Dependence of purine 8C-H exchange on nucleic acid conformation and base-pairing geometry: A dynamic probe of DNA and RNA secondary structures

Biopolymers ◽  
1985 ◽  
Vol 24 (4) ◽  
pp. 667-682 ◽  
Author(s):  
James M. Benevides ◽  
George J. Thomas
Keyword(s):  
Nucleic Acid ◽  
Secondary Structures ◽  
Base Pairing ◽  
Rna Secondary Structures ◽  
Dna And Rna ◽  
Nucleic Acid Conformation

scholarly journals Polyamines and Their Role in Virus Infection

2017 ◽  
Vol 81 (4) ◽  
Author(s):  
Bryan C. Mounce ◽  
Michelle E. Olsen ◽  
Marco Vignuzzi ◽  
John H. Connor
Keyword(s):  
Protein Synthesis ◽  
Nucleic Acid ◽  
Mammalian Cells ◽  
Cellular Proliferation ◽  
Polyamine Synthesis ◽  
Host Interactions ◽  
Dna And Rna ◽  
Rna Polymerization ◽  
Nucleic Acid Conformation

SUMMARY Polyamines are small, abundant, aliphatic molecules present in all mammalian cells. Within the context of the cell, they play a myriad of roles, from modulating nucleic acid conformation to promoting cellular proliferation and signaling. In addition, polyamines have emerged as important molecules in virus-host interactions. Many viruses have been shown to require polyamines for one or more aspects of their replication cycle, including DNA and RNA polymerization, nucleic acid packaging, and protein synthesis. Understanding the role of polyamines has become easier with the application of small-molecule inhibitors of polyamine synthesis and the use of interferon-induced regulators of polyamines. Here we review the diverse mechanisms in which viruses require polyamines and investigate blocking polyamine synthesis as a potential broad-spectrum antiviral approach.

scholarly journals Direct inference of base-pairing probabilities with neural networks improves RNA secondary structure prediction with pseudoknots

2018 ◽  
Author(s):  
Manato Akiyama ◽  
Yasubumi Sakakibara ◽  
Kengo Sato
Keyword(s):  
Neural Networks ◽  
Secondary Structure ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Secondary Structures ◽  
Support Vector ◽  
Base Pairing ◽  
Rna Secondary Structures ◽  
Decoding Algorithms ◽  
The Neural Networks

AbstractMotivationExisting approaches for predicting RNA secondary structures depend on howto decompose a secondary structure into substructures, so-called the architecture, to define their parameter space. However, the architecture has not been sufficiently investigated especially for pseudoknotted secondary structures.ResultsIn this paper, we propose a novel algorithm to directly infer base-pairing probabilities with neural networks that does not depend on the architecture of RNA secondary structures, followed by performing the maximum expected accuracy (MEA) based decoding algorithms; Nussinov-style decoding for pseudoknot-free structures, and IPknot-style decoding for pseudoknotted structures. To train the neural networks connected to each base-pair, we adopt a max-margin framework, called structured support vector machines (SSVM), as the output layer. Our benchmarks for predicting RNA secondary structures with and without pseudoknots show that our algorithm achieves the best prediction accuracy compared with existing methods.AvailabilityThe source code is available at https://github.com/keio-bioinformatics/neuralfold/[email protected]

scholarly journals STUDIES ON NUCLEIC ACID METACHROMASY

1965 ◽  
Vol 27 (2) ◽  
pp. 313-326 ◽  
Author(s):  
Michael E. Lamm ◽  
Lillian Childers ◽  
Merrill K. Wolf
Keyword(s):  
Nucleic Acid ◽  
Toluidine Blue ◽  
Binding Sites ◽  
Heat Denaturation ◽  
Color Contrast ◽  
Fluid Absorption ◽  
Tissue Sections ◽  
Dna And Rna ◽  
Nucleic Acid Conformation ◽  
Intense Color

The stacking coefficients (K's) of nucleic acids have been thought to influence the color contrast between DNA and RNA in tissue sections stained with metachromatic dyes. This idea was tested by titrating toluidine blue (TB) and acridine orange (AO) in solution against DNA and RNA, native or treated with formaldehyde, acrolein, or Carnoy's fluid. Absorption spectra at varying polymer-dye ratios were used to compute K values by the methods of Bradley and colleagues. Results with both dyes fit Bradley's stacking equations. Fixatives did not block dye-binding sites but markedly altered K values. K of DNA was low, unaffected by aldehyde fixative, increased by Carnoy's fluid or heat denaturation. K of RNA was higher than that of DNA and was increased greatly by formaldehyde, almost as much by acrolein, considerably less by Carnoy's fluid. Aldehyde effects were partially reversed upon removal of aldehyde by dialysis. These observations accord with known effects of aldehydes and denaturation upon nucleic acid conformation. Differences between K's of DNA and RNA were greater after aldehyde treatment than after Carnoy's, and were greater with AO than with TB. This is generally consistent with the magnitude of the color contrasts observed in tissues. Additional factors must contribute to the intense color contrast observed in acrolein-fixed tissues stained with TB.

