scholarly journals Conformation of G-quadruplex Controlled by Click Reaction

Molecules ◽  
2020 ◽  
Vol 25 (18) ◽  
pp. 4339
Author(s):  
Chao-Da Xiao ◽  
Zhi-Yong He ◽  
Chuan-Xin Guo ◽  
Xiang-Chun Shen ◽  
Yan Xu
Keyword(s):  
Click Chemistry ◽  
Dna Sequence ◽  
Click Reaction ◽  
Secondary Structures ◽  
Biological Processes ◽  
Biological Importance ◽  
Intense Fluorescence ◽  
G Quadruplex ◽  
First Time

G-quadruplexes are non-canonical four stranded secondary structures possessing great biological importance. Controlling G-quadruplex conformation for further regulating biological processes is both exciting and challenging. In this study, we described a method for regulating G-quadruplex conformation by click chemistry for the first time. 8-ethynyl-2′-deoxyguanosine was synthesized and incorporated into a 12-nt telomere DNA sequence. Such a sequence, at first, formed mixed parallel/anti-parallel G-quadruplexes, while it changed to anti-parallel after reaction with azidobenzene. Meanwhile, the click reaction can give the sequence intense fluorescence.

scholarly journals The Cellular Functions and Molecular Mechanisms of G-Quadruplex Unwinding Helicases in Humans

2021 ◽  
Vol 8 ◽  
Author(s):  
Yang Liu ◽  
Xinting Zhu ◽  
Kejia Wang ◽  
Bo Zhang ◽  
Shuyi Qiu
Keyword(s):  
Molecular Mechanisms ◽  
Secondary Structures ◽  
Biological Processes ◽  
Cellular Functions ◽  
General Introduction ◽  
Rna Sequences ◽  
Study Methods ◽  
G Quadruplex ◽  
And Function

G-quadruplexes (G4s) are stable non-canonical secondary structures formed by G-rich DNA or RNA sequences. They play various regulatory roles in many biological processes. It is commonly agreed that G4 unwinding helicases play key roles in G4 metabolism and function, and these processes are closely related to physiological and pathological processes. In recent years, more and more functional and mechanistic details of G4 helicases have been discovered; therefore, it is necessary to carefully sort out the current research efforts. Here, we provide a systematic summary of G4 unwinding helicases from the perspective of functions and molecular mechanisms. First, we provide a general introduction about helicases and G4s. Next, we comprehensively summarize G4 unfolding helicases in humans and their proposed cellular functions. Then, we review their study methods and molecular mechanisms. Finally, we share our perspective on further prospects. We believe this review will provide opportunities for researchers to reach the frontiers in the functions and molecular mechanisms of human G4 unwinding helicases.

scholarly journals Structural relation matching: an algorithm to identify structural patterns into RNAs and their interactions

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Michela Quadrini
Keyword(s):  
Hydrogen Bonding ◽  
Secondary Structure ◽  
Nucleotide Sequence ◽  
Thermus Thermophilus ◽  
Three Dimensional ◽  
Secondary Structures ◽  
Structural Effect ◽  
Biological Processes ◽  
Structural Pattern ◽  
Rna Molecules

Abstract RNA molecules play crucial roles in various biological processes. Their three-dimensional configurations determine the functions and, in turn, influences the interaction with other molecules. RNAs and their interaction structures, the so-called RNA–RNA interactions, can be abstracted in terms of secondary structures, i.e., a list of the nucleotide bases paired by hydrogen bonding within its nucleotide sequence. Each secondary structure, in turn, can be abstracted into cores and shadows. Both are determined by collapsing nucleotides and arcs properly. We formalize all of these abstractions as arc diagrams, whose arcs determine loops. A secondary structure, represented by an arc diagram, is pseudoknot-free if its arc diagram does not present any crossing among arcs otherwise, it is said pseudoknotted. In this study, we face the problem of identifying a given structural pattern into secondary structures or the associated cores or shadow of both RNAs and RNA–RNA interactions, characterized by arbitrary pseudoknots. These abstractions are mapped into a matrix, whose elements represent the relations among loops. Therefore, we face the problem of taking advantage of matrices and submatrices. The algorithms, implemented in Python, work in polynomial time. We test our approach on a set of 16S ribosomal RNAs with inhibitors of Thermus thermophilus, and we quantify the structural effect of the inhibitors.

