The structural shift of a DNA template between a hairpin and a dimer tunes the emission color of DNA-templated AgNCs

Nanoscale ◽  
2018 ◽  
Vol 10 (44) ◽  
pp. 20717-20722 ◽  
Author(s):  
Pratik Shah ◽  
Suk Won Choi ◽  
Riddhi Nagda ◽  
Reka Geczy ◽  
Seok Keun Cho ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Silver Nanoclusters ◽  
Dna Hairpin ◽  
Fluorescent Properties ◽  
Structural Shift ◽  
Emission Color ◽  
Dna Template

The structural shift of a DNA hairpin-dimer is as important as the DNA sequence in determining the fluorescent properties of DNA-stabilized silver nanoclusters (DNA/AgNCs).

scholarly journals Studies on the interactions of Ag(i) with DNA and their implication on the DNA-templated synthesis of silver nanoclusters and on the interaction with complementary DNA and RNA sequences

RSC Advances ◽  
2021 ◽  
Vol 11 (15) ◽  
pp. 9029-9042
Author(s):  
Alejandra de la Hoz ◽  
Alba Navarro ◽  
Anna Aviñó ◽  
Ramon Eritja ◽  
Raimundo Gargallo
Keyword(s):  
Secondary Structure ◽  
Dna Sequence ◽  
Analytical Signal ◽  
Silver Nanoclusters ◽  
Fluorescent Properties ◽  
Rna Sequences ◽  
Complementary Dna ◽  
Templated Synthesis ◽  
Dna And Rna ◽  
Hybridization Reaction

Variables affecting the fluorescent properties of DNA-stabilized silver nanoclusters are studied. The secondary structure of the AgNC-stabilizing DNA sequence dramatically affects the analytical signal behind the hybridization reaction.

scholarly journals Hg2+ Detection with Rational Design of DNA-Templated Fluorescent Silver Nanoclusters

Processes ◽  
2021 ◽  
Vol 9 (10) ◽  
pp. 1699
Author(s):  
Liam Yourston ◽  
Polikron Dhoqina ◽  
Nolan Marshall ◽  
Rujani Mahmud ◽  
Ethen Kuether ◽  
...  
Keyword(s):  
Optical Properties ◽  
Rational Design ◽  
Visible Spectral Range ◽  
Silver Nanoclusters ◽  
Hairpin Loop ◽  
Fluorescent Properties ◽  
Dna Oligonucleotides ◽  
Loop Sequence ◽  
Detectable Range ◽  
Additional Stability

Atomically precise silver nanoclusters (AgNCs) are small nanostructures consisting of only a few atoms of silver. The combination of AgNCs with cytosine-rich single-stranded oligonucleotides results in DNA-templated silver nanoclusters (DNA-AgNCs). DNA-AgNCs are highly luminescent and can be engineered with reproducible and unique fluorescent properties. Furthermore, using nucleic acids as templates for the synthesis of AgNCs provides additional practical benefits by expanding optical activity beyond the visible spectral range and creating the possibility for color tunability. In this study, we explore DNA oligonucleotides designed to fold into hairpin-loop (HL) structures which modulate optical properties of AgNCs based on the size of the loop containing different number of cytosines (HL-CN). Depending on the size of the loop, AgNCs can be manufactured to have either single or multiple emissive states. Such hairpin-loop structures provide an additional stability for AgNCs and further control over the base composition of the loop, allowing for the rational design of AgNCs’ optical properties. We demonstrate the potential of AgNCs in detecting Hg2+ by utilizing the HL-C13 design and its variants HL-T2C11, HL-T4C9, and HL-T6C7. The replacement of cytosines with thymines in the loop was intended to serve as an additional sink for mercury ions extending the detectable range of Hg2+. While AgNC@HL-T0C13 exhibits an interpretable quenching curve, AgNC@HL-T6C7 provides the largest detectable range of Hg2+. The results presented herein suggest that it is possible to use a rational design of DNA-AgNCs based on the composition of loop sequence in HL structures for creating biosensors to detect heavy metals, particularly Hg2+.

scholarly journals Corrigendum to “Formation of Silver Nanoclusters from a DNA Template Containing Ag(I)-Mediated Base Pairs”

2018 ◽  
Vol 2018 ◽  
pp. 1-1
Author(s):  
J. Christian Léon ◽  
Linda Stegemann ◽  
Martin Peterlechner ◽  
Stefanie Litau ◽  
Gerhard Wilde ◽  
...  
Keyword(s):  
Silver Nanoclusters ◽  
Base Pairs ◽  
Dna Template

DNA-Hairpin-Templated Silver Nanoclusters: A Study on Stem Sequence

2020 ◽  
Author(s):  
Yahui Guo ◽  
Fumiao Shen ◽  
Yuliang Cheng ◽  
Hang Yu ◽  
Yunfei Xie ◽  
...  
Keyword(s):  
Silver Nanoclusters ◽  
Dna Hairpin

