scholarly journals Recognition of Chelerythrine to Human Telomeric DNA and RNA G-quadruplexes

2014 ◽  
Vol 4 (1) ◽  
Author(s):  
Li-Ping Bai ◽  
Masaki Hagihara ◽  
Kazuhiko Nakatani ◽  
Zhi-Hong Jiang
Keyword(s):  
Telomeric Dna ◽  
Dna And Rna

scholarly journals Mass spectrometric studies on effects of counter ions of TMPyP4 on binding to human telomeric DNA and RNA G-quadruplexes

2014 ◽  
Vol 406 (22) ◽  
pp. 5455-5463 ◽  
Author(s):  
Li-Ping Bai ◽  
Jie Liu ◽  
Li Han ◽  
Hing-Man Ho ◽  
Renxiao Wang ◽  
...  
Keyword(s):  
Mass Spectrometric ◽  
Telomeric Dna ◽  
Dna And Rna ◽  
Counter Ions

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 Probing Human Telomeric DNA and RNA Topology and Ligand Binding in a Cellular Model by Using Responsive Fluorescent Nucleoside Probes

ChemBioChem ◽  
2017 ◽  
Vol 18 (16) ◽  
pp. 1604-1615 ◽  
Author(s):  
Sudeshna Manna ◽  
Cornelia H. Panse ◽  
Vyankat A. Sontakke ◽  
Sarangamath Sangamesh ◽  
Seergazhi G. Srivatsan
Keyword(s):  
Ligand Binding ◽  
Cellular Model ◽  
Telomeric Dna ◽  
Dna And Rna ◽  
Fluorescent Nucleoside

scholarly journals DNA and RNA Telomeric G-Quadruplexes: What Topology Features Can be Inferred from Ion Mobility Mass Spectrometry?

2019 ◽  
Author(s):  
Valentina D’Atri ◽  
Valerie Gabelica
Keyword(s):  
Mass Spectrometry ◽  
Gas Phase ◽  
Ion Mobility Spectrometry ◽  
Ion Mobility ◽  
Native Mass Spectrometry ◽  
Cation Binding ◽  
Telomeric Dna ◽  
Dna And Rna ◽  
G Quadruplex ◽  
Multiple Structures

Maintenance of the telomeres is key to chromosome integrity and cell proliferation. The G-quadruplex structures formed by telomeric DNA and RNA (TTAGGG and UUAGGG repeats, respectively) are key to this process. However, because these sequences are particularly polymorphic, solving high-resolution structures is not always possible, and there is a need for new methodologies to characterize the multiple structures coexisting in solution. In this context, we evaluated whether ion mobility spectrometry coupled to native mass spectrometry could help separate and assign the G-quadruplex topologies. We explored the circular dichroism spectra, multimer formation, cation binding, and ion mobility spectra of several 4-repeat and 8-repeat telomeric DNA and RNA sequences, both in NH<sub>4</sub><sup>+</sup> and in K<sup>+</sup>. In 1 mM K<sup>+</sup> and 100 mM trimethylammonium acetate, all RNAs fold intramolecularly (no multimer). In 8-repeat sequences, the subunits are not independent: in DNA the first subunit disfavors the folding of the second one, whereas in RNA the two subunits fold cooperatively via cation-mediated stacking. Ion mobility spectrometry shows that gas-phase structures keep a memory of the solution ones, but not identical. At the native charge states, the loops can rearrange in a variety of ways (unless they are constrained by pre-formed hydrogen bonds), thereby wrapping the core and masking the strand arrangements. Our study highlights that, to progress towards structural assignment from IM-MS experiments, deeper understanding of the solution-to-gas-phase rearrangement mechanisms is warranted. <br>

scholarly journals DNA and RNA Telomeric G-Quadruplexes: What Topology Features Can be Inferred from Ion Mobility Mass Spectrometry?

2019 ◽  
Author(s):  
Valentina D’Atri ◽  
Valerie Gabelica
Keyword(s):  
Mass Spectrometry ◽  
Gas Phase ◽  
Ion Mobility Spectrometry ◽  
Ion Mobility ◽  
Native Mass Spectrometry ◽  
Cation Binding ◽  
Telomeric Dna ◽  
Dna And Rna ◽  
G Quadruplex ◽  
Multiple Structures

Maintenance of the telomeres is key to chromosome integrity and cell proliferation. The G-quadruplex structures formed by telomeric DNA and RNA (TTAGGG and UUAGGG repeats, respectively) are key to this process. However, because these sequences are particularly polymorphic, solving high-resolution structures is not always possible, and there is a need for new methodologies to characterize the multiple structures coexisting in solution. In this context, we evaluated whether ion mobility spectrometry coupled to native mass spectrometry could help separate and assign the G-quadruplex topologies. We explored the circular dichroism spectra, multimer formation, cation binding, and ion mobility spectra of several 4-repeat and 8-repeat telomeric DNA and RNA sequences, both in NH<sub>4</sub><sup>+</sup> and in K<sup>+</sup>. In 1 mM K<sup>+</sup> and 100 mM trimethylammonium acetate, all RNAs fold intramolecularly (no multimer). In 8-repeat sequences, the subunits are not independent: in DNA the first subunit disfavors the folding of the second one, whereas in RNA the two subunits fold cooperatively via cation-mediated stacking. Ion mobility spectrometry shows that gas-phase structures keep a memory of the solution ones, but not identical. At the native charge states, the loops can rearrange in a variety of ways (unless they are constrained by pre-formed hydrogen bonds), thereby wrapping the core and masking the strand arrangements. Our study highlights that, to progress towards structural assignment from IM-MS experiments, deeper understanding of the solution-to-gas-phase rearrangement mechanisms is warranted. <br>

scholarly journals Oligonucleotide Models of Telomeric DNA and RNA Form a Hybrid G-quadruplex Structure as a Potential Component of Telomeres

2012 ◽  
Vol 287 (50) ◽  
pp. 41787-41796 ◽  
Author(s):  
Yan Xu ◽  
Takumi Ishizuka ◽  
Jie Yang ◽  
Kenichiro Ito ◽  
Hitoshi Katada ◽  
...  
Keyword(s):  
Telomeric Dna ◽  
Quadruplex Structure ◽  
Dna And Rna ◽  
G Quadruplex ◽  
Potential Component

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.

Scanning tunneling microscopy (STM) of DNA and RNA

1989 ◽  
Vol 47 ◽  
pp. 34-35
Author(s):  
Patricia G. Arscott ◽  
Gil Lee ◽  
Victor A. Bloomfield ◽  
D. Fennell Evans
Keyword(s):  
Molecular Structures ◽  
Inorganic Materials ◽  
Resolving Power ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Form And Function ◽  
Dna And Rna ◽  
Calf Thymus ◽  
And Function ◽  
The Relationship

STM is one of the most promising techniques available for visualizing the fine details of biomolecular structure. It has been used to map the surface topography of inorganic materials in atomic dimensions, and thus has the resolving power not only to determine the conformation of small molecules but to distinguish site-specific features within a molecule. That level of detail is of critical importance in understanding the relationship between form and function in biological systems. The size, shape, and accessibility of molecular structures can be determined much more accurately by STM than by electron microscopy since no staining, shadowing or labeling with heavy metals is required, and there is no exposure to damaging radiation by electrons. Crystallography and most other physical techniques do not give information about individual molecules.We have obtained striking images of DNA and RNA, using calf thymus DNA and two synthetic polynucleotides, poly(dG-me5dC)·poly(dG-me5dC) and poly(rA)·poly(rU).

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