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Basic Molecular Cloning of DNA and RNA
Published in Jay L. Nadeau, Introduction to Experimental Biophysics, 2017
The key to the specificity of ligations is that each restriction enzyme has its own distinct pattern of DNA cleavage. Rather than cut the double-stranded DNA molecule flush, the enzymes usually leave an overhang on the top or bottom strand; this overhang is known as a sticky end because it is readily ligated to its complement when DNA ligase is added. Overhangs that are not complementary to one another are incompatible sticky ends and will not ligate. Thus, the position and direction of a ligation can be controlled by matching compatible sticky ends (Figure 2.6).
Molecular Lithography Using DNA Nanostructures
Published in James E. Morris, Kris Iniewski, Graphene, Carbon Nanotubes, and Nanostructures, 2017
The DNA nanostructure is a complex arrangement of single-stranded DNA molecules that are partially hybridized along their subsegments. Fabrication of DNA nanostructures is mainly based on the self-assembly process. The idea is to design a stable motif with sticky ends first that can hybridize to form DNA nanostructures [60,61,63–66]. For example, four motifs with sticky ends are assembled to form a quadrilateral with additional sticky ends on the outside, further allowing the structure to form a two-dimensional (2D) lattice [60,65]. Some of the useful motif types found in DNA nanostructures are stem loop (also called hairpins), Holliday junction, and sticky ends. Stem loop is a single-stranded DNA that loops back to hybridize on itself and is often used to form patterns on DNA nanostructures. Sticky end is an unhybridized single-stranded DNA that protrudes from the end of a double helix and is often used to combine two DNA nanostructures via hybridization. Holliday junctions are formed by two parallel DNA helices with one strand of each DNA helix crossing over the other DNA helix. Holliday junctions are often used to hold together various parts of DNA nanostructures. To achieve complicated DNA assemblies, it is important to design stable motifs. The use of branched DNA junctions with sticky ends to construct 2D arrays often did not yield the desired stable nanostructure due to the flexible nature of branched DNA junctions. To address this challenge, Seeman and coworkers constructed branched complexes with greater rigidity called crossover tiles, such as double-crossover tiles (DX) [67,68]. Inspired by the DX motif, several other motifs were engineered, such as triple-crossover (TX) motif, paranemic crossover tiles (PX), three-, five-, and six-point star motifs, and T-junctions, to provide more options to fabricate DNA nanostructures. Examples of these structures are shown in Figure 10.1 [67–79].
Selection and Improvement of Industrial Organisms for Biotechnological Applications
Published in Nduka Okafor, Benedict C. Okeke, Modern Industrial Microbiology and Biotechnology, 2017
Nduka Okafor, Benedict C. Okeke
The single-stranded sticky or cohesive ends of DNA ends (Table 7.4A and Fig. 7.5) will join (anneal) with any DNA with sticky ends having complimentary bases regardless of the origin of the DNA provided that both DNA samples have been cut with the same restriction enzyme. Some restriction endonucleases and their recognition sequences are given in Table 7.4B.
Remediation of copper-contaminated soils using Tagetes patula L., earthworms and arbuscular mycorrhizal fungi
Published in International Journal of Phytoremediation, 2022
Lei Fu, Long Zhang, Pengcheng Dong, Jie Wang, Liang Shi, Chunlan Lian, Zhenguo Shen, Yahua Chen
PCR products were measured using 1.5% agar gel electrophoresis. The gel was recovered and purified using the Axygen PCR Purification Kit (Axygen, USA). The concentration of nucleic acid was determined using a spectrophotometer (NanoDrop 1000, Thermo Scientific). DNA fragments with sticky ends were repaired using 3′-5′ exonuclease and polymerase. Single base A was introduced to the 3′ end of repaired DNA fragments. There were T bases at the 3′ end of the adaptor, which guaranteed the complementary pairing of A and T between DNA fragments and adaptor and prevented coupling between DNA inserts. Adaptor-containing tags and DNA fragments were incubated in the presence of ligase. DNA fragments containing adaptors at both ends were enriched selectively using PCR and the DNA library was amplified. The DNA library was quantified using Pico green and fluorescence spectrophotometry. Quality control of PCR fragments was performed using Agilent 2100. The sizes of fragments in the DNA library and their distribution was confirmed. The multiplexed DNA libraries were diluted to 10 nM. Subsequent sequencing was then performed using Illumina Miseq (Shanghai Sunny Biotechnology Co., Ltd.).
Beyond the smiley face: applications of structural DNA nanotechnology
Published in Nano Reviews & Experiments, 2018
Aakriti Alisha Arora, Chamaree de Silva
The self-assembly process of DNA was first showcased with the creation of 2D nucleic acid junctions and lattice shapes [4]. These junctions were developed as clusters; the clusters were linked directly to each other, or with interspersed linear DNA pieces (later coined as ‘sticky ends’) [4]. Subsequently, creation of immobile branched junctions allowed for a building framework upon to which other molecules could be attached [5]. Specifically, a closed cube-like structure containing six faces, eight vertices, and 12 double helical edges was developed [5]. Ultimately, 2D crystalline DNA forms were developed from synthetic DNA double crossover molecules [6]. ‘Sticky ends’ of DNA allowed for intermolecular interactions between each unit, leading to the formation of specific patterned DNA crystals [6].
Spectrophotometric determination of single-stranded DNA with self-assembly hairpin DNA and silver nanoparticles
Published in Instrumentation Science & Technology, 2021
Zhikun Zhang, Qingqing Liu, Xiaojie Ye, Yapeng Cao, Cuixia Hu, Runjing Liu, Yumin Liu
The two sequences (H1 and H2) were designed with specific sticky ends, one of which can specifically complementary pair with target DNA. The self-assembly of the single stranded nucleic acids was triggered to synthesize the linear polymer DNA when target DNA was added into H1 and H2 solution (Figure 1a). The linear polymer DNA had a double-chain structure. Compared with single stranded DNA, the formation of polymeric DNA is able greatly strengthen the distance between the silver nanoparticles. This process results in a change in the absorbance when silver nanoparticles were dispersed in the presence of 30 mM NaCl (Figure 1b).