Dynamics of a bis-intercalator DNA complex by 1H-detected natural abundance 13C NMR spectroscopy

Base Dynamics in the HhaI Protein Binding Site

Protein-DNA interactions play an important role in numerous biological functions within the living cell. In many of these interactions, the DNA helix is significantly distorted upon protein-DNA complex formation. The HhaI restriction-modification system is one such system, where the methylation target is flipped out of the helix when bound to the methyltransferase. However, the base flipping mechanism is not well understood. The dynamics of the binding site of the HhaI methyltransferase and endonuclease (underlined) within the DNA oligomer [d(G1A2T3A4G5C6G7C8T9A10T11C12)]2 are studied using deuterium solid-state NMR (SSNMR). SSNMR spectra obtained from DNAs deuterated on the base of nucleotides within and flanking the [5'-GCGC-3']2 sequence indicate that all of these positions are structurally flexible. Previously, conformational flexibility within the phosphodiester backbone and furanose ring within the target sequence has been observed and hypothesized to play a role in the distortion mechanism. However, whether that distortion was occurring through an active or passive mechanism remained unclear. These NMR data demonstrate that although the [5'-GCGC-3']2 sequence is dynamic, the target cytosine is not passively flipping out of the double-helix on the millisecond-picosecond time scale. Additionally, although previous studies have shown that both the furanose ring and phosphodiester backbone experience a change in dynamics upon methylation, which may play a role in recognition and cleavage by the endonuclease, our observations here indicate that methylation has no effect on the dynamics of the base itself.

HI-NESS: a family of genetically encoded DNA labels based on a bacterial nucleoid-associated protein

The interplay between three-dimensional chromosome organisation and genomic processes such as replication and transcription necessitates in vivo studies of chromosome dynamics. Fluorescent organic dyes are often used for chromosome labelling in vivo. The mode of binding of these dyes to DNA cause its distortion, elongation, and partial unwinding. The structural changes induce DNA damage and interfere with the binding dynamics of chromatin-associated proteins, consequently perturbing gene expression, genome replication, and cell cycle progression. We have developed a minimally-perturbing, genetically encoded fluorescent DNA label consisting of a (photo-switchable) fluorescent protein fused to the DNA-binding domain of H-NS — a bacterial nucleoid-associated protein. We show that this DNA label, abbreviated as HI-NESS (H-NS-based indicator for nucleic acid stainings), is minimally-perturbing to genomic processes and labels chromosomes in eukaryotic cells in culture, and in zebrafish embryos with preferential binding to AT-rich chromatin.

Site-specific DNA structural and dynamic features revealed by nucleotide-independent nitroxide probes

In site-directed spin labeling, a covalently attached nitroxide probe containing a chemically inert unpaired electron is utilized to obtain information on the local environment of the parent macromolecule. Studies presented here examine the feasibility of probing local DNA structural and dynamic features using a class of nitroxide probes that are linked to chemically substituted phosphorothioate positions at the DNA backbone. Two members of this family, designated as R5 and R5a, were attached to eight different sites of a dodecameric DNA duplex without severely perturbing the native B-form conformation. Measured X-band electron paramagnetic resonance (EPR) spectra, which report on nitroxide rotational motions, were found to vary depending on the location of the label (e.g., duplex center vs termini) and the surrounding DNA sequence. This indicates that R5 and R5a can provide information on the DNA local environment at the level of an individual nucleotide. As these probes can be attached to arbitrary nucleotides within a nucleic acid sequence, they may provide a means to "scan" a given DNA molecule in order to interrogate its local structural and dynamic features.

Recent developments in the chemistry of deoxyribonucleic acid (DNA) intercalators: principles, design, synthesis, applications and trends

In the present overview, we describe the bases of intercalation of small molecules (cationic and polar neutral compounds) in DNA. We briefly describe the importance of DNA structure and principles of intercalation. Selected syntheses, possibilities and applications are shown to exemplify the importance, drawbacks and challenges in this pertinent, new, and exciting research area. Additionally, some clinical applications (molecular processes, cancer therapy and others) and trends are described.