scholarly journals Subtle structural alterations in G-quadruplex DNA regulate site specificity of fluorescence light-up probes

2020 ◽  
Vol 48 (3) ◽  
pp. 1108-1119 ◽  
Author(s):  
Rajendra Kumar ◽  
Karam Chand ◽  
Sudipta Bhowmik ◽  
Rabindra Nath Das ◽  
Snehasish Bhattacharjee ◽  
...  
Keyword(s):  
Rational Design ◽  
Dna Structure ◽  
Biological Processes ◽  
Chemical Research ◽  
Quadruplex Dna ◽  
Dna Structures ◽  
Future Studies ◽  
G4 Dna ◽  
G Quadruplex ◽  
Fluorescence Light

Abstract G-quadruplex (G4) DNA structures are linked to key biological processes and human diseases. Small molecules that target specific G4 DNA structures and signal their presence would therefore be of great value as chemical research tools with potential to further advance towards diagnostic and therapeutic developments. However, the development of these types of specific compounds remain as a great challenge. In here, we have developed a compound with ability to specifically signal a certain c-MYC G4 DNA structure through a fluorescence light-up mechanism. Despite the compound's two binding sites on the G4 DNA structure, only one of them result in the fluorescence light-up effect. This G-tetrad selectivity proved to originate from a difference in flexibility that affected the binding affinity and tilt the compound out of the planar conformation required for the fluorescence light-up mechanism. The intertwined relation between the presented factors is likely the reason for the lack of examples using rational design to develop compounds with turn-on emission that specifically target certain G4 DNA structures. However, this study shows that it is indeed possible to develop such compounds and present insights into the molecular details of specific G4 DNA recognition and signaling to advance future studies of G4 biology.

scholarly journals Construction of a cross-layer linked G-octamer via conformational control: a stable G-quadruplex in H-bond competitive solvents

2019 ◽  
Vol 10 (15) ◽  
pp. 4192-4199 ◽  
Author(s):  
Ying He ◽  
Yanbin Zhang ◽  
Lukasz Wojtas ◽  
Novruz G. Akhmedov ◽  
David Thai ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Cross Layer ◽  
Conformational Control ◽  
G Quadruplex ◽  
Improved Stability ◽  
First Time

A discrete and well-defined G-octamer system has been established through conformational design of monomers. The crystal structures of G-octamers were obtained for the first time. The covalent linked G-quadruplex exhibited significantly improved stability in both methanol and DMSO.

Lab in a tube: a fast-assembled colorimetric sensor for highly sensitive detection of oligonucleotides based on a hybridization chain reaction

RSC Advances ◽  
2015 ◽  
Vol 5 (55) ◽  
pp. 44714-44721 ◽  
Author(s):  
Siqi Zhang ◽  
Kun Wang ◽  
Zhenyu Li ◽  
Zhongmin Feng ◽  
Ting Sun
Keyword(s):  
Complex Formation ◽  
Dna Sequence ◽  
Self Assembly ◽  
The Self ◽  
Hybridization Chain Reaction ◽  
Chain Reaction ◽  
Highly Sensitive ◽  
G Quadruplex ◽  
Colored Product ◽  
Highly Sensitive Detection

Upon adding THBV, the self-assembly of THBV with H1 allows the rest of the DNA sequence of H1 to accelerate H1–H2 complex formation. The G-quadruplex at the end of the H1–H2 complex could catalyze TMB into a colored product.

