ChemInform Abstract: Developments in the Chemical Synthesis of Naturally Occurring DNA and RNA Sequences with Normal and Unusual Linkages.

ChemInform ◽  
1987 ◽  
Vol 18 (36) ◽  
Author(s):  
K. K. OGILVIE ◽  
M. J. DAMHA ◽  
N. USMAN ◽  
R. T. PON
Keyword(s):  
Chemical Synthesis ◽  
Rna Sequences ◽  
Dna And Rna ◽  
Naturally Occurring

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.

Tracking DNA and RNA Sequences at High Resolution

2013 ◽  
pp. 343-366 ◽  
Author(s):  
Dušan Cmarko ◽  
Anna Ligasová ◽  
Karel Koberna
Keyword(s):  
High Resolution ◽  
Rna Sequences ◽  
Dna And Rna

scholarly journals Same fold, different properties: polarizable molecular dynamics simulations of telomeric and TERRA G-quadruplexes

2019 ◽  
Vol 48 (2) ◽  
pp. 561-575 ◽  
Author(s):  
Justin A Lemkul
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dipole Moments ◽  
Sequence Motifs ◽  
Telomeric Dna ◽  
Rna Sequences ◽  
Dna And Rna ◽  
Induced Dipole ◽  
Dynamics Simulations

Abstract DNA and RNA sequences rich in guanine can fold into noncanonical structures called G-quadruplexes (GQs), which exhibit a common stem structure of Hoogsteen hydrogen-bonded guanine tetrads and diverse loop structures. GQ sequence motifs are overrepresented in promoters, origins of replication, telomeres, and untranslated regions in mRNA, suggesting roles in modulating gene expression and preserving genomic integrity. Given these roles and unique aspects of different structures, GQs are attractive targets for drug design, but greater insight into GQ folding pathways and the interactions stabilizing them is required. Here, we performed molecular dynamics simulations to study two bimolecular GQs, a telomeric DNA GQ and the analogous telomeric repeat-containing RNA (TERRA) GQ. We applied the Drude polarizable force field, which we show outperforms the additive CHARMM36 force field in both ion retention and maintenance of the GQ folds. The polarizable simulations reveal that the GQs bind bulk K+ ions differently, and that the TERRA GQ accumulates more K+ ions, suggesting different ion interactions stabilize these structures. Nucleobase dipole moments vary as a function of position and also contribute to ion binding. Finally, we show that the TERRA GQ is more sensitive than the telomeric DNA GQ to water-mediated modulation of ion-induced dipole-dipole interactions.

scholarly journals Using small samples to estimate neutral component size and robustness in the genotype–phenotype map of RNA secondary structure

2020 ◽  
Vol 17 (166) ◽  
pp. 20190784 ◽  
Author(s):  
Marcel Weiß ◽  
Sebastian E. Ahnert
Keyword(s):  
Secondary Structure ◽  
Rna Secondary Structure ◽  
Point Mutations ◽  
Local Environment ◽  
Small Samples ◽  
Sequence Length ◽  
Rna Sequences ◽  
Component Size ◽  
Naturally Occurring ◽  
Non Coding Rna

In genotype–phenotype (GP) maps, the genotypes that map to the same phenotype are usually not randomly distributed across the space of genotypes, but instead are predominantly connected through one-point mutations, forming network components that are commonly referred to as neutral components (NCs). Because of their impact on evolutionary processes, the characteristics of these NCs, like their size or robustness, have been studied extensively. Here, we introduce a framework that allows the estimation of NC size and robustness in the GP map of RNA secondary structure. The advantage of this framework is that it only requires small samples of genotypes and their local environment, which also allows experimental realizations. We verify our framework by applying it to the exhaustively analysable GP map of RNA sequence length L = 15, and benchmark it against an existing method by applying it to longer, naturally occurring functional non-coding RNA sequences. Although it is specific to the RNA secondary structure GP map in the first place, our framework can probably be transferred and adapted to other sequence-to-structure GP maps.

scholarly journals Structural characterization of DNA and RNA sequences recognized by the gene 5 protein of bacteriophage fd

1999 ◽  
Vol 339 (3) ◽  
pp. 525-531 ◽  
Author(s):  
Antony W. OLIVER ◽  
G. Geoff KNEALE
Keyword(s):  
Dna Sequence ◽  
Rna Structure ◽  
Gel Filtration ◽  
Rna Sequences ◽  
Rna Translation ◽  
Translational Repressor ◽  
Dna And Rna ◽  
Gene 5 Protein ◽  
Na Ions