DNA template-regulated intergrowth of a fluorescent silver nanocluster emitter pair

RSC Advances ◽  
2015 ◽  
Vol 5 (119) ◽  
pp. 98467-98471 ◽  
Author(s):  
Jin-Liang Ma ◽  
Bin-Cheng Yin ◽  
Bang-Ce Ye
Keyword(s):  
Silver Nanoclusters ◽  
Silver Nanocluster ◽  
Dna Template

We have developed a novel type of intensely fluorescent DNA-templated silver nanoclusters (DNA/AgNCs), which is in the form of the intergrowth of a Ag emitter pair.

scholarly journals DNA-Templated Fluorescent Silver Nanoclusters Inhibit Bacterial Growth While Being Non-Toxic to Mammalian Cells

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 4045
Author(s):  
Lewis Rolband ◽  
Liam Yourston ◽  
Morgan Chandler ◽  
Damian Beasock ◽  
Leyla Danai ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Antibacterial Properties ◽  
Silver Nanoclusters ◽  
Metal Nanoclusters ◽  
Fluorescent Properties ◽  
Dna Oligonucleotides ◽  
Mammalian Cell Lines ◽  
History Of ◽  
The Stability

Silver has a long history of antibacterial effectiveness. The combination of atomically precise metal nanoclusters with the field of nucleic acid nanotechnology has given rise to DNA-templated silver nanoclusters (DNA-AgNCs) which can be engineered with reproducible and unique fluorescent properties and antibacterial activity. Furthermore, cytosine-rich single-stranded DNA oligonucleotides designed to fold into hairpin structures improve the stability of AgNCs and additionally modulate their antibacterial properties and the quality of observed fluorescent signals. In this work, we characterize the sequence-specific fluorescence and composition of four representative DNA-AgNCs, compare their corresponding antibacterial effectiveness at different pH, and assess cytotoxicity to several mammalian cell lines.

scholarly journals Emerging roles for R-loop structures in the management of topological stress

2020 ◽  
Vol 295 (14) ◽  
pp. 4684-4695 ◽  
Author(s):  
Frederic Chedin ◽  
Craig J. Benham
Keyword(s):  
Dna Sequence ◽  
Single Molecule ◽  
Genome Instability ◽  
Dna Topology ◽  
Loop Structure ◽  
Loop Modeling ◽  
Loop Formation ◽  
Dna Structures ◽  
Recent Developments ◽  
Dna Template

R-loop structures are a prevalent class of alternative non-B DNA structures that form during transcription upon invasion of the DNA template by the nascent RNA. R-loops form universally in the genomes of organisms ranging from bacteriophages, bacteria, and yeasts to plants and animals, including mammals. A growing body of work has linked these structures to both physiological and pathological processes, in particular to genome instability. The rising interest in R-loops is placing new emphasis on understanding the fundamental physicochemical forces driving their formation and stability. Pioneering work in Escherichia coli revealed that DNA topology, in particular negative DNA superhelicity, plays a key role in driving R-loops. A clear role for DNA sequence was later uncovered. Here, we review and synthesize available evidence on the roles of DNA sequence and DNA topology in controlling R-loop formation and stability. Factoring in recent developments in R-loop modeling and single-molecule profiling, we propose a coherent model accounting for the interplay between DNA sequence and DNA topology in driving R-loop structure formation. This model reveals R-loops in a new light as powerful and reversible topological stress relievers, an insight that significantly expands the repertoire of R-loops' potential biological roles under both normal and aberrant conditions.

scholarly journals Effect of low nucleotide concentrations on abortive elongation catalysed by wheat-germ RNA polymerase II

1987 ◽  
Vol 244 (1) ◽  
pp. 151-157 ◽  
Author(s):  
C Job ◽  
J Dietrich ◽  
D Shire ◽  
M Teissere ◽  
D Job
Keyword(s):  
Escherichia Coli ◽  
Substrate Specificity ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Dna Sequence ◽  
Wheat Germ ◽  
Starting Point ◽  
Dna Template ◽  
Plant Enzyme ◽  
Productive Elongation

A kinetic study of the effect of elongating nucleotide concentration on the reactions of abortive elongation catalysed by wheat-germ RNA polymerase II on a poly[d(A-T)] template suggests that the shift from abortive to productive elongation may involve the participation of at least two nucleotides, according to a mechanism very similar to that reported for Escherichia coli RNA polymerase. Experiments performed with non-complementary nucleotides with respect to the DNA template, and with substrate derivatives, allow an analysis of the substrate specificity during these reactions. Similar experiments performed with poly[d(A-A-T)].poly[d(T-T-A)] as template provide a starting point for a better understanding of the effect of DNA sequence on the rates of abortive and productive elongation catalysed by the plant enzyme.

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