G4-PROTAC: Targeted degradation of a G-quadruplex binding protein

2021 ◽  
Author(s):  
Kiran Patil ◽  
Danielle Chin ◽  
Hui Ling Seah ◽  
Qi Shi ◽  
Kah Wai Lim ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Binding Protein ◽  
Interaction Networks ◽  
Biological Processes ◽  
G Quadruplex

G-quadruplex (G4)-binding proteins regulate important biological processes, but their interaction networks are poorly understood. We report the first use of G4 as warhead of a proteolysis-targeting chimera (G4-PROTAC) for targeted...

scholarly journals Sequences of the second internal transcribed spacer of ribosomal DNA for three species of Trichostrongylus (Nematoda: Trichostrongylidae) from sheep in Russia

2007 ◽  
Vol 44 (2) ◽  
pp. 43-46 ◽  
Author(s):  
D. Kuznetsov ◽  
N. Kuznetsova
Keyword(s):  
Dna Sequence ◽  
Intraspecific Variation ◽  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Moscow Region ◽  
Dna Sequence Data ◽  
Interspecific Differences ◽  
Second Internal Transcribed Spacer ◽  
First Time

AbstractFor the first time, DNA sequence data were obtained for three species of Trichostrongylus from Russia. Internal transcribed spacer (ITS-2) of ribosomal DNA was sequenced for T. axei, T. colubriformis and T. probolurus from sheep from the Moscow region. ITS-2 rDNA length was estimated as 238 nucleotides for T. colubriformis and T. probolurus and 237 nucleotides for T. axei. The G+C content of the ITS-2 sequences of T. colubriformis, T. axei and T. probolurus were 31 %, 32 % and 34 % respectively. The level of interspecific differences in ITS-2 of rDNA of T. axei, T. probolurus and T. colubriformis ranged from 3 to 4 %. The ITS-2 sequences from the Russian specimens were compared with those of T. axei, T. probolurus and T. colubriformis from Australia and Germany. Intraspecific variation ranged from 0 % in T. colubriformis to 3.0 % in T. axei.

scholarly journals Pif1 is essential for efficient replisome progression through lagging strand G-quadruplex DNA secondary structures

2018 ◽  
Vol 46 (22) ◽  
pp. 11847-11857 ◽  
Author(s):  
Danielle Dahan ◽  
Ioannis Tsirkas ◽  
Daniel Dovrat ◽  
Melanie A Sparks ◽  
Saurabh P Singh ◽  
...  
Keyword(s):  
Secondary Structures ◽  
Quadruplex Dna ◽  
G Quadruplex ◽  
Dna Secondary Structures ◽  
Lagging Strand

Fully biodegradable antibacterial hydrogels via thiol–ene “click” chemistry

2014 ◽  
Vol 5 (13) ◽  
pp. 4002-4008 ◽  
Author(s):  
Hong Du ◽  
Guangyu Zha ◽  
Lilong Gao ◽  
Huan Wang ◽  
Xiaodong Li ◽  
...  
Keyword(s):  
Ethylene Glycol ◽  
Click Chemistry ◽  
Click Reaction ◽  
Poly Ethylene Glycol ◽  
Physiological Conditions ◽  
Poly Ethylene

Novel biodegradable antimicrobial hydrogels, which are promising for use as biomaterials, were prepared facilely via a thiol–ene “click” reaction under human physiological conditions using multifunctional poly(ethylene glycol) (PEG) derivatives as precursors.

scholarly journals SYNTHESIS OF AN AZIDE–THIOL LINKER FOR HETEROGENEOUS POLYMER FUNCTIONALIZATION VIA THE “CLICK” REACTION

2018 ◽  
Vol 55 (1B) ◽  
pp. 152
Author(s):  
Thuy Thu Truong
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Click Reaction ◽  
Proton Nuclear Magnetic Resonance ◽  
Reaction Yield ◽  
Reaction Conditions ◽  
Click Reactions ◽  
Heterogeneous Polymer ◽  
Ft Ir ◽  
First Time ◽  
Layer Chromatography

In this study, the synthesis of a telechelic linker bearing both azide and thiol functional groups was described. The reaction conditions were investigated to optimize the reaction yield. The product was analyzed using thin layer chromatography (TLC) and proton nuclear magnetic resonance (1H NMR). The employment of the obtained azide–thiol linker in heterogeneous polymer “click” functionalization was demonstrated for the first time, which was monitored by an online FT–IR method. The obtained telechelic azide–thiol linker is envisioned to be useful chemical tools to link macromolecular chains via orthogonal click reactions.

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