scholarly journals 5-Fluoro pyrimidines: labels to probe DNA and RNA secondary structures by 1D 19 F NMR spectroscopy

2009 ◽  
Vol 37 (22) ◽  
pp. 7728-7740 ◽  
Author(s):  
Barbara Puffer ◽  
Christoph Kreutz ◽  
Ulrike Rieder ◽  
Marc-Olivier Ebert ◽  
Robert Konrat ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Secondary Structures ◽  
Rna Secondary Structures ◽  
Dna And Rna ◽  
19 F Nmr

scholarly journals Evolutionary analyses of base-pairing interactions in DNA and RNA secondary structures

2018 ◽  
Author(s):  
Michael Golden ◽  
Ben Murrell ◽  
Oliver G. Pybus ◽  
Darren Martin ◽  
Jotun Hein
Keyword(s):  
Secondary Structure ◽  
Secondary Structures ◽  
Sequence Evolution ◽  
Base Pairing ◽  
Sequence Alignments ◽  
Dna Viruses ◽  
Dna And Rna ◽  
Subtype B ◽  
Dna Secondary Structures ◽  
Hiv 1

AbstractPairs of nucleotides within functional nucleic acid secondary structures often display evidence of coevolution that is consistent with the maintenance of base-pairing. Here we introduce a sequence evolution model, MESSI, that infers coevolution associated with base-paired sites in DNA or RNA sequence alignments. MESSI can estimate coevolution whilst accounting for an unknown secondary structure. MESSI can also use GPU parallelism to increase computational speed. We used MESSI to infer coevolution associated with GC, AU (AT in DNA), GU (GT in DNA) pairs in non-coding RNA alignments, and in single-stranded RNA and DNA virus alignments. Estimates of GU pair coevolution were found to be higher at base-paired sites in single-stranded RNA viruses and non-coding RNAs than estimates of GT pair coevolution in single-stranded DNA viruses, suggesting that GT pairs do not stabilise DNA secondary structures to the same extent that GU pairs do in RNA. Additionally, MESSI estimates the degrees of coevolution at individual base-paired sites in an alignment. These estimates were computed for a SHAPE-MaP-determined HIV-1 NL4-3 RNA secondary structure and two corresponding alignments. We found that estimates of coevolution were more strongly correlated with experimentally-determined SHAPE-MaP pairing scores than three non-evolutionary measures of base-pairing covariation. To assist researchers in prioritising substructures with potential functionality, MESSI automatically ranks substructures by degrees of coevolution at base-paired sites within them. Such a ranking was created for an HIV-1 subtype B alignment, revealing an excess of top-ranking substructures that have been previously identified as having structure-related functional importance, amongst several uncharacterised top-ranking substructures.

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 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 Comparative Sequence Analysis and Patterns of Covariation in RNA Secondary Structures

Genetics ◽  
2000 ◽  
Vol 154 (2) ◽  
pp. 909-921 ◽  
Author(s):  
John Parsch ◽  
John M Braverman ◽  
Wolfgang Stephan
Keyword(s):  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Rnase P ◽  
Secondary Structures ◽  
Comparative Sequence Analysis ◽  
Small Subunit ◽  
Physical Parameters ◽  
Small Subunit Rrna ◽  
Base Pairing ◽  
Compensatory Evolution

Abstract A novel method of RNA secondary structure prediction based on a comparison of nucleotide sequences is described. This method correctly predicts nearly all evolutionarily conserved secondary structures of five different RNAs: tRNA, 5S rRNA, bacterial ribonuclease P (RNase P) RNA, eukaryotic small subunit rRNA, and the 3′ untranslated region (UTR) of the Drosophila bicoid (bcd) mRNA. Furthermore, covariations occurring in the helices of these conserved RNA structures are analyzed. Two physical parameters are found to be important determinants of the evolution of compensatory mutations: the length of a helix and the distance between base-pairing nucleotides. For the helices of bcd 3′ UTR mRNA and RNase P RNA, a positive correlation between the rate of compensatory evolution and helix length is found. The analysis of Drosophila bcd 3′ UTR mRNA further revealed that the rate of compensatory evolution decreases with the physical distance between base-pairing residues. This result is in qualitative agreement with Kimura's model of compensatory fitness interactions, which assumes that mutations occurring in RNA helices are individually deleterious but become neutral in appropriate combinations.

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