13C relaxation studies of the DNA target sequence for hhai methyltransferase reveal unique motional properties

The goal of this work was to examine if sequence-dependent conformational flexibility in DNA plays a role in base extrusion, a common conformational change induced by many DNA-modifying enzymes. We studied the dynamics of the double-stranded DNA target of the HhaI methyltransferase by recording an extensive set of (13)C NMR relaxation parameters. We observe that the cytidine furanose rings experience fast (picosecond to nanosecond) motions that are not present in other nucleotides; the methylation site experiences particularly high mobility. We also observe that the bases of guanosine and cytidine residues within the HhaI recognition sequence GCGC experience motions on a much slower (1-100 micros) time scale. We compare these observations with previous solution and solid-state NMR studies of the EcoRI nuclease target sequence, and solid-state NMR studies of a similar HhaI target construct. While an increased mobility of cytidine furanose rings compared to those of other nucleotides is observed for both sequences, the slower motions are only observed in the HhaI target DNA. We propose that this inherent flexibility lowers the energetic barriers that must occur when the DNA binds to the HhaI methyltransferase and for extrusion of the cytidine prior to its methylation.

Solid-state nuclear magnetic resonance spectroscopy studies of furanose ring dynamics in the DNA HhaI binding site

The dynamics of the furanose rings in the GCGC moiety of the DNA oligomer [d(G 1A 2T 3A 4 G 5 C 6 G 7 C 8T 9A 10T 11C 12)] 2 are studied by using deuterium solid-state NMR (SSNMR). SSNMR spectra obtained from DNAs selectively deuterated on the furanose rings of nucleotides within the 5'-GCGC-3' moiety indicated that all of these positions are structurally flexible. The furanose ring within the deoxycytidine that is the methylation target displays the largest-amplitude structural changes according to the observed deuterium NMR line shapes, whereas the furanose rings of nucleotides more remote from the methylation site have less-mobile furanose rings (i.e., with puckering amplitudes < 0.3 A). Previous work has shown that methylation reduces the amplitude of motion in the phosphodiester backbone of the same DNA, and our observations indicate that methylation perturbs backbone dynamics through the furanose ring. These NMR data indicate that the 5'-GCGC-3' is dynamic, with the largest-amplitude motions occurring nearest the methylation site. The inherent flexibility of this moiety in DNA makes the molecule more amenable to the large-amplitude structural rearrangements that must occur when the DNA binds to the HhaI methyltransferase.

NMR and MD studies of the temperature-dependent dynamics of RNA YNMG-tetraloops

In a combined NMR/MD study, the temperature-dependent changes in the conformation of two members of the RNA YNMG-tetraloop motif (cUUCGg and uCACGg) have been investigated at temperatures of 298, 317 and 325 K. The two members have considerable different thermal stability and biological functions. In order to address these differences, the combined NMR/MD study was performed. The large temperature range represents a challenge for both, NMR relaxation analysis (consistent choice of effective bond length and CSA parameter) and all-atom MD simulation with explicit solvent (necessity to rescale the temperature). A convincing agreement of experiment and theory is found. Employing a principle component analysis of the MD trajectories, the conformational distribution of both hairpins at various temperatures is investigated. The ground state conformation and dynamics of the two tetraloops are indeed found to be very similar. Furthermore, both systems are initially destabilized by a loss of the stacking interactions between the first and the third nucleobase in the loop region. While the global fold is still preserved, this initiation of unfolding is already observed at 317 K for the uCACGg hairpin but at a significantly higher temperature for the cUUCGg hairpin.

