scholarly journals Facile synthesis and fundamental properties of an N-methylguanidine-bridged nucleic acid (GuNA[NMe])

2018 ◽  
Vol 16 (35) ◽  
pp. 6531-6536 ◽  
Author(s):  
Naohiro Horie ◽  
Shinji Kumagai ◽  
Yutaro Kotobuki ◽  
Takao Yamaguchi ◽  
Satoshi Obika
Keyword(s):  
Nucleic Acid ◽  
Modified Oligonucleotides ◽  
Facile Synthesis ◽  
Single Stranded Dna ◽  
Enzymatic Stability ◽  
Fundamental Properties ◽  
Dna And Rna

The GuNA[NMe]-modified oligonucleotides exhibited excellent duplex-forming ability towards the complementary single-stranded DNA and RNA, and showed robust enzymatic stability.

Synthesis and properties of GuNA purine/pyrimidine nucleosides and oligonucleotides

2020 ◽  
Vol 18 (46) ◽  
pp. 9461-9472
Author(s):  
Shinji Kumagai ◽  
Hiroaki Sawamoto ◽  
Tomo Takegawa-Araki ◽  
Yuuki Arai ◽  
Shuhei Yamakoshi ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Modified Oligonucleotides ◽  
Robust Method ◽  
Facile Synthesis ◽  
Pyrimidine Nucleosides ◽  
Thymine Adenine ◽  
Purine Pyrimidine

Facile synthesis of GuNA (guanidine-bridged nucleic acid) phosphoramidites bearing thymine, adenine, guanine, and 5-methylcytosine nucleobases and a robust method for the preparation of GuNA-modified oligonucleotides are described.

Highly stable triple helix formation by homopyrimidine (l)-acyclic threoninol nucleic acids with single stranded DNA and RNA

2015 ◽  
Vol 13 (8) ◽  
pp. 2366-2374 ◽  
Author(s):  
Vipin Kumar ◽  
Venkitasamy Kesavan ◽  
Kurt V. Gothelf
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Triple Helix ◽  
Helical Structures ◽  
Single Stranded Dna ◽  
Dna And Rna ◽  
Helix Formation ◽  
Triple Helix Formation

Homopyrimidine acyclic (l)-threoninol nucleic acid (aTNA) was synthesized and found to form highly stable (l)-aTNA–DNA–(l)-aTNA and (l)-aTNA–RNA–(l)-aTNA triple helical structures.

scholarly journals Hydroxyapatite-Mediated Separation of Double-Stranded DNA, Single-Stranded DNA, and RNA Genomes from Natural Viral Assemblages

2010 ◽  
Vol 76 (15) ◽  
pp. 5039-5045 ◽  
Author(s):  
Cynthia Andrews-Pfannkoch ◽  
Douglas W. Fadrosh ◽  
Joyce Thorpe ◽  
Shannon J. Williamson
Keyword(s):  
Nucleic Acid ◽  
Significant Similarity ◽  
Metagenomic Sequence ◽  
Single Stranded Dna ◽  
Dna And Rna ◽  
Double Stranded Dna ◽  
Marine Viruses ◽  
Viral Communities ◽  
Environmental Sequences ◽  
Dsdna Viruses

ABSTRACT Metagenomics can be used to determine the diversity of complex, often unculturable, viral communities with various nucleic acid compositions. Here, we report the use of hydroxyapatite chromatography to efficiently fractionate double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), dsRNA, and ssRNA genomes from known bacteriophages. Linker-amplified shotgun libraries were constructed to generate sequencing reads from each hydroxyapatite fraction. Greater than 90% of the reads displayed significant similarity to the expected genomes at the nucleotide level. These methods were applied to marine viruses collected from the Chesapeake Bay and the Dry Tortugas National Park. Isolated nucleic acids were fractionated using hydroxyapatite chromatography followed by linker-amplified shotgun library construction and sequencing. Taxonomic analysis demonstrated that the majority of environmental sequences, regardless of their source nucleic acid, were most similar to dsDNA viruses, reflecting the bias of viral metagenomic sequence databases.

