ArticleNucleic acids research2008
Rigid spin-labeled nucleoside C: a nonperturbing EPR probe of nucleic acid conformation.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Rational Design of a Cu(II) Spin Label Improves the Sensitivity of Distance Measurements.The journal of physical chemistry letters · 2025Article
- Caught in the Middle: A Rigid DNA Label That Provides an Incisive Picture of DNA Conformational Flexibility in Protein-DNA Complexes.Journal of the American Chemical Society · 2025Article
- Investigating the Conformational Diversity of the TMR-3 Aptamer.Journal of the American Chemical Society · 2025Article
- Spin-Labeled Riboswitch Synthesized from a Protected TPA Phosphoramidite Building Block.Chemistry (Weinheim an der Bergstrasse, Germany) · 2022Article
- Paramagnetic Chemical Probes for Studying Biological Macromolecules.Chemical reviews · 2022Review
- Advanced preparation of fragment libraries enabled by oligonucleotide-modified 2',3'-dideoxynucleotides.Communications chemistry · 2022Article
- Orientation and dynamics of CuPhysical chemistry chemical physics : PCCP · 2020Article
- Cu2+-based distance measurements by pulsed EPR provide distance constraints for DNA backbone conformations in solution.Nucleic acids research · 2020Article
- Phosphoramidite building blocks with protected nitroxides for the synthesis of spin-labeled DNA and RNA.Beilstein journal of organic chemistry · 2018Article
- TEMPO-derived spin labels linked to the nucleobases adenine and cytosine for probing local structural perturbations in DNA by EPR spectroscopy.Beilstein journal of organic chemistry · 2015Article
- A fully enzymatic method for site-directed spin labeling of long RNA.Nucleic acids research · 2014Article
- A novel paramagnetic relaxation enhancement tag for nucleic acids: a tool to study structure and dynamics of RNA.ACS chemical biology · 2013Article
- mtsslSuite:Molecular physics · 2013Article
- Protein-induced changes in DNA structure and dynamics observed with noncovalent site-directed spin labeling and PELDOR.Nucleic acids research · 2013Article
- Site-directed spin-labeling of nucleotides and the use of in-cell EPR to determine long-range distances in a biologically relevant environment.Nature protocols · 2013Article
- Structural changes of an abasic site in duplex DNA affect noncovalent binding of the spin label ç.Nucleic acids research · 2012Article
- Functionalized polystyrene supports for solid-phase synthesis of glycyl-, alanyl-, and isoleucyl-RNA conjugates as hydrolysis-resistant mimics of peptidyl-tRNAs.Bioorganic & medicinal chemistry · 2011Article
- Crystal structure of a DNA containing the planar, phenoxazine-derived bi-functional spectroscopic probe C.Nucleic acids research · 2011Article
- Site-specific DNA structural and dynamic features revealed by nucleotide-independent nitroxide probes.Biochemistry · 2009Article
- Folding of the cocaine aptamer studied by EPR and fluorescence spectroscopies using the bifunctional spectroscopic probe Ç.Nucleic acids research · 2009Article
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Authors and funding
5 authors.
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Abstract
Rigid spin-labeled nucleoside C, an analog of deoxycytidine that base-pairs with deoxyguanosine, was incorporated into DNA oligomers by chemical synthesis. Thermal denaturation experiments and circular dichroism (CD) measurements showed that C has a negligible effect on DNA duplex stability and conformation. Nucleoside C was incorporated into several positions within single-stranded DNA oligomers that can adopt two hairpin conformations of similar energy, each of which contains a four-base loop. The relative mobility of nucleotides in the alternating C/G hairpin loops, 5'-d(GCGC) and 5'-d(CGCG), was determined by electron paramagnetic resonance (EPR) spectroscopy. The most mobile nucleotide in the loop is the second one from the 5'-end, followed by the third, first and fourth nucleotides, consistent with previous NMR studies of DNA hairpin loops of different sequences. The EPR hairpin data were also corroborated by fluorescence spectroscopy using oligomers containing reduced C (C(f)), which is fluorescent. Furthermore, EPR spectra of duplex DNAs that contained C at the end of the helix showed features that indicated dipolar coupling between two spins. These data are consistent with end-to-end duplex stacking in solution, which was only observed when G was paired to C, but not when C was paired with A, C or T.
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