Nucleic acid X-ray crystallography via direct selenium derivatization

X-ray crystallography has proven to be an essential tool for structural studies of bio-macromolecules at the atomic level. There are two major bottle-neck problems in the macromolecular crystal structure determination: phasing and crystallization. Although the selenium derivatization is routinely used for solving novel protein structures through the MAD phasing technique, the phase problem is still a critical issue in nucleic acid crystallography. The background and current progress of using direct selenium-derivatization of nucleic acids (SeNA) to solve the phase problem and to facilitate nucleic acid crystallization for X-ray crystallography are summarized in this tutorial review.     

Internal derivatization of oligonucleotides with selenium for X-ray crystallography using MAD.

We have developed a route for the synthesis of 2'-selenium uridine analogues and oligonucleotides containing selenium labels, and have demonstrated for the first time a new strategy to covalently derivatize nucleotides with selenium for phase and structure determination in X-ray crystallography.     

Chemical synthesis of selenium-modified oligoribonucleotides and their enzymatic ligation leading to an U6 SnRNA stem-loop segment

The derivatization of nucleic acids with selenium is highly promising to facilitate nucleic acids structure determination by X-ray crystallography using the multiwavelength anomalous dispersion (MAD) technique. The foundation for such an approach has been laid by Huang, Egli, and co-workers and was exemplified on small DNA duplexes. Here, we present a comprehensive study on the preparation of RNAs containing 2'-Se-methylpyrimidine nucleoside labels. This includes the synthesis of a novel 2'-Se-methylcytidine phosphoramidite 11 and its incorporation into oligoribonucleotides by solid-phase synthesis. Deprotection of the oligonucleotides is achieved in the presence of millimolar amounts of threo-1,4-dimercapto-2,3-butandiol (DTT). With this additive, oxidation products and follow-up side-products are suppressed and acceptable HPLC traces of the crude material are obtained, so far tested for sequences of up to 22-mers. Moreover, an extensive investigation on the enzymatic ligation of the selenium-containing oligoribonucleotides demonstrates the high flexibility of the selenium approach. Our target sequence, an U6 snRNA stem-loop motif comprising all naturally occurring nucleoside modifications beside the Se-label is achieved by ligation using T4 RNA ligase.     

Synthesis of a 2'-Se-thymidine phosphoramidite and its incorporation into oligonucleotides for crystal structure study

[reaction: see text] To investigate nucleic acids with selenium derivatization for crystallography, we report the first synthesis of 2'-methylseleno-thymidine phosphoramidite and its incorporation into DNAs and RNAs by solid-phase synthesis with over 99% coupling yield. The d(GT(Se)GTACAC)2 crystal structure was also determined at 1.40 A resolution using Se phasing, revealing that this Se derivatization did not cause significant structure perturbation, consistent with our UV melting study. In addition, we observed that the Se modification largely facilitated the crystallization.     

The Synthesis of Oligo- and Polynucleotides

Problems and results of the synthesis of oligonucleotides are reviewed. The central role of the nucleic acids in biochemistry is a challenge to synthesize nucleic acids of known base sequence and chain length. Oligomers with various sequences of up to 12 members and homo-oligomers with a maximum chain length of 30 nucleotides can be obtained by chemical synthesis. The enzymatic synthesis of ribonucleic acids can be directed in such a way that polynucleotides with definite sequences are produced.     

Probing the Binding Region of the Single-Stranded DNA-Binding Domain of Rat DNA Polymerase β Using Nanosecond-Pulse Laser-Induced Cross-Linking and Mass Spectrometry

In recent years, there has been a significant number of studies in which UV light has been used as a reagent to induce cross-links in nucleic acid-protein complexes. An area of considerable interest among those interested in structural biology is the garnering of information about the sites of cross-linking within the protein and nucleic acid members of photolinked conjugates, under the assumption that such knowledge should lead to identification of contact regions or sites within the native complexes. In this paper, we present our results from a photocross-linking study of the complex of the single-stranded DNA-binding domain of rat DNA polymerase β (pol β-ss) with the oligonucleotide d(ATATATA). In this study, we have used single nanosecond laser pulses as the cross-linking reagent and matrix-assisted laser desorp-tion/ionization-time of flight mass spectrometry as an analytical tool to identify cross-linked peptides purified from proteolytic digests of the cross-linked complex. Six cross-linked peptides have been identified in tryptic digests of the protein-oligonucleotide conjugates that result from irradiation of the pol β-ss-d(ATATATA) complex with a single laser pulse. Comparisons with NMR data in the literature for the same complex show that each of the cross-linked peptides contains amino acids that are in contact with the nucleic acid component of the complex.     

