Structural insights of non-canonical U*U pair and Hoogsteen interaction probed with Se atom.

Unlike DNA, in addition to the 2'-OH group, uracil nucleobase and its modifications play essential roles in structure and function diversities of non-coding RNAs. Non-canonical U•U base pair is ubiquitous in non-coding RNAs, which are highly diversified. However, it is not completely clear how uracil plays the diversifing roles. To investigate and compare the uracil in U-A and U•U base pairs, we have decided to probe them with a selenium atom by synthesizing the novel 4-Se-uridine ((Se)U) phosphoramidite and Se-nucleobase-modified RNAs ((Se)U-RNAs), where the exo-4-oxygen of uracil is replaced by selenium. Our crystal structure studies of U-A and U•U pairs reveal that the native and Se-derivatized structures are virtually identical, and both U-A and U•U pairs can accommodate large Se atoms. Our thermostability and crystal structure studies indicate that the weakened H-bonding in U-A pair may be compensated by the base stacking, and that the stacking of the trans-Hoogsteen U•U pairs may stabilize RNA duplex and its junction. Our result confirms that the hydrogen bond (O4(…)H-C5) of the Hoogsteen pair is weak. Using the Se atom probe, our Se-functionalization studies reveal more insights into the U•U interaction and U-participation in structure and function diversification of nucleic acids.

Novel complex MAD phasing and RNase H structural insights using selenium oligonucleotides.

The crystal structures of protein-nucleic acid complexes are commonly determined using selenium-derivatized proteins via MAD or SAD phasing. Here, the first protein-nucleic acid complex structure determined using selenium-derivatized nucleic acids is reported. The RNase H-RNA/DNA complex is used as an example to demonstrate the proof of principle. The high-resolution crystal structure indicates that this selenium replacement results in a local subtle unwinding of the RNA/DNA substrate duplex, thereby shifting the RNA scissile phosphate closer to the transition state of the enzyme-catalyzed reaction. It was also observed that the scissile phosphate forms a hydrogen bond to the water nucleophile and helps to position the water molecule in the structure. Consistently, it was discovered that the substitution of a single O atom by a Se atom in a guide DNA sequence can largely accelerate RNase H catalysis. These structural and catalytic studies shed new light on the guide-dependent RNA cleavage.

Simple ultraviolet and high-performance liquid chromatography methods for the evaluation of sunscreen efficacy.

BACKGROUND: To prevent DNA damage caused by the ultraviolet (UV) radiation of sunlight, sunscreens are commonly used to protect human skin. Current analysis of sunscreens' effectiveness is done through complicated procedures, including human exposure. OBJECTIVE: We sought to design a simple system using thymidine-thymidine (TT) dinucleotides to analyze the effectiveness of sunscreens. METHODS: We can directly analyze sunscreen effectiveness and the formation of TT photolesions simply by using UV spectrophotometry and high-performance liquid chromatography (HPLC). Efficient sunscreen has protective effects against UV irradiation damage. RESULTS: We have developed a simple method using TT dinucleotide, UV, and HPLC for the analysis of sunscreen effectiveness. Our research indicates that the analytical results from UV are consistent with those of HPLC, which is used to monitor the formation of the TT photolesions. Moreover, both UV and HPLC analyses indicate that TT dinucleotides are better protected against UV damage, using the sunscreens with higher UVB sun protection factor (SPF) value, and that sunscreens with higher SPF lead to reduced photolesion formation. Our UV and HPLC analyses confirm the SPF grading of commercial sunscreens. LIMITATIONS: In this experiment, only sunscreens were tested. The experiment, therefore, does not apply to other commercial products, such as cosmetic materials that claim UV protection as a secondary benefit. CONCLUSION: In conclusion, we have established a simple strategy to analyze the effectiveness of sunscreens and the quality of these potential cancer-preventive products.

Synthesis and crystal structure of 2'-se-modified guanosine containing DNA.

Selenium modification of nucleic acids is of great importance in X-ray crystal structure determination and functional study of nucleic acids. Herein, we describe a convenient synthesis of a new building block, the 2'-SeMe-modified guanosine (G(Se)) phosphoramidite, and report the first incorporation of the 2'-Se-G moiety into DNA. The X-ray crystal structure of the 2'-Se-modified octamer DNA (5'-GTG(Se)TACAC-3') was determined at a resolution of 1.20 A. We also found that the 2'-Se modification points to the minor groove and that the modified and native structures are virtually identical. Furthermore, we observed that the 2'-Se-G modification can significantly facilitate the crystal growth with respect to the corresponding native DNA.

Derivatization of DNAs with selenium at 6-position of guanine for function and crystal structure studies.

