Modified Nucleobases

2014 ◽  
pp. 209-243 ◽  
Author(s):  
Spiridoula Matsika
Keyword(s):  
Modified Nucleobases

scholarly journals Thermochemical and Structural Analysis of Tautomers of Sulfur and Selenium Modified RNA Nucleobases

2019 ◽  
Vol 2 (2) ◽  
pp. 47-48
Author(s):  
Megan Joy ◽  
Alex Brown ◽  
Arturo Mora Gomez ◽  
Maria Rossano-Tapia ◽  
Shyam Parshotam
Keyword(s):  
Ir Spectra ◽  
Structural Changes ◽  
Chemical Properties ◽  
Hydrogen Atoms ◽  
Relative Population ◽  
Geometry Analysis ◽  
Physical And Chemical ◽  
Modified Nucleobases ◽  
Relative Gibbs Free Energy ◽  
And Chemical Properties

Nucleobases (adenine, cytosine, guanine, and uracil), the four molecules that forms RNA, have been found to be useful in probing in the human body when modified because they can emit light. Non-modified nucleobases do not exhibit emissive properties and cannot be used as probes. Some of the modifications include the substitution of nitrogen atoms with sulfur and selenium, and the resulting modified nucleobases give place to the so-called tz- and ts- RNA alphabets, respectively. Therefore, the aim of this project was to provide insights about the viability, from a computational perspective, of using the modified nucleobases as probes, evaluating the differences in thermochemical, structural and emissive properties of the modified nucleobases with respect to the non-modified ones. Nucleobases can coexist with other modified nucleobases or tautomers, molecules that differ due to the change in position of hydrogen atoms in a molecule’s structure and as a result have different physical and chemical properties. The thermochemical properties evaluation mainly consisted in the computation of the relative Gibbs Free Energy (G), which is related to the fraction F, an index of the relative population among tautomers. This was done using Gaussian 09 software by performing geometry analysis and frequency computations on each one of the tautomers. By comparing the equilibrium fractions, it was determined that in both cases, tz- and ts- guanine and cytosine exist principally in the form of one of their tautomers (Cytosine 2 and Guanine 2) as in the case of the non-modified cases. After confirming which tz- and ts- tautomers were the ones with the largest probable population, infrared (IR) and ultraviolet-visible (UV-vis) spectra were obtained. The IR spectra of selenium and sulfur tautomers of guanine and cytosine indicated that the tautomers had peaks at similar frequencies with respect to each other, however, the intensities varied, implying slight structural changes between the tautomers. On the other hand, the UV-vis spectra showed a change in peak positions between the tautomers with sulfur and selenium, suggesting that the change between sulfur and selenium has an effect on the spectra by shifting the peaks from the original molecules’ λmax values. Their relative population fractions show that only the canonical forms of the modified nucleobases exist in a larger extent than the rest of their tautomer forms. In addition, the features in their UV-vis and IR spectra allow these tautomers to be differentiated from each other.

Semiconductive and Magnetic One-Dimensional Coordination Polymers of Cu(II) with Modified Nucleobases

2013 ◽  
Vol 52 (19) ◽  
pp. 11428-11437 ◽  
Author(s):  
Pilar Amo-Ochoa ◽  
Oscar Castillo ◽  
Carlos J. Gómez-García ◽  
Khaled Hassanein ◽  
Sandeep Verma ◽  
...  
Keyword(s):  
Coordination Polymers ◽  
One Dimensional ◽  
Modified Nucleobases

scholarly journals Directed Evolution of Aptamer Discovery Technologies

2021 ◽  
Author(s):  
Diana Wu ◽  
Chelsea Gordon ◽  
John Shin ◽  
Michael Eisenstein ◽  
Hyongsok Tom Soh
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Click Reaction ◽  
Clinical Diagnostics ◽  
High Quality ◽  
Affinity Reagents ◽  
Wide Range ◽  
Target Binding ◽  
Modified Nucleobases ◽  
Parallel Fashion

Although antibodies are a powerful tool for molecular biology and clinical diagnostics, there are many emerging applications for which nucleic acid-based aptamers can be advantageous. However, generating high-quality aptamers with sufficient affinity and specificity for biomedical applications is a challenging feat for most research laboratories. In this Account, we describe four techniques developed in our lab to accelerate the discovery of high quality aptamer reagents that can achieve robust binding even for challenging molecular targets. The first method is particle display, in which we convert solution-phase aptamers into aptamer particles that can be screened via fluorescence-activated cell sorting (FACS) to quantitatively isolate individual aptamer particles based on their affinity. This enables the efficient isolation of high-affinity aptamers in fewer selection rounds than conventional methods, thereby minimizing selection biases and reducing the emergence of artifacts in the final aptamer pool. We subsequently developed the multi-parametric particle display (MPPD) method, which employs two-color FACS to isolate aptamer particles based on both affinity and specificity, yielding aptamers that exhibit excellent target binding even in complex matrices like serum. The third method is a click chemistry-based particle display (click-PD) that enables the generation and high-throughput screening of non-nattural aptamers with a wide range of base modifications. We have shown that these base-modified aptamers can achieve robust affinity and specificity for targets that have proven challenging or inaccessible with natural nucleotide-based aptamer libraries. Lastly, we describe the non-natural aptamer array (N2A2) platform, in which a modified benchtop sequencing instrument is used to characterize base-modified aptamers in a massively parallel fashion, enabling the efficient identification of molecules with excellent affinity and specificity for their targets. This system first generates aptamer clusters on the flow-cell surface that incorporate alkyne-modified nucleobases, and then performs a click reaction to couple those nucleobases to an azide-modified chemical moiety. This yields a sequence-defined array of tens of millions of base-modified sequences, which can then be characterized in a high-throughput fashion. Collectively, we believe that these advancements are helping to make aptamer technology more accessible, efficient, and robust, thereby enabling the use of these affinity reagents for a wider range of molecular recognition and detection-based applications.

