scholarly journals Non-Canonical Helical Structure of Nucleic Acids Containing Base-Modified Nucleotides

2021 ◽  
Vol 22 (17) ◽  
pp. 9552
Author(s):  
Thananjeyan Balasubramaniyam ◽  
Kwnag-Im Oh ◽  
Ho-Seong Jin ◽  
Hye-Bin Ahn ◽  
Byeong-Seon Kim ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Genetic Diseases ◽  
Helical Structure ◽  
Biological Functions ◽  
Modified Nucleotides ◽  
Helical Structures ◽  
Chemically Modified ◽  
Research Fields ◽  
G Quadruplex ◽  
Modified Nucleobases

Chemically modified nucleobases are thought to be important for therapeutic purposes as well as diagnosing genetic diseases and have been widely involved in research fields such as molecular biology and biochemical studies. Many artificially modified nucleobases, such as methyl, halogen, and aryl modifications of purines at the C8 position and pyrimidines at the C5 position, are widely studied for their biological functions. DNA containing these modified nucleobases can form non-canonical helical structures such as Z-DNA, G-quadruplex, i-motif, and triplex. This review summarizes the synthesis of chemically modified nucleotides: (i) methylation, bromination, and arylation of purine at the C8 position and (ii) methylation, bromination, and arylation of pyrimidine at the C5 position. Additionally, we introduce the non-canonical structures of nucleic acids containing these modifications.

Chemical-biology approaches to probe DNA and RNA G-quadruplex structures in the genome

2020 ◽  
Vol 56 (9) ◽  
pp. 1317-1324 ◽  
Author(s):  
Federica Raguseo ◽  
Souroprobho Chowdhury ◽  
Aisling Minard ◽  
Marco Di Antonio
Keyword(s):  
Nucleic Acids ◽  
Chemical Biology ◽  
Secondary Structures ◽  
Biological Functions ◽  
Physiological Conditions ◽  
Dna And Rna ◽  
G Quadruplex

G-quadruplexes are nucleic-acids secondary structures that can be formed under physiological conditions. In this review, we critically present the most relevant chemical-biology methods to probe the biological functions of G-quadruplex structures.

scholarly journals Transcription of 4′-thioDNA templates to natural RNA in vitro and in mammalian cells

2015 ◽  
Vol 51 (37) ◽  
pp. 7887-7890 ◽  
Author(s):  
Hideto Maruyama ◽  
Kazuhiro Furukawa ◽  
Hiroyuki Kamiya ◽  
Noriaki Minakawa ◽  
Akira Matsuda
Keyword(s):  
Nucleic Acids ◽  
Mammalian Cells ◽  
Genetic Material ◽  
Rna Polymerases ◽  
Chemically Modified ◽  
Biological Studies ◽  
Modified Nucleic Acids

Synthetic chemically modified nucleic acids, which are compatible with DNA/RNA polymerases, have great potential as a genetic material for synthetic biological studies.

scholarly journals Triazole-Modified Nucleic Acids for the Application in Bioorganic and Medicinal Chemistry

Biomedicines ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 628
Author(s):  
Dagmara Baraniak ◽  
Jerzy Boryski
Keyword(s):  
Nucleic Acids ◽  
State Of The Art ◽  
Modified Oligonucleotides ◽  
Synthetic Genes ◽  
Chemically Modified ◽  
Amide Linkage ◽  
Dna And Rna ◽  
Modified Dna ◽  
Modified Nucleic Acids ◽  
Non Coding Rnas

This review covers studies which exploit triazole-modified nucleic acids in the range of chemistry and biology to medicine. The 1,2,3-triazole unit, which is obtained via click chemistry approach, shows valuable and unique properties. For example, it does not occur in nature, constitutes an additional pharmacophore with attractive properties being resistant to hydrolysis and other reactions at physiological pH, exhibits biological activity (i.e., antibacterial, antitumor, and antiviral), and can be considered as a rigid mimetic of amide linkage. Herein, it is presented a whole area of useful artificial compounds, from the clickable monomers and dimers to modified oligonucleotides, in the field of nucleic acids sciences. Such modifications of internucleotide linkages are designed to increase the hybridization binding affinity toward native DNA or RNA, to enhance resistance to nucleases, and to improve ability to penetrate cell membranes. The insertion of an artificial backbone is used for understanding effects of chemically modified oligonucleotides, and their potential usefulness in therapeutic applications. We describe the state-of-the-art knowledge on their implications for synthetic genes and other large modified DNA and RNA constructs including non-coding RNAs.

scholarly journals Thermal Stability Changes in Telomeric G-Quadruplex Structures Due to N6-Methyladenine Modification

Epigenomes ◽  
2021 ◽  
Vol 5 (1) ◽  
pp. 5 ◽  
Author(s):  
Ryohei Wada ◽  
Wataru Yoshida
Keyword(s):  
Thermal Stability ◽  
Base Pair ◽  
Genomic Dna ◽  
Biological Functions ◽  
Duplex Structure ◽  
Stacking Interaction ◽  
Hybrid Type ◽  
G Quadruplex ◽  
Melting Analysis ◽  
Thermal Stability Of

