited by 6 •
2019
This article presents a detailed protocol for T4 ligation and denaturing PAGE purification of small circular DNA molecules, annealing and native PAGE analysis of circular tiles, assembling and AFM imaging of 1D and 2D DNA nanostructures, as well as agarose gel electrophoresis and centrifugation purification of finite DNA nanostructures.
14:28
Peptide-based Identification of Functional Motifs and their Binding Partners
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Cited by 2 •
2013
Techniques to dissect the mechanisms underlying the secretion of HIV-1 Nef in exosomes are described. Specific short peptides derived from Nef and protein transfection were exploited to determine the structure, function, and binding partners of Nef’s Secretion Modification Region. These procedures have general relevance in many mechanistic studies.
07:55
Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
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Cited by 3 •
2011
A straight-forward and robust method to identify potential regulatory motifs in co-regulated genes is presented. SCOPE does not require any user parameters and returns motifs that represent excellent candidates for regulatory signals. The identification of such regulatory signals helps to understand the underlying biology.
08:59
High-Speed Atomic Force Microscopy Imaging of DNA Three-Point-Star Motif Self Assembly Using Photothermal Off-Resonance Tapping
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2024
Here, we show the imaging protocol for observing biomolecular interactions with photothermal off-resonance tapping (PORT), where we optimized imaging parameters, identified system limits, and investigated potential improvements in imaging three-point-star DNA motif assembly.
13:16
Assessment of DNA Contamination in RNA Samples Based on Ribosomal DNA
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Cited by 26 •
2018
Here, we present a protocol for tracing genomic DNA (gDNA) contamination in RNA samples. The presented method utilizes primers specific for the internal transcribed spacer region (ITS) of ribosomal DNA (rDNA) genes. The method is suited for reliable and sensitive detection of DNA contamination in most eukaryotes and prokaryotes.
FAQs
Formation begins when mildly acidic conditions protonate cytosine residues, allowing a protonated cytosine to pair with a neutral cytosine. These hemiprotonated C·C+ pairs then intercalate, meaning they stack within the folded strand rather than simply remaining adjacent in sequence. This sequence of protonation, pairing, and intercalation creates the compact architecture that distinguishes the structure.
Intercalation is important because it converts local base pairing into a higher-order fold with a compact molecular shape. That altered architecture can change how the nucleic acid presents recognition features and responds to its chemical surroundings. In bioengineering, controlling this fold provides a way to connect sequence and environment to the behavior of a programmable nucleic acid system.
pH dependence gives the DNA i-motif a reversible response rather than a permanently fixed fold. Changes toward suitable mildly acidic conditions can promote the protonation and C·C+ pairing needed for folding, whereas changing the chemical environment can favor the alternative state. This reversibility supports designs that repeatedly couple environmental conditions to molecular switching.
Researchers can use this pH-responsive behavior as a switching element in biosensors, DNA nanotechnology, and responsive biomaterials. The i-motif supplies a structural transition that can be linked to a designed system’s state, allowing chemical conditions to influence molecular organization. Its value is therefore not only the fold itself, but the ability to build reversible, programmable responses into nucleic-acid-based materials.
Design starts with the cytosine-rich sequence, but sequence alone does not determine the outcome. The surrounding chemical environment affects cytosine protonation, while higher-order folding influences the final architecture and recognition behavior. Considering these variables together helps bioengineers tune whether an i-motif forms and how its structure contributes to a responsive nucleic acid design.
Within bioengineering, these structures provide a model for connecting molecular recognition with programmable folding. Their pH-dependent architecture can be incorporated into systems whose organization changes with chemical conditions, including responsive biomaterials and nucleic acid nanotechnology. Studying the relationship among sequence, environment, and folding also helps guide designs that use DNA in controllable molecular systems.