Study of the Reaction between Nucleic Acids and Tb-BPMPHD-CTMAB Complex and its Analytical Application

The direct use of the fluorescence emission properties of nucleic acids in the investigation of their biological properties is limited, whereas the use of metal complexes as fluorescence probe to study nucleic acids has increased remarkbly. Recently we found that the Tb-l,6-bi(1'-phenyl-3'-methyl-5'-pyrazolone-4'-)hezane-dione(BPMPHD)-trimethyl am-monium bromide(CTMAB) complex can be used as a sensitive fluorescence probe for the determination of nucleic acids.     

聚二烯丙基二甲基氯化铵与核酸相互作用的共振光散射光谱及分析应用

实验基于核酸与聚阳离子聚二烯丙基二甲基氯化铵(PDDA)的相互作用导致共振光散射(RLS)增强的现象来测定核酸。考察了pH值、PDDA浓度和离子强度对体系共振光散射强度的影响。在优化条件下,建立了用RLS光谱测定微量核酸的新方法。方法的抗干扰能力较强,可允许大部分的常见金属离子、核苷酸、氨基酸、糖、蛋白质等干扰物质的存在。同时用于合成样品的分析,结果令人满意。     

"Molecular chameleons". Design and synthesis of C-4-substituted imidazole fleximers

The synthesis of two flexible nucleosides is presented. The "fleximers" feature the purine ring system split into its imidazole and pyrimidine components. This modification serves to introduce flexibility to the nucleoside while still retaining the elements essential for molecular recognition. As a result, these structurally innovative nucleosides can more readily adapt to capricious binding sites and, as such, should find use for investigating enzyme-coenzyme as well as nucleic acid-protein interactions.     

Exploring the Nature of Hydrogen Bonding between RNA and Proteins: A Comprehensive Analysis of RNA : Protein Complexes

A nonredundant dataset of ∼300 high (up to 2.5 Å) resolution X-ray structures of RNA : protein complexes were analyzed for hydrogen bonds between amino-acid residues and canonical ribonucleotides (rNs). The identified 17100 contacts were classified based on the identity (rA, rC, rG or rU) and interacting fragment (base, sugar, or ribose) of the rN, the nature (polar or nonpolar) and interacting moiety (main chain or side chain) of the amino-acid residue, as well as the rN and amino-acid atoms participating in the hydrogen bonding. 80 possible hydrogen-bonding combinations (4 (rNs)×20 (amino acids)) involve a wide variety of RNA and protein types and are present in multiple occurrences in almost all PDB files. Comparison with the analogously-selected DNA:protein complexes reveals that the absence of 2′-OH group in DNA mainly accounts for the differences in DNA:protein and RNA : protein hydrogen bonding. Search for intrinsically-stable base:amino acid pairs containing single or multiple hydrogen bonds reveals 37 unique pairs, which may act as well-defined RNA : protein interaction motifs. Overall, our work collectively analyzes the largest set of nucleic acid-protein hydrogen bonds to date, and therefore highlights several trends that may help frame structural rules governing the physiochemical characteristics of RNA : protein recognition.     

Pyrrolidine-5,5-trans-lactams. 2. The use of X-ray crystal structure data in the optimization of P3 and P4 substituents

[reaction: see text] In this, the second of two letters, we describe the elaboration of the pyrrolidine-5,5-trans-lactam template to delineate the requirements for optimal substitution of the pyrrolidine and lactam nitrogen atoms. Central to the strategy is the use of rapid iterative synthesis in conjunction with X-ray crystal structure determination of ligand-protein complexes.     

Perspectives on analyses of nucleic acid constituents: the basis of genomics

The recent mapping of the human genome was a tremendous achievement made possible to a large degree by the development of analytical methods for sequencing purine and pyrimidine bases in nucleic acids. In the last 3 decades, the number of analyses of nucleic acids and their constituents by HPLC and capillary electrophoresis (CE) has exploded. These techniques have been used not only for genomics, but also for the determination of free nucleotides, nucleosides and their bases in body fluids and tissues. Although a large number of HPLC and CE papers have been published on nucleic acid constituent applications, relatively little has been written on the mechanisms of the separations. However, to optimize analytical conditions knowledgeably and rapidly, it is important to know why and how these separations occur and the factors that affect them. The HPLC methods for the analysis of nucleic acid constituents and the information available on some of the mechanisms of separation of nucleotides, nucleosides and their bases, as well as the analysis of these compounds by CE and the factors that affect these separations are discussed.     