High-resolution nucleic acid sequence mapping via in situ hybridization at the Electron Microscope level

1995 ◽  
Vol 53 ◽  
pp. 752-753
Author(s):  
B.A. Hamkalo ◽  
S. Narayanswami ◽  
A.P. Kausch
Keyword(s):  
Nucleic Acid ◽  
Interphase Nucleus ◽  
Genome Mapping ◽  
Precise Location ◽  
Electron Microscope Level ◽  
Rna Sequences ◽  
Fundamental Interest ◽  
Whole Cells ◽  
Dna And Rna

The availability of nonradioactive methods to label nucleic acids an the resultant rapid and greater sensitivity of detection has catapulted the technique of in situ hybridization to become the method of choice to locate of specific DNA and RNA sequences on chromosomes and in whole cells in cytological preparations in many areas of biology. It is being applied to problems of fundamental interest to basic cell and molecular biologists such as the organization of the interphase nucleus in the context of putative functional domains; it is making major contributions to genome mapping efforts; and it is being applied to the analysis of clinical specimens. Although fluorescence detection of nucleic acid hybrids is routinely used, certain questions require greater resolution. For example, very closely linked sequences may not be separable using fluorescence; the precise location of sequences with respect to chromosome structures may be below the resolution of light microscopy(LM); and the relative positions of sequences on very small chromosomes may not be feasible.

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 Sulfur Modification in Natural RNA and Therapeutic Oligonucleotides

2021 ◽  
Author(s):  
Ya Ying Zheng ◽  
Ying Wu ◽  
Thomas Begley ◽  
Jia Sheng
Keyword(s):  
Nucleic Acid ◽  
Dna And Rna ◽  
Sulfur Modification ◽  
Oxygen Atoms

Sulfur modifications have been discovered on both DNA and RNA. Sulfur substitution of oxygen atoms at nucleobase or backbone locations in the nucleic acid framework led to a wide variety...

scholarly journals A mini DNA-RNA hybrid origami nanobrick

2021 ◽  
Author(s):  
Lifeng Zhou ◽  
Arun Richard Chandrasekaran ◽  
Mengwen Yan ◽  
Vibhav A. Valsangkar ◽  
Jeremy I. Feldblyum ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Dna Origami ◽  
Complex Geometries ◽  
Single Stranded Dna ◽  
Dna Scaffold

DNA origami is typically used to fold a long single-stranded DNA scaffold into nanostructures with complex geometries using many short DNA staple strands. Integration of RNA into nucleic acid nanostructures...

scholarly journals Urea Facilitates the Translocation of Single-Stranded DNA and RNA Through the α-Hemolysin Nanopore

2010 ◽  
Vol 98 (9) ◽  
pp. 1856-1863 ◽  
Author(s):  
Deanpen Japrung ◽  
Marsiyana Henricus ◽  
Qiuhong Li ◽  
Giovanni Maglia ◽  
Hagan Bayley
Keyword(s):  
Single Stranded Dna ◽  
Dna And Rna

scholarly journals Recent developments in nucleic acid based techniques for use in rumen manipulation

2009 ◽  
Vol 38 (spe) ◽  
pp. 341-351 ◽  
Author(s):  
Christopher McSweeney ◽  
Seungha Kang ◽  
Emma Gagen ◽  
Carl Davis ◽  
Mark Morrison ◽  
...  
Keyword(s):  
Microbial Community ◽  
Nucleic Acid ◽  
Microbial Communities ◽  
Marker Gene ◽  
Molecular Ecology ◽  
Functional Gene ◽  
Rumen Microorganisms ◽  
Dna And Rna ◽  
Conventional Culture ◽  
Reference Strains

Nucleic acid-based techniques which can be used to characterise complex microbial communities without incubation are now being employed regularly in ruminant nutrition studies. Conventional culture-based methods for enumerating rumen microorganisms (bacteria, archaea, protozoa, and fungi) have been superseded and are now used mainly to obtain pure isolates of novel organisms and reference strains that are required for the development and validation of the nucleic acid approaches. These reference strains are also essential for physiological studies of the lifestyle of the organisms as well as sources of genomic DNA and RNA that can be analysed for functional gene activity. The foundation of the molecular ecology techniques is 16S/18S rDNA sequence analysis which has provided a phylogenetically based classification scheme for enumeration and identification of microbial community members. The use of this marker gene in assays involving the use of single nucleic acid probes or primer sets is rapidly evolving to high throughput approaches such as microarray analysis and new generation sequencing technologies. While these analyses are very informative for determining the composition of the microbial community and monitoring changes in population size, they can only infer function based on these observations. The focus of nucleic acid research is now shifting to the functional analysis of the ecosystem which involves the measurement of functional genes and their expression in the predominant or specific members of the rumen microbial community. Functional gene studies are less developed than 16S rDNA-based analysis of community structure. Also for gene expression studies there are inherent problems involved in extracting high quality RNA from digesta, and priming cDNA synthesis from bacterial mRNA. This paper reviews nucleic acid based molecular methods which have recently been developed for studying the structure and function of rumen microbial communities.

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