5′-Phosphorylation Strengthens Sticky-End Cohesions

Zhe Li; Mengxi Zheng; Longfei Liu; Nadrian C. Seeman; Chengde Mao

doi:10.1021/jacs.1c07279

Unusual sequence length-dependent gold nanoparticles aggregation of the ssDNA sticky end and its application for enzyme-free and signal amplified colorimetric DNA detection

Scientific Reports ◽

10.1038/srep30878 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 19

Author(s):

Hongfei He ◽

Jianyuan Dai ◽

Zhijuan Duan ◽

Baozhan Zheng ◽

Yan Meng ◽

...

Keyword(s):

Gold Nanoparticles ◽

Dna Detection ◽

Sequence Length ◽

Sticky End

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Pathway Complexity in Fuel-Driven DNA Nanostructures with Autonomous Reconfiguration of Multiple Dynamic Steady States

10.26434/chemrxiv.10059131.v1 ◽

2019 ◽

Author(s):

Jie Deng ◽

Andreas Walther

Keyword(s):

Molecular Recognition ◽

Enzymatic Reaction ◽

Reaction Network ◽

Steady States ◽

Hierarchical Level ◽

Dna Nanostructures ◽

Structural Dynamic ◽

Systems Chemistry ◽

Sticky End ◽

Autonomous Evolution

We introduce pathway complexity on a multicomponent systems level in chemically fueled transient DNA polymerization system. The systems are based on a monomeric species pool that is fueled by ATP and orchestrated by an enzymatic reaction network (ERN) of ATP-powered ligation and concurrent cleavage. Such systems display autonomous evolution over multiple structural dynamic steady states from monomers to dimers, oligomer of dimers to ultimately randomized polymer structure before being ultimately degraded back to monomers once the fuel is consumed. The enabling key principle is to design monomer species having kinetically selected molecular recognition with respect to the structure-forming step (ATP-powered ligation) by encoding different sticky-end overhangs into the ligation area. However, all formed structures are equally degraded, and the orthogonal molecular recognition of the different starting species are harmonized during the constantly occurring restriction process, leading in consequence to a reconfiguration of the driven dynamic nanostructures on a higher hierarchical level. This non-equilibrium systems chemistry approach to pathway complexity provides new conceptual insights in fuel-driven automatons and autonomous materials design.

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Restriction Enzyme Double Digestion v1

10.17504/protocols.io.by9hpz36 ◽

2021 ◽

Author(s):

Zhenfeng Fu

Keyword(s):

Restriction Enzyme ◽

Enzyme Digestion ◽

Dna Molecule ◽

Double Digestion ◽

Carrier Molecule ◽

Sticky End

Enzyme digestion is to cut the DNA molecule and the carrier molecule at the sticky end to obtain the corresponding sticky end connection.

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A chromomeric model for nuclear and chromosome structure

Journal of Cell Science ◽

10.1242/jcs.108.9.2927 ◽

1995 ◽

Vol 108 (9) ◽

pp. 2927-2935 ◽

Cited By ~ 7

Author(s):

P.R. Cook

Keyword(s):

Transcription Factors ◽

Chromosome Structure ◽

Rna Polymerases ◽

Stable Structure ◽

Structural Elements ◽

Transcription Factories ◽

Chromatin Loops ◽

Sticky End

The basic structural elements of chromatin and chromosomes are reviewed. Then a model involving only three architectural motifs, nucleosomes, chromatin loops and transcription factories/chromomeres, is presented. Loops are tied through transcription factors and RNA polymerases to factories during interphase and to the remnants of those factories, chromomeres, during mitosis. On entry into mitosis, increased adhesiveness between nucleosomes and between factories drives a ‘sticky-end’ aggregation to the most compact and stable structure, a cylinder of nucleosomes around an axial chromomeric core.

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Mitigating the Non-Specific Amplification in RCA: Assessment of the Role of Ligation and Exonuclease Digestion in Circular DNA Preparation

10.26434/chemrxiv.14577975 ◽

2021 ◽

Author(s):

Vandana Kuttappan Nair ◽

Chandrika Sharma ◽

Mrittika Sengupta ◽

Souradyuti Ghosh

Keyword(s):

Nucleic Acid ◽

Real Time ◽

False Positive ◽

Rolling Circle Amplification ◽

Circular Dna ◽

Rolling Circle ◽

Specific Amplification ◽

Exonuclease Digestion ◽

Sticky End

<b>Layman Summary: </b>Rolling circle amplification (RCA) is a popular and extensively used bioanalytical tool. Like any nucleic acid amplifications, non-specific amplification may occur in it and risk generating false positive readouts. The work described in the manuscript investigates non-specific amplification in RCA as a function of ligation and exonuclease digestion assays during the synthesis of circular DNA. In particular, it investigates and compares the role of three different ligation techniques, namely splint-padlock ligation, cohesive end (sticky end ligation), and self-annealing ligation. In addition, it also probes the role of single exonuclease vs dual exonuclease digestions. We employed real time fluorescence to quantify the effect of these factors. Finally, our work hypothesizes the possible origins of non-specific amplification in RCA.

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