Enzymatic sequence-specific spin labeling of a DNA fragment containing the recognition sequence of EcoRI endonuclease

Structure and dynamics of nucleic acids

In this chapter we describe the application of CW and pulsed EPR methods for the investigation of structural and dynamical properties of RNA and DNA molecules and their interaction with small molecules and proteins. Special emphasis will be given to recent applications of dipolar spectroscopy on nucleic acids.

Site-directed spin labeling studies on nucleic acid structure and dynamics

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.

Spin labeling of oligonucleotides with the nitroxide TPA and use of PELDOR, a pulse EPR method, to measure intramolecular distances

In this protocol, we describe the facile synthesis of the nitroxide spin-label 2,2,5,5-tetramethyl-pyrrolin-1-oxyl-3-acetylene (TPA) and then its coupling to DNA/RNA through Sonogashira cross-coupling during automated solid-phase synthesis. Subsequently, we explain how to perform distance measurements between two such spin-labels on RNA/DNA using the pulsed electron paramagnetic resonance method pulsed electron double resonance (PELDOR). This combination of methods can be used to study global structure elements of oligonucleotides in frozen solution at RNA/DNA amounts of approximately 10 nmol. We especially focus on the Sonogashira cross-coupling step, the advantages of the ACE chemistry together with the appropriate parameters for the RNA synthesizer and on the PELDOR data analysis. This procedure is applicable to RNA/DNA strands of up to approximately 80 bases in length and PELDOR yields reliably spin-spin distances up to approximately 6.5 nm. The synthesis of TPA takes approximately 5 days and spin labeling together with purification approximately 4 days. The PELDOR measurements usually take approximately 16 h and data analysis from an hour up to several days depending on the extent of analysis.

Long-range distance determinations in biomacromolecules by EPR spectroscopy

Electron paramagnetic resonance (EPR) spectroscopy provides a variety of tools to study structures and structural changes of large biomolecules or complexes thereof. In order to unravel secondary structure elements, domain arrangements or complex formation, continuous wave and pulsed EPR methods capable of measuring the magnetic dipole coupling between two unpaired electrons can be used to obtain long-range distance constraints on the nanometer scale. Such methods yield reliably and precisely distances of up to 80 A, can be applied to biomolecules in aqueous buffer solutions or membranes, and are not size limited. They can be applied either at cryogenic or physiological temperatures and down to amounts of a few nanomoles. Spin centers may be metal ions, metal clusters, cofactor radicals, amino acid radicals, or spin labels. In this review, we discuss the advantages and limitations of the different EPR spectroscopic methods, briefly describe their theoretical background, and summarize important biological applications. The main focus of this article will be on pulsed EPR methods like pulsed electron-electron double resonance (PELDOR) and their applications to spin-labeled biosystems.

Distance measurements on spin-labelled biomacromolecules by pulsed electron paramagnetic resonance

The biological function of protein, DNA, and RNA molecules often depends on relative movements of domains with dimensions of a few nanometers. This length scale can be accessed by distance measurements between spin labels if pulsed electron paramagnetic resonance (EPR) techniques such as electron-electron double resonance (ELDOR) and double-quantum EPR are used. The approach does not require crystalline samples and is well suited to biomacromolecules with an intrinsic flexibility as distributions of distances can be measured. Furthermore, oligomerization or complexation of biomacromolecules can also be studied, even if it is incomplete. The sensitivity of the technique and the reliability of the measured distance distribution depend on careful optimization of the experimental conditions and procedures for data analysis. Interpretation of spin-to-spin distance distributions in terms of the structure of the biomacromolecules furthermore requires a model for the conformational distribution of the spin labels.

Site-specific dynamics in DNA: experiments

This chapter reviews the dynamics information obtained from experimental magnetic resonance studies of site-specifically labeled duplex DNA. A previous review (43) discusses the dynamics of duplex DNA; it develops a theory that shows how magnetic resonance experiments are used to detect those dynamics. The methods for obtaining information about dynamics as well as a summary of what is now known about the site-specific dynamics of DNA are presented. This review contains two methods sections which present results using electron paramagnetic resonance and nuclear magnetic resonance active probes.

Overall and internal dynamics of DNA as monitored by five-atom-tethered spin labels

