Internal motions in ribonucleic acid duplexes as determined by electron spin resonance with site-specifically spin-labeled uridines

Kao, Shih Chung; Polnaszek, Carl F.; Toppin, Charles R.; Bobst, Albert M.

doi:10.1021/bi00293a017

Cited by 28 publications

(47 citation statements)

References 30 publications

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“…Site-specific covalent spin-labeling methods for nucleic acids have been carried out in some selected tRNAs containing minor bases in positions known from sequencing (Bobst, 1979). Direct attachment of a spin-labeled probe to DNA has been accomplished using both enzymatic and chemical syntheses (Bobst et al, 1984;Kao & Bobst, 1985;Pauly et al, 1987;Spaltenstein et al, 1989;Kirchner et al, 1990). It is clear from these studies that the length and structure of the tether which connects the nitroxide reporter group to the DNA have a profound influence on the EPR spectra obtained.…”

mentioning

confidence: 99%

Spin-Labeled Psoralen Probes for the Study of DNA Dynamics

Hp¹,

Dy²,

Ng³

et al. 1995

Biochemistry

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Six nitroxide spin-labeled psoralen derivatives have been synthesized and evaluated as probes for structural and dynamic studies. Sequence specific photoaddition of these derivatives to DNA oligonucleotides resulted in site-specifically cross-linked and spin-labeled oligomers. Comparison of the general line shape features of the observed electron paramagnetic resonance (EPR) spectra of several duplexes ranging in size from 8 to 46 base pairs with simulated EPR spectra indicate that the nitroxide spin-label probe reports the global tumbling motion of the oligomers. While there is no apparent large amplitude motion of the psoralen other than the overall tumbling of the DNA on the time scales investigated, there are indications of bending and other residual motions. The (A)BC excinuclease DNA repair system detects structural or dynamic features of the DNA that distinguish between damaged and undamaged DNA and are independent of the intrinsic structure of the lesion. NMR studies have shown that psoralencross-linked DNA has altered backbone dynamics and conformational populations in the immediate vicinity Psoralen-damaged DNA serves as an excellent substrate for the study of structural and dynamic motifs that DNA repair enzyme systems may recognize. Psoralens are photoreagents which form a well-characterized set of covalent nucleic acid adducts through photochemical addition ( Figure 1) (Straub et al., 1981; Kanne et al., 1982a,b). The primary reaction is cyclobutane ring formation between the 5,6 double bond of thymidine in DNA and either the 4',5' or 3,4 double bonds of the psoralen. Reaction at the 4'3' double bond creates a furanside monoadduct (MAf),' which can react further at a site with opposed and adjacent pyrimidines to create an interstrand cross-link (XL). The XL is a rigid unit formed by the psoralen and the opposite and adjacent pyrimidine bases, linking the two strands together. Reaction at the 3,4 double bond of the psoralen first creates a pyroneside monoadduct (MAP), which cannot form an interstrand cross-link.Psoralen-DNA monoadducts and cross-links are recognized and removed by the excision repair system in both

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mentioning

confidence: 99%

Spin-Labeled Psoralen Probes for the Study of DNA Dynamics

Hp¹,

Dy²,

Ng³

et al. 1995

Biochemistry

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“…Two SLE-based simulation approaches have been developed in studies of nitroxides attached to bases within DNA duplexes (25,97). The Bobst group developed a base disk model, in which the spin-labeled base is considered an axially symmetric diffusing system (25,29).…”

Section: Spectral Simulations In the Slow-motionmentioning

confidence: 99%

“…The Bobst group developed a base disk model, in which the spin-labeled base is considered an axially symmetric diffusing system (25,29). The principle motion is characterized by two correlation times: τ ‖ describes rotational diffusion about the principle axis as defined by the average position of the bonds that connect the base to the nitroxide, and τ ⊥ describes the motion about the axis perpendicular to the tether bond.…”

Section: Spectral Simulations In the Slow-motionmentioning

confidence: 99%

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Site-directed Spin Labeling Studies on Nucleic Acid Structure and Dynamics

Sowa¹,

Qin²

2008

Progress in Nucleic Acid Research and Molecular Biology

104

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Site-directed spin labeling (SDSL) uses electron paramagnetic resonance (EPR) spectroscopy to monitor the behavior of a stable nitroxide radical attached at specific locations within a macromolecule such as protein, DNA, or RNA. Parameters obtained from EPR measurements, such as internitroxide distances and descriptions of the rotational motion of a nitroxide, provide unique information on features near the labeling site. With recent advances in solid-phase synthesis of nucleic acids and developments in EPR methodologies, particularly pulsed EPR technologies, SDSL has been increasingly used to study the structure and dynamics of DNA and RNA at the level of the individual nucleotides. This chapter summarizes the current SDSL studies on nucleic acids, with discussions focusing on literature from the last decade.

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“…However, it is difficult to introduce a covalently bound site-specific EPR label into nucleic acids by chemical or enzymatic means. Direct attachment of a spin-labeled probe to DNA has been accomplished using both enzymatic and chemical syntheses (Bobst et al, 1984;Kao and Bobst, 1985;Kirchner et al, 1990;Spaltenstein et al, 1989). It is clear from these studies that the length and structure of the tether which connects the nitroxide reporter group to the DNA has a profound influence on the EPR spectra obtained.…”

mentioning

confidence: 99%

The application of psoralens to the study of DNA structure, function and dynamics

Spielmann

1991

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Internal motions in ribonucleic acid duplexes as determined by electron spin resonance with site-specifically spin-labeled uridines

Cited by 28 publications

References 30 publications

Spin-Labeled Psoralen Probes for the Study of DNA Dynamics

Spin-Labeled Psoralen Probes for the Study of DNA Dynamics

Site-directed Spin Labeling Studies on Nucleic Acid Structure and Dynamics

The application of psoralens to the study of DNA structure, function and dynamics

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