To investigate nucleic acid base pairing and stacking via atom-specific mutagenesis and crystallography, we have synthesized for the first time the 6-Se-deoxyguanosine phosphoramidite and incorporated it into DNAs via solid-phase synthesis with a coupling yield over 97%. We found that the UV absorption of the Se-DNAs red-shifts over 100 nm to 360 nm (epsilon = 2.3 x 10(4) M(-1) cm(-1)), the Se-DNAs are yellow colored, and this Se modification is relatively stable in water and at elevated temperature. Moreover, we successfully crystallized a ternary complex of the Se-G-DNA, RNA and RNase H. The crystal structure determination and analysis reveal that the overall structures of the native and Se-modified nucleic acid duplexes are very similar, the selenium atom participates in a Se-mediated hydrogen bond (Se ... H-N), and the (Se)G and C form a base pair similar to the natural G-C pair though the Se-modification causes the base-pair to shift (approximately 0.3 A). Our biophysical and structural studies provide new insights into the nucleic acid flexibility, duplex recognition and stability. Furthermore, this novel selenium modification of nucleic acids can be used to investigate chemogenetics and structure of nucleic acids and their protein complexes.

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.

Synthesis of a 2'-Se-uridine phosphoramidite and its incorporation into oligonucleotides for structural study.

[chemical reaction: see text]. We report here the synthesis of the 5'-[benzhydryloxybis(trimethylsilyloxy)]silyl-2'-methylseleno-2'-deoxyuridine phosphoramidite and its incorporation into oligonucleotides by solid-phase synthesis. The coupling yield of this phosphoramidite into oligonucleotides is higher than 99%. We also demonstrate that this 2'-methylselenophosphoramidite is compatible with the 5'-silyl-2'-ACE chemistry, for longer Se-RNA solid-phase synthesis. Our preliminary NMR study on the synthesized 2'-Se-DNA has revealed a U(Se)-A base pair and a duplex structure formation when its complementary strand was present.

Covalent and noncovalent labeling schemes for near-infrared dyes in capillary electrophoresis protein applications.

Capillary electrophoresis (CE) is experiencing increased use in the field of separation science. Part of its growing popularity of capillary electrophoresis can be attributed to the high efficiency of the separations achievable with the technique, making it an attractive tool for bioanalytical applications. Laser-induced fluorescence (LIF) is a common detection method for CE. One of the problems frequently experienced when using visible LIF detection is matrix autofluorescence which has the effect of degrading the overall sensitivity of the technique. However, the use of near-infrared (NIR) laser induced fluorescence nearly eliminates matrix autofluorescence, as very few molecules have intrinsic fluorescence in this region. This chapter describes the use of covalent and noncovalent labeling schemes for tagging biomolecules with near infrared dyes. To fully appreciate the advantages that the NIR LIF technique can supply, we also review applications that employ detection schemes other than NIR LIF. Specific applications to be discussed include drug-protein studies by CE, as well as capillary electrophoretic immunoassays.

Noncovalent labeling of biomolecules with red and near- infrared dyes.

Biopolymers such as proteins and nucleic acids can be labeled with a fluorescent marker to allow for their detection. Covalent labeling is achieved by the reaction of an appropriately functionalized dye marker with a reactive group on a biomolecule. The recent trend, however, is the use of noncovalent labeling that results from strong hydrophobic and/or ionic interactions between the marker and biomolecule of interest. The main advantage of noncovalent labeling is that it affects the functional activity of the biomolecule to a lesser extent. The applications of luminescent cyanine and squarylium dyes are reviewed.

Synthesis of 6-Se-guanosine RNAs for structural study.

6-Se-guanosine phosphoramidite and RNAs have been synthesized by selenium substitution of the 6-oxygen atom, and it is revealed that the Se-derivatization is relatively stable and that bulge and wobble structures can better accommodate a large Se atom than a duplex. This Se-modification is useful in the structural study of RNAs and their protein complexes.

Mild detritylation of nucleic acid hydroxyl groups by warming up.

It is challenging to effectively deprotect hydroxyl groups of acid-or-base sensitive bio-macromolecules without causing even minor defects and compromising high quality of final products. We report here a mild detritylation strategy in mildly acidic buffers to remove the DMTr protection from the 5'-hydroxyl groups of synthetic nucleic acids. The DMTr-groups can be easily and effectively removed at pH 4.5 or 5.0 with slight warming up (40 °C), offering virtually quantitative deprotection. This warming-up strategy is particularly useful for deprotection of the modified nucleic acids that are sensitive to the conventional acid deprotection. As a first step towards our long-term goal of synthesizing defect-free nucleic acids, our novel and simple strategy further increases the quality of synthetic nucleic acids.

1-Methyl-1H-imidazo[4,5-f]quinolin-6-ium chloride monohydrate.

The title compound, C(11)H(10)N(3)(+) x Cl(-) x H(2)O, belongs to the N1-methyl-substituted imidazo[4,5-f]quinoline family, in which the heterocyclic ring is protonated at the pyridine rather than at the imidazole N atom. The molecule as a whole is almost exactly planar. The molecular structure has been compared with that of the 2-amino analogue described in the literature, and it was found that the extra amino group of the latter is involved in conjugation with the adjacent double bond, i.e. the conjugation does not extend over the entire heterocyclic system. The cation of the title compound forms a strong hydrogen bond with the Cl(-) anion and the anions are interconnected by the water solvent molecule.