The Role of Mg(II) in DNA Cleavage Site Recognition in Group II Intron Ribozymes

Skilandat, Miriam; Sigel, Roland K. O.

doi:10.1074/jbc.m113.542381

Cited by 13 publications

(13 citation statements)

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“…S2). Out of a total of four sequences, two are derived from the group IIB intron Sc.ai5g and have been previously investigated by NMR 38,39 and smFRET 41,42 (d3 0 EBS1* IBS1*, PDB entries 2m23 and 2m24; d3 0 EBS1* dIBS1*, PDB entry 2m1v). The other set of cyanine labeled oligonucleotides (hereafter termed sCy3/sCy5-DNA or sCy3/sCy5-RNA respectively) has been designed to hybridize to a regulatory RNA located in the 5 0 -untranslated region of the btuB gene from E. coli.…”

Section: Magnesium(ii) Mediates Rna-dye Interactionsmentioning

confidence: 99%

“…S2). 39,42 surface decouple the global correlation time t r,global from the local wobbling-in-cone, the stacked dye population can provide valuable information on the rotational diffusion of the host molecule.…”

Section: Bioconjugation Interferes With Photoisomerizationmentioning

confidence: 99%

“…The structures of d3 0 EBS1* IBS1* (RNA/RNA) and d3 0 EBS1* dIBS1* (RNA/DNA) were previously solved by NMR 38,39 while the other RNAs (19/44 nt) were constructed using RNAComposer 40 on the basis of a secondary structure prediction with Mfold. 38 Sulfonated carbocyanine fluorophores (sCy3/sCy5) were attached terminally via a C6 amino linker using PyMOL (Schro ¨dinger LLC).…”

Section: Lifetime Quantum Yields and Dynamic Anisotropymentioning

confidence: 99%

“…Error bars are estimated from triplicates of the sCy3-DNA titration (b) van der Waals surface of d3 0 EBS1* (PDB: 2m24) including the tetraU overhang color coded with the electrostatic surface potential (ESP, calculated with APBS62,63 ). The putative location of the Mg 2+ ion is indicated by a violet sphere and is based on the ESP and previously recorded NMR chemical shifts38,42 between G4ÁC26 and A6ÁU24 (nucleotide labeling according to ESI, † Fig.S2) 39,42.…”

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confidence: 99%

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An atomistic view on carbocyanine photophysics in the realm of RNA

Steffen

Sigel

Börner

2016

Phys. Chem. Chem. Phys.

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Carbocyanine dyes have a long-standing tradition in fluorescence imaging and spectroscopy, due to their photostability and large spectral separation between individual dye species. Herein, we explore the versatility of cyanine dyes to probe the dynamics of nucleic acids and we report on the interrelation of fluorophores, RNA, and metal ions, namely K and Mg. Photophysical parameters including the fluorescence lifetime, quantum yield and dynamic anisotropy are monitored as a function of the nucleic acid composition, conformation, and metal ion abundance. Occasional excursions to a non-fluorescent cis-state hint at the remarkable sensitivity of carbocyanines to their local environment. Comparison of time-correlated single photon experiments with all-atom molecular dynamics simulations demonstrate that the propensity of photoisomerization is dictated by sterical constraints imposed on the fluorophore. Structural features in the vicinity of the dye play a crucial role in RNA recognition and have far-reaching implications on the mobility of the fluorescent probe. An atomic level description of the mutual interactions will ultimately benefit the quantitative interpretation of single-molecule FRET measurements on large RNA systems.

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Section: Magnesium(ii) Mediates Rna-dye Interactionsmentioning

confidence: 99%

Section: Bioconjugation Interferes With Photoisomerizationmentioning

confidence: 99%

Section: Lifetime Quantum Yields and Dynamic Anisotropymentioning

confidence: 99%

mentioning

confidence: 99%

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An atomistic view on carbocyanine photophysics in the realm of RNA

Steffen

Sigel

Börner

2016

Phys. Chem. Chem. Phys.

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“…Furthermore, non-Watson-Crick base-pairing (wobble, Hoogsteen) can shift pK a s toward neutrality. 10 Unlike proteins, RNAs rely largely on metal cofactors 14,15 or general acid-base chemistry to achieve catalysis. 16 The hepatitis delta virus (HBV) ribozyme, 17 for example, has a catalytically essential cytosine whose pK a is shifted from the normal value of 4.1 in cytidine monophosphate to 6.4 in the active site of the HDV ribozyme.…”

Section: Pk a Perturbation Depending On Microenvironmentmentioning

confidence: 99%

Properties and reactivity of nucleic acids relevant to epigenomics, transcriptomics, and therapeutics

2016

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Developments in epigenomics, toxicology, and therapeutic nucleic acids all rely on a precise understanding of nucleic acid properties and chemical reactivity. In this review we discuss the properties and chemical reactivity of each nucleobase and attempt to provide some general principles for nucleic acid targeting or engineering. For adenine-thymine and guaninecytosine base pairs, we review recent quantum chemical estimates of their Watson-Crick interaction energy, - stacking energies, as well as the nuclear quantum effects on tautomerism. Reactions that target nucleobases have been crucial in the development of new sequencing technologies and we believe further developments in nucleic acid chemistry will be required to deconstruct the enormously complex transcriptome.

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