Studies of DNA-protein interactions by gel electrophoresis

The use of gel electrophoresis in studies of nucleic acid-protein (especially DNA-protein) interactions has yielded much qualitative and quantitative information about a variety of such systems. The reduction in mobility of complexes relative to free DNA allows isolation and characterization of the complexes as well as determination of thermodynamic and kinetic properties of the interactions. This article begins with a review of recent applications of the "gel retardation" assay, by way of introduction to experiments in two areas. In the first, a hypothesis is tested regarding whether a DNA molecule with sizable proteins bound very near to each end migrates through a polyacrylamide gel differently than does the corresponding complex having the proteins in the middle of the DNA fragment. The data show little mobility differences for these types of complexes, implying that both may move in a linear, "snakelike", manner through the gel. The experiments also provide results pertaining to questions of DNA bending caused by the binding of the E. coli catabolite activator protein (CAP) and RNA polymerase to the lactose promoter region. It appears that DNA bending by CAP at its wild type lac binding site is retained in complexes where RNA polymerase is bound simultaneously at the lac UV5 promoter.     

Synthesis of the First Tellurium‐Derivatized Oligonucleotides for Structural and Functional Studies

We report here the first synthesis of Te‐nucleoside phosphoramidites and Te‐modified oligonucleotides. We protected the 2′‐tellurium functionality by alkylation and found that the Te functionality is compatible with solid‐phase synthesis and that the Te oligonucleotides are stable during deprotection and purification. In addition, the redox properties of the Te functionalities have been explored. We found that the telluride and telluoxide DNAs are interchangeable by redox reactions. At elevated temperature, the Te‐DNA can also be site‐specifically fragmented oxidatively or reductively when 2′‐TePh functionality is present, whereas elimination of the nucleobase is observed in the presence of 2′‐TeMe. Moreover, the stability of the DNA duplexes derivatized with the Te functionalities has been investigated. Our Te derivatization of nucleic acids provides a novel approach for investigating DNA damage as well as for structure and function studies of nucleic acids and their protein complexes.     

QUENCHING OF TYROSINE FLUORESCENCE BY PHOSPHATE IONS: A MODEL STUDY FOR PROTEIN-NUCLEIC ACID COMPLEXES

Abstract— In order to test the ability of phosphate groups to quench the tyrosine fluorescence in nucleic acid-protein complexes, we have studied the effect of several phosphate ions on the fluorescence of tyrosine derivatives. Mono and bianions (H₂PO₄ and HPO₄^2–) which are good proton acceptors quenched the fluorescence of all the phenolic compounds studied except that of O -methyl tyrosine. With the other derivatives (tyrosine, N -acetyl tyrosinamide and lysyl-tyrosyl-α lysine) fluorescence inhibition was accompanied by the appearance of a long wavelength emission (345 nm) attributed to tyrosinate anions. The quenching of tyrosine emission was due to the deprotonation of the phenolic group promoted in the excited state by phosphate ions and leading to the weakly fluorescent tyrosinate ion. Mono and dianions of phosphate mono ester inhibited tyrosine fluorescence as did unesterified phosphates. However, phosphate diester did not have any effect on the fluorescence of tyrosine derivatives. We conclude from this study that in nucleic acid-protein complexes phosphate groups are not able to quench tyrosine fluorescence except at the end of polynucleotide chains. Since monoester and diester monoanions have a different behavior, we propose that quenching of tyrosine fluorescence by monoanions requires the formation of two hydrogen bonds. This complex cannot form with diesters which consequently do not quench tyrosine fluorescence.     

Empirical energy functions for energy minimization and dynamics of nucleic acids

An improved empirical energy function for energy minimization and dynamics calculations of nucleic acids is developed and evaluated by an examination of its representation of both static and dynamic properties of model systems. Among the properties studied and used for parameter optimization are base pairing interactions, sugar and phosphate energy surfaces, small crystal heats of sublimation, base, phosphate and sugar analogue vibration spectra, and the overall behavior of a DNA hexamer duplex in vacuum molecular dynamics simulations. The results obtained are compared with those from two other energy functions that have been used recently for nucleic acids. Parameters for two energy functions are given; one includes heavy atoms and only polar hydrogens and the other includes all atoms.     