NMR studies of dynamics in RNA and DNA by 13C relaxation

RNA and DNA molecules experience motions on a wide range of time scales, ranging from rapid localized motions to much slower collective motions of entire helical domains. The many functions of RNA in biology very often require this molecule to change its conformation in response to biological signals in the form of small molecules, proteins or other nucleic acids, whereas local motions in DNA may facilitate protein recognition and allow enzymes acting on DNA to access functional groups on the bases that would otherwise be buried in Watson-Crick base pairs. Although these statements make a compelling case to study the sequence dependent dynamics in nucleic acids, there are few residue-specific studies of nucleic acid dynamics. Fortunately, NMR studies of dynamics of nucleic acids and nucleic acids-protein complexes are gaining increased attention. The aim of this review is to provide an update of the recent progress in studies of nucleic acid dynamics by NMR based on the application of solution relaxation techniques.

Alternate-site isotopic labeling of ribonucleotides for NMR studies of ribose conformational dynamics in RNA

Heteronuclear NMR spin relaxation studies of conformational dynamics are coming into increasing use to help understand the functions of ribozymes and other RNAs. Due to strong 13C-13C magnetic interactions within the ribose ring, however, these studies have thus far largely been limited to (13)C and (15)N resonances on the nucleotide base side chains. We report here the application of the alternate-site (13)C isotopic labeling scheme, pioneered by LeMaster for relaxation studies of amino acid side chains, to nucleic acid systems. We have used different strains of E. coli to prepare mononucleotides containing (13)C label in one of two patterns: Either C1' or C2' in addition to C4', termed (1'/2',4') labeling, or nearly complete labeling at the C2' and C4' sites only, termed (2',4') labeling. These patterns provide isolated 13C-1H spin systems on the labeled carbon atoms and thus allow spin relaxation studies without interference from 13C-13C scalar or dipolar coupling. Using relaxation studies of AMP dissolved in glycerol at varying temperature to produce systems with correlation times characteristic of different size RNAs, we demonstrate the removal of errors due to 13C-13C interaction in T (1) measurements of larger nucleic acids and in T (1rho) measurements in RNA molecules. By extending the applicability of spin relaxation measurements to backbone ribose groups, this technology should greatly improve the flexibility and completeness of NMR analyses of conformational dynamics in RNA.

Dynamics-based amplification of RNA function and its characterization by using NMR spectroscopy

The ever-increasing cellular roles ascribed to RNA raise fundamental questions regarding how a biopolymer composed of only four chemically similar building-block nucleotides achieves such functional diversity. Here, I discuss how RNA achieves added mechanistic and chemical complexity by undergoing highly controlled conformational changes in response to a variety of cellular signals. I examine pathways for achieving selectivity in these conformational changes that rely to different extents on the structure and dynamics of RNA. Finally, I review solution-state NMR techniques that can be used to characterize RNA structural dynamics and its relationship to function.

Entropy production mapping on stretched DNA interacted with proteins

This paper presents an entropy production mapping (EPM) method for detecting a higher-order structure change of a stretched and immobilized DNA molecule on a cover slip through measuring and mapping an increment of the orientational entropy (defined as "entropy production") of the Watson-Crick base pairs by the interaction of biological factors such as proteins; the stretched DNA molecule undergoes a higher-order structure change by the interaction, so that the orientational entropy at the interaction regions increases because the alignment of the base pairs is reduced at the regions. We demonstrated the utility of this "EPM method" by using a histone-lambda DNA system. It is revealed that the histone interaction region is clearly distinguished from no interaction regions on a stretched lambda DNA molecule immobilized on a cover slip.

Chlorination effect on the fluorescence of nucleic acid staining dyes

An alternative to culture methods for the control of drinking water disinfection would use fluorescent dyes that could evidence the nucleic acid damages provoked by sodium hypochlorite treatment. The two dyes selected in this study, SYBR Green II RNA gel stain and TOTO-1 iodide, efficiently stain nucleic acids (DNA and RNA) and quite poorly the other biomolecules considered (Bovine serum albumin, palmitic acid and dextrane). After treatment of nucleic acid solutions with increasing amounts of sodium hypochlorite, a decrease of fluorescence intensity is observed for both DNA and RNA stained with either SYBR-II or TOTO-1. However, the two fluorochromes do not lead to the same results, which shows that the two dyes are not bound to nucleic acids in the same way. Contrary to TOTO-1, SYBR-II reveals to be sufficiently sensitive to indicate both DNA or RNA damages as soon as the latter are in contact with hypochlorite even at concentrations of HClO lower than 10 micromol/L. Moreover, SYBR-II offers the opportunity to make quantitative titration of chlorine treated DNA and therefore seems to be the appropriate candidate to control the efficiency of the hypochlorite disinfection process of drinking water samples.