Asymmetric and Symmetric Dicopper(II) Paddle-Wheel Units with Modified Nucleobases

2015 ◽  
Vol 15 (11) ◽  
pp. 5485-5494 ◽  
Author(s):  
Khaled Hassanein ◽  
Oscar Castillo ◽  
Carlos J. Gómez-García ◽  
Félix Zamora ◽  
Pilar Amo-Ochoa
Keyword(s):  
Paddle Wheel ◽  
Modified Nucleobases

scholarly journals Reading canonical and modified nucleobases in 16S ribosomal RNA using nanopore native RNA sequencing

PLoS ONE ◽  
2019 ◽  
Vol 14 (5) ◽  
pp. e0216709 ◽  
Author(s):  
Andrew M. Smith ◽  
Miten Jain ◽  
Logan Mulroney ◽  
Daniel R. Garalde ◽  
Mark Akeson
Keyword(s):  
Rna Sequencing ◽  
Ribosomal Rna ◽  
16S Ribosomal Rna ◽  
Modified Nucleobases

Supramolecular Porous Network Formed by Molecular Recognition between Chemically Modified Nucleobases Guanine and Cytosine

2010 ◽  
Vol 122 (49) ◽  
pp. 9563-9567 ◽  
Author(s):  
Wei Xu ◽  
Jian-guo Wang ◽  
Mikkel F. Jacobsen ◽  
Manuela Mura ◽  
Miao Yu ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Porous Network ◽  
Chemically Modified ◽  
Modified Nucleobases

scholarly journals Diagnostic optical sequencing

2019 ◽  
Author(s):  
Lee E. Korshoj ◽  
Prashant Nagpal
Keyword(s):  
Single Molecule ◽  
Point Of Care ◽  
Cost Effective ◽  
Diagnostic Methods ◽  
Sequencing Platform ◽  
Molecular Variants ◽  
Cost Effective Method ◽  
Wide Range ◽  
Lactamase Gene ◽  
Modified Nucleobases

AbstractAdvances in precision medicine require high-throughput, inexpensive, point-of-care diagnostic methods with multi-omics capability for detecting a wide range of biomolecules and their molecular variants. Optical techniques have offered many promising advances towards such diagnostics. However, the inability to squeeze light with several hundred-nanometer wavelengths into angstrom-scale volume for single nucleotide measurements has hindered further progress. Recently, a block optical sequencing (BOS) method has been shown for determining relative nucleobase content in DNA k-mer blocks with Raman spectroscopy, and a block optical content scoring (BOCS) algorithm was developed for robust content-based genetic biomarker database searching. Here, we performed BOS measurements on positively-charged silver nanoparticles to achieve 93.3% accuracy for predicting nucleobase content in DNA k-mer blocks (where k=10), as well as measurements on RNA and chemically-modified nucleobases for extensions to transcriptomic and epigenetic studies. Our high-accuracy BOS measurements were then used with BOCS to correctly identify a β-lactamase gene from the MEGARes antibiotic resistance database and confirm the Pseudomonas aeruginosa pathogen of origin from <12 content measurements (<15% coverage) of the gene. These results prove the integration of BOS/BOCS as a diagnostic optical sequencing platform. With the versatile range of available plasmonic substrates offering simple data acquisition, varying resolution (single-molecule to ensemble), and multiplexing, this optical sequencing platform has potential as the rapid, cost-effective method needed for broad-spectrum biomarker detection.

scholarly journals Non-Canonical Helical Structure of Nucleic Acids Containing Base-Modified Nucleotides

2021 ◽  
Vol 22 (17) ◽  
pp. 9552
Author(s):  
Thananjeyan Balasubramaniyam ◽  
Kwnag-Im Oh ◽  
Ho-Seong Jin ◽  
Hye-Bin Ahn ◽  
Byeong-Seon Kim ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Genetic Diseases ◽  
Helical Structure ◽  
Biological Functions ◽  
Modified Nucleotides ◽  
Helical Structures ◽  
Chemically Modified ◽  
Research Fields ◽  
G Quadruplex ◽  
Modified Nucleobases

Chemically modified nucleobases are thought to be important for therapeutic purposes as well as diagnosing genetic diseases and have been widely involved in research fields such as molecular biology and biochemical studies. Many artificially modified nucleobases, such as methyl, halogen, and aryl modifications of purines at the C8 position and pyrimidines at the C5 position, are widely studied for their biological functions. DNA containing these modified nucleobases can form non-canonical helical structures such as Z-DNA, G-quadruplex, i-motif, and triplex. This review summarizes the synthesis of chemically modified nucleotides: (i) methylation, bromination, and arylation of purine at the C8 position and (ii) methylation, bromination, and arylation of pyrimidine at the C5 position. Additionally, we introduce the non-canonical structures of nucleic acids containing these modifications.

scholarly journals Higher order structures involving post transcriptionally modified nucleobases in RNA

RSC Advances ◽  
2017 ◽  
Vol 7 (57) ◽  
pp. 35694-35703 ◽  
Author(s):  
Preethi S. P. ◽  
Purshotam Sharma ◽  
Abhijit Mitra
Keyword(s):  
Quantum Chemical ◽  
Higher Order ◽  
Chemical Studies ◽  
Quantum Chemical Studies ◽  
Modified Nucleobases ◽  
Order Structures

Quantum chemical studies are carried out to understand the structures and stabilities of higher order structures involving post-transcriptionally modified nucleobases in RNA.

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