Shape, flexibility and packing of proteins and nucleic acids in complexes

Determining the change in topological properties like shape, flexibility and packing of proteins and nucleic acids on complexation is important in characterizing the role of induced structural changes and various interactions which control the functional specificity of proteins and nucleic acids. To this end, we have analyzed and compared the three dimensional structures of several protein-protein, protein-DNA and protein-RNA complexes available in the Protein Data Bank (PDB) and the Nucleic Acid Data Bank (NDB). The size of complexed proteins and nucleic acids, as measured by the radius of gyration, follows Flory's scaling law. The change in the scaling exponents for proteins, RNA and DNA reflects the changes in their respective sizes due to complexation. The anisotropy in the shape of proteins, DNA and RNA in complexes is measured by considering the asphericity and shape parameter, which are calculated from the eigenvalues of the moment of inertia tensor. The distribution of asphericity and shape shows that complexed proteins are mostly spherically symmetrical, while DNA and RNA in complexed states are largely prolate and considerably more aspherical compared to the proteins. Persistence length characterizes the intrinsic flexibility/rigidity of proteins and nucleic acids. The flexibility of all biomolecules decreases with the chain length. For small DNA molecules (6-147 base pairs), persistence length is larger compared to RNA and proteins in protein-protein and protein-RNA complexes. The flexibility of DNA increases, while RNA decreases, in their respective complexed states as compared to that of proteins which remain almost unchanged. The two body contact analysis confirms that the side-chain-backbone contacts are predominant compared to sidechain-sidechain and backbone-backbone contacts in the complexed proteins. The average packing density of proteins decreases in their complexed states, which is measured by the mean value of the contact density of their alpha carbon atoms. The average number of hydrogen bonds are found to be less in the interface region of protein-protein complexes compared to that in protein-DNA and protein-RNA complexes.     

核苷酸、聚核苷酸和核酸猝灭Tb3+-钛铁试剂络合物荧光的机理研究

研究了核苷酸、聚核苷酸和核酸对Tb³⁺－钛铁试剂(TR)络合物的荧光碎灭机理,认为荧光猝灭过程是核苷酸、聚核苷酸和核酸分子中的磷酸基组分与TR竞争Tb³⁺离子,生成实验条件下无荧光的二元络合物的静态猝灭过程;用Tb³⁺－TR络合物荧光探针研究DNA嵌入剂和金属离子与DNA相互作用的实验结果说明这一机理是合理的.     

Interactions of Cu(I) with selenium-containing amino acids determined by NMR, XAS, and DFT studies

Cu(I) coordination by organoselenium compounds was recently reported as a mechanism for their prevention of copper-mediated DNA damage. To establish whether direct Se-Cu coordination may be involved in selenium antioxidant activity, Cu(I) coordination of the selenoamino acids methyl-Se-cysteine (MeSeCys) and selenomethionine (SeMet) was investigated. NMR results in D(2)O indicate that Cu(I) binds to the Se atom of both MeSeCys and SeMet as well as the carboxylic acid oxygen atom(s) or amine nitrogen atoms. X-ray absorption spectroscopy (XAS) and density functional theory (DFT) results confirm Se-Cu coordination, with the identification of a 2.4 ? Se-Cu vector in both the Se- and Cu-EXAFS data. XAS studies also show Cu(I) in an unusual three-coordinate environment with the additional two ligands arising from O/N (2.0 ?). DFT models of 1:1 Cu-selenoamino acid complexes suggest that both selenoamino acids coordinate Cu(I) through the selenium and amino groups, with the third ligand assumed to be water. These compounds represent the first structurally characterized copper(I) complexes with sulfur- or selenium-containing amino acids.     

Identifying similarities and differences between analogous bisdithiolene and bisdiselenolene complexes: A computational study

Due to ligand non‐innocence and reversible one‐electron‐transfer processes dithiolene complexes have been intensively studied both experimentally and computationally. While the substitution of the ligating sulfur atoms by selenium provides a means to delicately tune the behavior of dithiolene compounds, diselenolene complexes have not been as thoroughly examined. Yet, the search for such ligands has been ongoing since the 1970s. Thus, we have looked at several metal‐bisdiselenolene complexes and have compared key properties of these complexes with their bisdithiolene analogues to determine the effect of substituting the chalcogen atom. The results herein show that substitution of the sulfur atoms by selenium within these complexes only subtly changes the thermodynamics and kinetic reactivity of bisdithiolene complexes while not significantly affecting the geometries of the complexes. The significance being that the relatively minor structural changes that occur upon redox is a key feature of dithiolene complexes. Due to ligand non‐innocence and reversible one‐electron‐transfer processes dithiolene complexes have been intensively studied, however, diselenolene complexes have not. First‐principles calculations show that substitution of the sulfur atoms by selenium within the investigated complexes does offer the ability to subtly tune the thermodynamics and kinetic reactivity of bisdithiolene complexes, while not significantly affecting the geometries of the complexes. © 2015 Wiley Periodicals, Inc.