Oriented and vectorial immobilization of linear M13 dsDNA between interdigitated electrodes--towards single molecule DNA nanostructures

The ability to control molecules at a resolution well below that offered by photolithography has gained much interest recently. DNA is a promising candidate for this task since it offers excellent specificity in base-pairing combined with addressability at the nanometer scale. New applications in biosensing, e.g. interaction analysis at the single molecule level, or nanobiotechnology, e.g. ultradense DNA microarrays, have been devised that rely on stretched DNA bridges. The basic technology required is the ability to deposit spatially defined, stretched DNA-bridges between anchoring structures on surfaces. In this paper we present two techniques for spanning 2 microm long dsDNA bridges between neighboring interdigitated electrodes (IDEs). The extended DNA used was linearized M13 dsDNA (M13mp18 7231 bp, ca. 2.5 microm length), either unmodified, or with chemical modifications at both ends. The first approach is based on the dielectrophoretic (DEP) concentration and alignment of linearized wild-type dsDNA. IDEs with 1.7 microm spacing are driven with an AC voltage around 1 MHz leading to field strengths in the order of 1 MV m(-1). The dsDNA is polarized and linearized by the force field and accumulates in the gap between two neighboring electrodes. This process is reversible and was visualized by fluorescence staining of M13 DNA using PicoGreen, as intercalating dye. The resulting dsDNA bridges and their orientation are discernible under the fluorescence microscope using fluorescent particles of different color. The particles are tagged with sequence specific peptide nucleic acid (PNA) probes that bind to the DNA double strand at specific sites. The second approach is based on asymmetric electrochemical modification of a gold IDE with 2.0 microm spacings followed by spontaneous or stimulated deposition of a chemically modified M13-DNA. One side of the IDE was selectively coated with streptavidin by electropolymerization of a novel hydrophilic conductive polymer in the presence of the binding protein. The second side was modified with gold nanoparticles by reductive plating from aqueous gold chloride solution. An asymmetric double stranded (ds) M13 DNA carrying a 5'-thiol group at one end and a 5'-biotin at the other end was obtained by polymerase chain reaction (PCR) using two differently labeled primers. For DNA bridges to form spontaneously the modified IDE was incubated over night with a 50 nM solution of the modified M13 DNA. Potential applications of DNA-bridge formation in biosensing and biotechnology are discussed.

Structural differences in the NOE-derived structure of G-T mismatched DNA relative to normal DNA are correlated with differences in (13)C relaxation-based internal dynamics

Detailed description of the characteristics of mismatched DNA that are distinct from normal DNA is vital to the understanding of how mismatch repair proteins are able to recognize and repair these DNA lesions. To this end, we have used nuclear Overhauser effect spectroscopy (NOESY)-based distance restraints and (13)C relaxation measurements to solve the solution structures and measure some of the internal dynamics of the G-T mismatched DNA oligomer d(CCATGCGTGG)(2) (GT) and its parent DNA sequence d(CCACGCGTGG)(2) (GC). In GT, the mismatched G7 is structurally perturbed much more than the mismatched T4 relative to their corresponding bases in GC. The degree of G7 displacement differs from previous high-resolution structures of G-T mismatch-containing B-DNA, suggesting a dependence of G-T mismatch-induced structural perturbation on sequence context. The internal dynamics of GC and GT differ on multiple timescales. The mismatched G7 of GT contains spins that decrease significantly in order in GT compared to GC, while spins in C6, T8, and A3 have significantly higher order in GT compared to GC. Linear correlations between helical parameters of GC and GT and the order of C-1' and aromatic methine carbon atoms relate differences in internal dynamics to the structures quantitatively. The dynamic differences between the normal and mismatched DNA signify changes in local flexibility that may be exploited by the mismatch repair system to bind mismatched DNA preferentially while ignoring normal DNA.