Electron paramagnetic resonance (EPR) spectra of the two-atom-tethered six-membered ring thymidylate spin label (DUMTA) incorporated into duplexes of different sizes were found to display a helix length dependence and a local-order parameter S = 0.32 +/- 0.01 for B-DNA based on the dynamic cylinder model (Keyes, R. S., and A. M. Bobst. 1995. Detection of internal and overall dynamics of a two-atom-tethered spin-labeled DNA. Biochemistry. 34:9265-9276). This sensitivity to size, which reflects global tumbling, is now reported for the more flexible five-atom-tethered five-membered ring thymidylate spin label (DUAP) that can be readily incorporated enzymatically and sequence specifically into nucleic acids of different sizes. The DUAPs containing B-DNA systems were simulated with the same dynamic cylinder model, giving S = 0.20 +/- 0.01 for the more flexibly tethered spin label. This shows that S is dependent on tether length but not on global motion. An analysis with the same motional model of the B-Z transition in a (dG-dC)n polymer containing the five-atom-tethered six-membered ring cytidylate spin label (DCAT) (Strobel, O. K., R. S. Keyes, and A. M. Bobst. 1990b. Base dynamics of local Z-DNA conformations as detected by electron paramagnetic resonance with spin-labeled deoxycytidine analogues. Biochemistry. 29:8522-8528) revealed an increase in S from 0.15 +/- 0.01 to 0.26 +/- 0.01 in response to the B- to Z-DNA transition. This indicates that S is not only sensitive to tether length, but also to conformational changes in DNA. Both the DUAP- and the DCAT-labeled systems were also simulated with a base disk model. From the DUAP spectral series, the perpendicular component of the correlation time tau perpendicular describing the spin-labeled base diffusion was found to be sensitive to global tumbling, confirming earlier results obtained with DUMTA. The DCAT polymer results demonstrated that tau perpendicular monitors a conformational change from B- to Z-DNA, indicating that tau perpendicular is also sensitive to local base dynamics. These results confirm that the dynamics of five-atom-tethered nitroxides are coupled to the nucleic acid dynamics and, as with two-atom-tethered spin labels, can be characterized by S and tau perpendicular. The analyses of both spin-labeled systems provide good evidence for spin-labeled base motions within double-stranded DNA occurring on the nanosecond time scale, and establish that both labels can be used to monitor changes in global tumbling and local order parameter due to variations in DNA conformation and protein-DNA interactions.

Spin-labeled nucleotide mobility in the boundary of the EcoRI endonuclease binding site

A complex consisting of the EcoRI endonuclease site-specifically bound to spin-labeled DNA 26mers was prepared to provide a model system for studying possible conformational changes resulting from protein binding. EPR was used to monitor the mobility of the spin labels that were strategically placed in position 6, 9, or 11 with respect to the dyad axis of the 26mer. These positions are located within the flanking region on either side of the EcoRI hexamer binding site. This allows the monitoring of potential distal structural changes in the DNA helix caused by protein binding. The spectral line shapes indicate that the spin label closest to the EcoRI endonuclease binding site, i.e., in position 6, is most influenced by the binding event. The EPR data are analyzed according to a model that distinguishes between spectral effects due to a change in the hydrodynamic shape of the complex and those resulting from local variations in the spin-label mobility as characterized by a local order parameter S. S reflecting the motional restriction of the spin-labeled base is 0.20 +/- 0.01 for all three oligomers as well as for the two complexes with the label in position 9 or 11, while the position 6 labeled complex yields S = 0.25. To further evaluate the origin of the slightly larger EPR effect observed with position 6 labeled material, molecular dynamics (MD) simulations were used to explore the space accessible to the probes in positions 6, 9, and 11. MD results gave similar nitroxide trajectories for all three labeled 26mers in the absence or presence of EcoRI. Thus, the small position 6 effect is attributed to a structural distortion in the major groove of the DNA at this location possibly corresponding to a bend induced by protein binding. The observation that the spectral changes are small indicates the absence of any significant structural disruption being propagated along the helix as a result of protein binding. Also, the fact that the line shape of the 26mers did not change as expected from hydrodynamic theory in view of the significant increase in molecular volume upon protein binding suggests that there are additional relaxation processes involving the protein and nucleic acid.

Spectroscopic probe for the detection of local DNA bending at an AAA triplet

Spectroscopic evidence of a DNA bend in solution is presented by analyzing model 15-mer duplexes spin-labeled with the five-atom-tethered nitroxide DUAP located in the major groove. Three 15-mers containing AATT with DUAP enzymatically incorporated into three different positions yielded nearly identical line shapes while a fourth 15-mer containing AAATT produced an EPR spectrum with significant additional line broadening. These results are interpreted according to the dynamic cylinder model where the DNA dynamics are decoupled into overall and internal contributions. It is shown that the AAATT sequence induces a change in the internal dynamics characterized by local ordering of DUAP. The increase in ordering evident in 15-mers containing AAATT rather than AATT suggests that the former sequence gives rise to a bend toward the major groove resulting in spatial restriction of the probe.

An electron paramagnetic resonance probe to detect local Z-DNA conformations

We present spectroscopic evidence for an electron paramagnetic resonance (EPR) probe to detect local Z-DNA conformations in synthetic DNA. A spin labeled deoxycytidine-5'-triphosphate (pppDCAT) was co-polymerized with Micrococcus luteus DNA polymerase to yield the spin active alternating co-polymer (dG-dC,DCAT)n. The EPR spectrum of (dG-dC,DCAT)n in the Z-DNA conformation indicates a decrease in the local base dynamics by about a factor of two as compared to that computed for B-DNA. A control experiment conducted with (dA-dT, DUAT)n under similar salt conditions rules out the possibility of observing salt induced artifacts.

Nick translation of lambda phage DNA with a deoxycytidine analog spin labeled in the 5 position

The synthesis and properties of a novel C(5)-spin-labeled 2'-deoxycytidine 5'-triphosphate which serves as a suitable substrate for the template-directed enzyme Escherichia coli DNA polymerase I are reported. The spin label is readily incorporated into lambda phage DNA by nick translation where it reports the characteristic local base motion for double- and single-stranded DNA as determined by electron spin resonance. The high-frequency deoxycytidine motion is similar to the previously reported thymidine motion in double-stranded lambda phage DNA.