How G-quadruplex topology and loop sequences affect optical properties of DNA-templated silver nanoclusters

Nano Research ◽  
2018 ◽  
Vol 11 (4) ◽  
pp. 2237-2247 ◽  
Author(s):  
Guangyu Tao ◽  
Yang Chen ◽  
Ruoyun Lin ◽  
Jiang Zhou ◽  
Xiaojing Pei ◽  
...  
Keyword(s):  
Optical Properties ◽  
Silver Nanoclusters ◽  
G Quadruplex

scholarly journals Unravelling the cellular emission fingerprint of the benchmark G-quadruplex-interactive compound Phen-DC3

2020 ◽  
Vol 56 (91) ◽  
pp. 14251-14254
Author(s):  
Marco Deiana ◽  
Jan Jamroskovic ◽  
Ikenna Obi ◽  
Nasim Sabouri
Keyword(s):  
Optical Properties ◽  
Cancer Cells ◽  
Binding Interactions ◽  
G Quadruplex

The G4-interactive binding interactions enable one to tune the optical properties of Phen-DC3, allowing the detection of G4 structures in cancer cells.

scholarly journals N-methyl mesoporphyrin IX as a highly selective light-up probe for G-quadruplex DNA

2019 ◽  
Vol 23 (11n12) ◽  
pp. 1195-1215 ◽  
Author(s):  
Ariana Yett ◽  
Linda Yingqi Lin ◽  
Dana Beseiso ◽  
Joanne Miao ◽  
Liliya A. Yatsunyk
Keyword(s):  
Optical Properties ◽  
Small Molecules ◽  
Genomic Stability ◽  
Water Soluble ◽  
Biological Processes ◽  
Binding Properties ◽  
Quadruplex Dna ◽  
Dna Structures ◽  
G Quadruplex ◽  
High Fluorescence

[Formula: see text]-methyl mesoporphyrin IX (NMM) is a water-soluble, non-symmetric porphyrin with excellent optical properties and unparalleled selectivity for G-quadruplex (GQ) DNA. G-quadruplexes are non-canonical DNA structures formed by guanine-rich sequences. They are implicated in genomic stability, longevity, and cancer. The ability of NMM to selectively recognize GQ structures makes it a valuable scaffold for designing novel GQ binders. In this review, we survey the literature describing the GQ-binding properties of NMM as well as its wide utility in chemistry and biology. We start with the discovery of the GQ-binding properties of NMM and the development of NMM-binding aptamers. We then discuss the optical properties of NMM, focusing on the light-switch effect — high fluorescence of NMM induced upon its binding to GQ DNA. Additionally, we examine the affinity and selectivity of NMM for GQs, as well as its ability to stabilize GQ structures and favor parallel GQ conformations. Furthermore, a portion of the review is dedicated to the applications of NMM-GQ complexes as biosensors for heavy metals, small molecules ([Formula: see text] ATP and pesticides), DNA, and proteins. Finally and importantly, we discuss the utility of NMM as a probe to investigate the roles of GQs in biological processes.

Optimization of fluorescent 8-heteroaryl-guanine probes for monitoring protein-mediated duplex → G-quadruplex exchange

2016 ◽  
Vol 14 (19) ◽  
pp. 4409-4419 ◽  
Author(s):  
Kaila L. Fadock ◽  
Richard A. Manderville ◽  
Purshotam Sharma ◽  
Stacey D. Wetmore
Keyword(s):  
Optical Properties ◽  
G Quadruplex

In this study, we describe the thermal and optical properties of the thrombin binding aptamer (TBA) that has been modified at syn-G-tetrad postions with fluorescent 8-heteroaryl-2′-deoxyguanosine derivatives that light-up upon thrombin binding.

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 First Step Towards Larger DNA-Based Assemblies of Fluorescent Silver Nanoclusters: Template Design and Detailed Characterization of Optical Properties

Nanomaterials ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 613 ◽  
Author(s):  
Liam E. Yourston ◽  
Alexander Y. Lushnikov ◽  
Oleg A. Shevchenko ◽  
Kirill A. Afonin ◽  
Alexey V. Krasnoslobodtsev
Keyword(s):  
Optical Properties ◽  
Dna Sequences ◽  
Silver Nanoclusters ◽  
Conformational Heterogeneity ◽  
Individual Element ◽  
Double Stranded Dna ◽  
Close Proximity ◽  
Template Design ◽  
Fluorescent Nanomaterials

Besides being a passive carrier of genetic information, DNA can also serve as an architecture template for the synthesis of novel fluorescent nanomaterials that are arranged in a highly organized network of functional entities such as fluorescent silver nanoclusters (AgNCs). Only a few atoms in size, the properties of AgNCs can be tuned using a variety of templating DNA sequences, overhangs, and neighboring duplex regions. In this study, we explore the properties of AgNCs manufactured on a short DNA sequence—an individual element designed for a construction of a larger DNA-based functional assembly. The effects of close proximity of the double-stranded DNA, the directionality of templating single-stranded sequence, and conformational heterogeneity of the template are presented. We observe differences between designs containing the same AgNC templating sequence—twelve consecutive cytosines, (dC)12. AgNCs synthesized on a single “basic” templating element, (dC)12, emit in “red”. The addition of double-stranded DNA core, required for the larger assemblies, changes optical properties of the silver nanoclusters by adding a new population of clusters emitting in “green”. A new population of “blue” emitting clusters forms only when ssDNA templating sequence is placed on the 5′ end of the double-stranded core. We also compare properties of silver nanoclusters, which were incorporated into a dimeric structure—a first step towards a larger assembly.

A Ratiometric Fluorescent DNA Radar Based on Contrary Response of DNA/Silver Nanoclusters and G-Quadruplex/Crystal Violet

2019 ◽  
Vol 11 (28) ◽  
pp. 25066-25073 ◽  
Author(s):  
Shuang Wang ◽  
Shasha Lu ◽  
Jiahui Zhao ◽  
Xiurong Yang
Keyword(s):  
Crystal Violet ◽  
Silver Nanoclusters ◽  
G Quadruplex

FRET-based Ratiometric MicroRNA Detection with G-quadruplex-stabilized Silver Nanoclusters

2017 ◽  
Vol 75 (11) ◽  
pp. 1103 ◽  
Author(s):  
Ruoyun Lin ◽  
Yang Chen ◽  
Guangyu Tao ◽  
Xiaojing Pei ◽  
Feng Liu ◽  
...  
Keyword(s):  
Silver Nanoclusters ◽  
Microrna Detection ◽  
G Quadruplex

Optical Properties of Silver Nanoclusters Synthesized in Surface-Grafted Polyacrylic Acid at Different Grafting Densities

2019 ◽  
Vol 126 (2) ◽  
pp. 150-153
Author(s):  
A. A. Gorbachev ◽  
N. I. Sushko ◽  
P. P. Pershukevich ◽  
O. N. Tretinnikov
Keyword(s):  
Optical Properties ◽  
Polyacrylic Acid ◽  
Silver Nanoclusters

scholarly journals Control of synthesis and optical properties of DNA templated silver nanoclusters by varying DNA length and sequence

RSC Advances ◽  
2011 ◽  
Vol 1 (5) ◽  
pp. 802 ◽  
Author(s):  
Guo-Yu Lan ◽  
Wei-Yu Chen ◽  
Huan-Tsung Chang
Keyword(s):  
Optical Properties ◽  
Silver Nanoclusters
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