NMR evidence for mechanical coupling of phosphate B(I)-B(II) transitions with deoxyribose conformational exchange in DNA

The conformational exchange of the phosphate and deoxyribose groups of the DNA oligomers d(GCGTACGC)(2) and d(CGCTAGCG)(2) have been investigated using a combination of homonuclear and heteronuclear NMR techniques. Two-state exchange between phosphate B(I) and B(II) conformations and deoxyribose N and S conformations was expressed as percent population of the major conformer, %B(I) or %S. Sequence context-dependent variations in %B(I) and %S were observed. The positions of the phosphate and deoxyribose equilibria provide a quantitative measure of the ps to ns timescale dynamic exchange processes in the DNA backbone. Linear correlations between %B(I), %S, and previously calculated model free (13)C order parameters (S(2)) were observed. The %B(I) of the phosphates were found to be correlated to the S(2) of the flanking C3' and C4' atoms. The %B(I) was also found to be correlated with the %S and C1' S(2) of the deoxyribose ring 5' of the phosphates. The %B(I) of opposing phosphates is correlated, while the %B(I) of sequential phosphates is anti-correlated. These correlations suggest that conformational exchange processes in DNA are coupled to each other and are modulated by DNA base sequence, which may have important implications for DNA-protein interactions.

Relationship of DNA structure to internal dynamics: correlation of helical parameters from NOE-based NMR solution structures of d(GCGTACGC)(2) and d(CGCTAGCG)(2) with (13)C order parameters implies conformational coupling in dinucleotide units

The coupling between the conformational properties of double-stranded DNA and its internal dynamics has been examined. The solution structures of the isomeric DNA oligomers d(GCGTACGC)(2) (UM) and d(CGCTAGCG)(2) (CTSYM) were determined with (1)H NMR spectroscopy by utilizing distance restraints from total relaxation matrix analysis of NOESY cross-peak intensities in restrained molecular dynamics calculations. The root-mean-square deviation of the coordinates for the ensemble of structures was 0.13 A for UM and 0.49 A for CTSYM, with crystallographic equivalent R(c)=0.41 and 0.39 and sixth-root residual R(x)=0.11 and 0.10 for UM and CTSYM, respectively. Both UM and CTSYM are B-form with straight helical axes and show sequence-dependent variations in conformation. The internal dynamics of UM and CTSYM were previously determined by analysis of (13)C relaxation parameters in the context of the Lipari & Szabo model-free formalism. Helical parameters for the two DNA oligomers were examined for linear correlations with the order parameters (S(2)) of groups of (13)C spins in base-pairs and dinucleotide units of UM and CTSYM. Correlations were found for six interstrand base-pair parameters tip, y-displacement, inclination, buckle and stretch with various combinations of S(2) for atoms in Watson-Crick base-pairs and for two inter-base-pair parameters, rise and roll with various combinations of S(2) for atoms in dinucleotides. The correlations for the interstrand base-pair helical parameters indicate that the conformations of the deoxyribose residues of each strand are dynamically coupled. Also, the inter-base-pair separation has a profound effect on the local internal motions available to the DNA, supporting the idea that rise is a principal degree of freedom for DNA conformational variability. The correlations indicate collective atomic motions of spins that may represent specific motional modes in DNA, and that base sequence has a predictable effect on the relative order of groups of spins both in the bases and in the deoxyribose ring of the DNA backbone. These observations suggest that an important functional outcome of DNA base sequence is the modulation of both the conformation and dynamic behavior of the DNA backbone.