The single-stranded DNA sequence d(GT5G4CT4C) occurs close to the origin of replication within the intergenic region of the viral strand of bacteriophage fd. The RNA analogue of this sequence r(GU5G4CU4C) forms part of the untranslated leader sequence of the gene 2 mRNA and is specifically bound by the fd gene 5 protein in its role as a translational repressor. The structure of these sequences is likely to have an important role in the control of both DNA replication and RNA translation in the phage. We show that this 16 nt sequence, in both a DNA and an RNA context, can exist in a structured and unstructured form as determined by high-resolution gel filtration and non-denaturing gel electrophoresis. The CD spectrum of the structured form is characteristic of parallel guanine tetraplexes. The structured form of the DNA sequence melts at approx. 47 °C in the presence of Na+ ions but the structure is stabilized up to 75 °C in the presence of K+ ions. The RNA structure is more stable than the equivalent DNA structure (melting temperature approx. 62 °C), and its stability is further enhanced in the presence of K+ ions. Two of the central guanine residues are fully protected from cleavage as determined by dimethyl sulphate protection experiments, whereas methylation interference studies show that methylation of any of the four central guanine residues inhibits structure formation. Our results demonstrate that the structured form of the nucleic acid is mediated through the formation of a guanine-tetraplex core region, in RNA this might be further stabilized by the presence of weaker uracil quartets.

DNA and RNA induced enantioselectivity in chemical synthesis

2007 ◽  
Vol 3 (2) ◽  
pp. 126-135 ◽  
Author(s):  
Gerard Roelfes
Keyword(s):  
Chemical Synthesis ◽  
Dna And Rna

scholarly journals Detection of viral DNA and RNA by in situ hybridization.

1986 ◽  
Vol 34 (1) ◽  
pp. 33-38 ◽  
Author(s):  
J K McDougall ◽  
D Myerson ◽  
A M Beckmann
Keyword(s):  
Dna Sequences ◽  
Viral Dna ◽  
Rna Sequences ◽  
Hpv Dna ◽  
Dna And Rna ◽  
Common Warts ◽  
Anogenital Region ◽  
Simplex Virus ◽  
Human Viruses

Using cloned restriction endonuclease fragments of Herpes simplex virus (HSV), human papillomavirus (HPV), and cytomegalovirus (CMV) DNA as probes, viral DNA and RNA sequences have been detected in human tissues. The probes were labeled either with a radioactive isotope, for subsequent detection by autoradiography, or with biotin. This latter technique has been successfully used to visualize HPV DNA in tissues that have been fixed in formalin and embedded in paraffin, and is therefore of value in retrospective studies of histological specimens. HPV DNA was detected under non-stringent conditions (Tm = -42 degrees C) with heterologous probes in plantar and common warts, laryngeal papillomas, and anogenital condylomas. The specific type of HPV was established using stringent hybridization conditions (Tm = - 17 degrees C). Results from these and from malignant tissues show the distribution and localization of HSV and HPV RNA and DNA sequences in malignancies of squamous cell origin in the anogenital region. Both HSV and HPV DNA sequences have occasionally been detected in the same tumor, providing a further impetus to test the hypothesis that an initiator-promoter relationship might involve these common human viruses in the development of some tumors.

scholarly journals Structure and synthesis of naturally occurring anhydrovitamin A2

1979 ◽  
Vol 177 (3) ◽  
pp. 791-799 ◽  
Author(s):  
A B Barua ◽  
K Verma ◽  
S R Das
Keyword(s):  
Chemical Synthesis ◽  
Freshwater Fish ◽  
Mass Spectra ◽  
Chemical Conversion ◽  
Naturally Occurring

The structure of naturally occurring anhydrovitamin A2 was elucidated as 3-hydroxyanhydroretinol from study of its u.v.–visible, i.r., n.m.r. and mass spectra. The structure has been confirmed by a chemical synthesis. Saccobranchus fossils, a freshwater fish, can convert 3-hydroxyretinol into 3-hydroxyanhydroretinol, which in turn is converted into-3-dehydroretinol. Chemical conversion of 3-hydroxyretinol into 3-dehydroretinol was also carried out.

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