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

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.

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Spectroscopic Characterization of Mitochondrial G-Quadruplexes

International Journal of Molecular Sciences ◽

10.3390/ijms23020925 ◽

2022 ◽

Vol 23 (2) ◽

pp. 925

Author(s):

Sara Illodo ◽

Cibrán Pérez-González ◽

Ramiro Barcia ◽

Flor Rodríguez-Prieto ◽

Wajih Al-Soufi ◽

...

Keyword(s):

Crucial Role ◽

Spectroscopic Characterization ◽

Rna Sequences ◽

Conserved Sequence ◽

Dna And Rna ◽

Sodium Cations ◽

Topology Changes ◽

Spectroscopy Studies ◽

Rna Transcript

Guanine quadruplexes (G4s) are highly polymorphic four-stranded structures formed within guanine-rich DNA and RNA sequences that play a crucial role in biological processes. The recent discovery of the first G4 structures within mitochondrial DNA has led to a small revolution in the field. In particular, the G-rich conserved sequence block II (CSB II) can form different types of G4s that are thought to play a crucial role in replication. In this study, we decipher the most relevant G4 structures that can be formed within CSB II: RNA G4 at the RNA transcript, DNA G4 within the non-transcribed strand and DNA:RNA hybrid between the RNA transcript and the non-transcribed strand. We show that the more abundant, but unexplored, G6AG7 (37%) and G6AG8 (35%) sequences in CSB II yield more stable G4s than the less profuse G5AG7 sequence. Moreover, the existence of a guanine located 1 bp upstream promotes G4 formation. In all cases, parallel G4s are formed, but their topology changes from a less ordered to a highly ordered G4 when adding small amounts of potassium or sodium cations. Circular dichroism was used due to discriminate different conformations and topologies of nucleic acids and was complemented with gel electrophoresis and fluorescence spectroscopy studies.

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Physical mapping and characterization of the mitochondrial DNA and RNA sequences from mit- mutants defective in cytochrome oxidase peptide 1 (OXI 3)

MGG Molecular & General Genetics ◽

10.1007/bf00268576 ◽

1979 ◽

Vol 170 (1) ◽

pp. 1-9 ◽

Cited By ~ 21

Author(s):

Richard Morimoto ◽

Alfred Lewin ◽

Murray Rabinowitz

Keyword(s):

Mitochondrial Dna ◽

Cytochrome Oxidase ◽

Physical Mapping ◽

Rna Sequences ◽

Dna And Rna

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

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100140130 ◽

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.

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New ultrastructural findings about Borrelia burgdorferi by cryofixation, negative staining, thin sectioning and scanning techniques

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100160467 ◽

1990 ◽

Vol 48 (3) ◽

pp. 582-583

Author(s):

S. F. Hayes ◽

M. D. Corwin ◽

T. G. Schwan ◽

D. W. Dorward ◽

W. Burgdorfer

Keyword(s):

Lyme Disease ◽

Borrelia Burgdorferi ◽

Structural Characterization ◽

Negative Staining ◽

Low Speed ◽

Thin Sectioning ◽

Ultrastructural Findings

Characterization of Borrelia burgdorferi strains by means of negative staining EM has become an integral part of many studies related to the biology of the Lyme disease organism. However, relying solely upon negative staining to compare new isolates with prototype B31 or other borreliae is often unsatisfactory. To obtain more satisfactory results, we have relied upon a correlative approach encompassing a variety EM techniques, i.e., scanning for topographical features and cryotomy, negative staining and thin sectioning to provide a more complete structural characterization of B. burgdorferi.For characterization, isolates of B. burgdorferi were cultured in BSK II media from which they were removed by low speed centrifugation. The sedimented borrelia were carefully resuspended in stabilizing buffer so as to preserve their features for scanning and negative staining. Alternatively, others were prepared for conventional thin sectioning and for cryotomy using modified procedures. For thin sectioning, the fixative described by Ito, et al.

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