N6-methyladenine modification (m6dA) has recently been identified in eukaryote genomic DNA. The methylation destabilizes the duplex structure when the adenine forms a Watson–Crick base pair, whereas the methylation on a terminal unpaired adenine stabilizes the duplex structure by increasing the stacking interaction. In this study, the effects of m6dA modification on the thermal stability of four distinct telomeric G-quadruplex (G4) structures were investigated. The m6dA-modified telomeric oligonucleotide d[AGGG(TTAGGG)3] that forms a basket-type G4 in Na+, d[(TTAGGG)4TT] that forms a hybrid-type G4 in K+ (Form-2), d[AAAGGG(TTAGGG)3AA] that forms a hybrid-type G4 in K+ (Form-1), and d[GGG(TTAGGG)3T] that forms a basket-type G4 with two G-tetrads in K+ (Form-3) were analyzed. Circular dichroism melting analysis demonstrated that (1) A7- and A19-methylation destabilized the basket-type G4 structure that formed in Na+, whereas A13-methylation stabilized the structure; (2) A15-methylation stabilized the Form-2 G4 structure; (3) A15- and A21-methylations stabilized the Form-1 G4 structure; and (4) A12-methylation stabilized the Form-3 G4 structure. These results suggest that m6dA modifications may affect the thermal stability of human telomeric G4 structures in regulating the biological functions.

scholarly journals Nucleic Acids Chemistry and Engineering: Special Issue on Nucleic Acid Conjugates for Biotechnological Applications

2021 ◽  
Vol 11 (8) ◽  
pp. 3594
Author(s):  
Tamaki Endoh ◽  
Eriks Rozners ◽  
Takashi Ohtsuki
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Genetic Information ◽  
Biotechnological Applications ◽  
Biological Functions ◽  
Primary Sequence ◽  
Special Issue

Nucleic acids not only store genetic information in their primary sequence but also exhibit biological functions through the formation of their unique structures [...]

Characterization of Heme–DNA Complexes Composed of Some Chemically Modified Hemes and Parallel G-Quadruplex DNAs

Biochemistry ◽  
2015 ◽  
Vol 54 (49) ◽  
pp. 7168-7177 ◽  
Author(s):  
Yasuhiko Yamamoto ◽  
Masashi Kinoshita ◽  
Yuya Katahira ◽  
Haruna Shimizu ◽  
Yue Di ◽  
...  
Keyword(s):  
Dna Complexes ◽  
Chemically Modified ◽  
G Quadruplex

scholarly journals Encapsulation and Ultrasound-Triggered Release of G-Quadruplex DNA in Multilayer Hydrogel Microcapsules

Polymers ◽  
2018 ◽  
Vol 10 (12) ◽  
pp. 1342 ◽  
Author(s):  
Aaron Alford ◽  
Brenna Tucker ◽  
Veronika Kozlovskaya ◽  
Jun Chen ◽  
Nirzari Gupta ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Defense Mechanisms ◽  
The Body ◽  
Stimuli Responsive ◽  
Triggered Release ◽  
Quadruplex Dna ◽  
Nucleic Acid Therapeutics ◽  
Wide Range ◽  
G Quadruplex ◽  
Hydrogel Capsules

Nucleic acid therapeutics have the potential to be the most effective disease treatment strategy due to their intrinsic precision and selectivity for coding highly specific biological processes. However, freely administered nucleic acids of any type are quickly destroyed or rendered inert by a host of defense mechanisms in the body. In this work, we address the challenge of using nucleic acids as drugs by preparing stimuli responsive poly(methacrylic acid)/poly(N-vinylpyrrolidone) (PMAA/PVPON)n multilayer hydrogel capsules loaded with ~7 kDa G-quadruplex DNA. The capsules are shown to release their DNA cargo on demand in response to both enzymatic and ultrasound (US)-triggered degradation. The unique structure adopted by the G-quadruplex is essential to its biological function and we show that the controlled release from the microcapsules preserves the basket conformation of the oligonucleotide used in our studies. We also show that the (PMAA/PVPON) multilayer hydrogel capsules can encapsulate and release ~450 kDa double stranded DNA. The encapsulation and release approaches for both oligonucleotides in multilayer hydrogel microcapsules developed here can be applied to create methodologies for new therapeutic strategies involving the controlled delivery of sensitive biomolecules. Our study provides a promising methodology for the design of effective carriers for DNA vaccines and medicines for a wide range of immunotherapies, cancer therapy and/or tissue regeneration therapies in the future.

scholarly journals Cockayne Syndrome B protein selectively interacts and resolves intermolecular DNA G-quadruplex structures

2021 ◽  
Author(s):  
Denise Liano ◽  
Marco Di Antonio
Keyword(s):  
Ribosomal Dna ◽  
Living Cells ◽  
Cockayne Syndrome ◽  
Biological Functions ◽  
Loss Of Function ◽  
Endogenous Protein ◽  
G Quadruplex ◽  
Dna Strands ◽  
Low Probability ◽  
Dna Strand

AbstractGuanine-rich DNA can fold into secondary structures known as G-quadruplexes (G4s). G4s can form from a single DNA-strand (intramolecular) or from multiple DNA-strands (intermolecular), but studies on their biological functions have been often limited to intramolecular G4s, owing to the low probability of intermolecular G4s to form within genomic DNA. Herein, we report that the endogenous protein Cockayne Syndrome B (CSB) binds with picomolar affinity to intermolecular G4s, whilst displaying negligible binding towards intramolecular structures. We also observed that CSB can selectively resolve intermolecular G4s in an ATP independent fashion. Our study demonstrates that intermolecular G4s formed within ribosomal DNA are natural substrates for CSB, strongly suggesting that these structures might be formed in the nucleolus of living cells. Given that CSB loss of function elicits premature ageing phenotypes, our findings indicate that the interaction between CSB and ribosomal DNA intermolecular G4s is essential to maintain cellular homeostasis.

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