- Radiolabeled 5-iodo-3′-O-(17β-succinyl-5α-androstan-3-one) -2′-deoxyuridine and its 5′-monophosphate for imaging and therapy of androgen receptor-positive cancers: Synthesis and biological evaluation
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High levels of androgen receptor (AR) are often indicative of recurrent, advanced, or metastatic cancers. These conditions are also characterized by a high proliferative fraction. 5-Radioiodo-3′-O-(17β-succinyl-5α- androstan-3-one)-2′-deoxyuridine 8 and 5
- Kortylewicz, Zbigniew P.,Nearman, Jessica,Baranowska-Kortylewicz, Janina
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Read Online
- Nucleic Acid Conformation Influences Postsynthetic Suzuki-Miyaura Labeling of Oligonucleotides
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Chemoselective transformations that work under physiological conditions have emerged as powerful tools to label nucleic acids in cell-free and cellular environments. However, detailed studies investigating the influence of nucleic acid conformation on the
- Walunj, Manisha B.,Srivatsan, Seergazhi G.
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Read Online
- Primer extension reaction assays for incorporation of deoxynucleotide analogue into DNA
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Incorporation of deoxynucleotide analogues into DNA is important for the expansion of DNA functions. Primer extension reactions are commonly used for the assay of such reaction events. However, current assay protocols generally rely on radiolabeling, fluo
- Wang, Xilong,Chen, Xun,Liu, Yonghui,Zhu, Jin
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Read Online
- Synthesis of Phosphoramidite Monomers Equipped with Complementary Bases for Solid-Phase DNA Oligomerization
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We describe the preparation of two monomers that bear complementary nucleobases at the edges (guanine-2′-deoxycytidine and 2-aminoadenine-2′-deoxyuridine) and that are conveniently protected and activated for solid-phase automated DNA synthesis. We report the optimized synthetic routes leading to the four nucleobase derivatives involved, their cross-coupling reactions into dinucleobase-containing monomers, and their oligomerization in the DNA synthesizer.
- Romero-Pérez, Sonia,López-Martín, Isabel,Martos-Maldonado, Manuel C.,Somoza, álvaro,González-Rodríguez, David
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Read Online
- Tuning the Stereoselectivity of a DNA-Catalyzed Michael Addition through Covalent Modification
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Complexes of G-quadruplex DNA and CuIIions have previously been applied as catalysts in asymmetric reactions, but the largely unspecific and noncovalent nature of the interaction has impeded understanding of the structural basis of catalysis. T
- Dey, Surjendu,J?schke, Andres
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Read Online
- Design and Development of a Two-Color Emissive FRET Pair Based on a Photostable Fluorescent Deoxyuridine Donor Presenting a Mega-Stokes Shift
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We report the synthesis and site-specific incorporation in oligodeoxynucleotides (ODNs) of an emissive deoxyuridine analog electronically conjugated on its C5-position with a 3-methoxychromone moiety acting as a fluorophore. When incorporated in ODNs, thi
- Barthes, Nicolas P. F.,Gavvala, Krishna,Bonhomme, Dominique,Dabert-Gay, Anne Sophie,Debayle, Delphine,Mély, Yves,Michel, Beno?t Y.,Burger, Alain
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Read Online
- Introducing structural flexibility into porphyrin-DNA zipper arrays
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A more flexible nucleotide building block for the synthesis of new DNA based porphyrin-zipper arrays is described. Changing the rigid acetylene linker between the porphyrin substituent and the 2′-deoxyuridine to a more flexible propargyl amide containing
- Brewer, Ashley,Siligardi, Guiliano,Neylon, Cameron,Stulz, Eugen
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Read Online
- Metallocene - DNA: Synthesis, molecular and electronic structure and DNA incorporation of C5-ferrocenylthymidine derivatives
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Ferrocenylthymidine derivatives have been prepared by Pd-catalysed cross-coupling between ethynylferrocene or vinylferrocene and 5-iodo-2′-deoxyuridine. In the latter case a mixture of trans (2a) and gem (2b) isomers was obtained. The cis-vinylferrocenyl
- Pike, Andrew R.,Ryder, Lyndsey C.,Horrocks, Benjamin R.,Clegg, William,Elsegood, Mark R. J.,Connolly, Bernard A.,Houlton, Andrew
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Read Online
- Intelligent fluorescent nucleoside in sensing cytosine base: Importance of hydrophobic nature of perylene fluorophore
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Fluorescence response upon hybridization of perylene labeled oligonucleotide probes depends on the microenvironment experienced by the perylene fluorophore. In mismatched duplex (PerU-C), enhanced fluorescence was observed while in matched dupl
- Bag, Subhendu Sekhar,Saito, Yoshio,Hanawa, Kazuo,Kodate, Satoshi,Suzuka, Isamu,Saito, Isao
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Read Online
- Norepinephrine-Transporter-Targeted and DNA-Co-Targeted Theranostic Guanidines
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High risk neuroblastoma often recurs, even with aggressive treatments. Clinical evidence suggests that proliferative activities are predictive of poor outcomes. This report describes syntheses, characterization, and biological properties of theranostic guanidines that target norepinephrine transporter and undergo intracellular processing, and subsequently their catabolites are efficiently incorporated into DNA of proliferating neuroblastoma cells. Radioactive guanidines are synthesized from 5-radioiodo-2′-deoxyuridine, a molecular radiotherapy platform with clinically proven minimal toxicities and DNA-targeting properties. The transport of radioactive guanidines into neuroblastoma cells is active as indicated by the competitive suppression of cellular uptake by meta-iodobenzylguanidine. The rate of intracellular processing and DNA uptake is influenced by the agent's catabolic stability and cell population doubling times. The radiotoxicity is directly proportional to DNA uptake and duration of exposure. Biodistribution of 5-[125I]iodo-3′-O-(?-guanidinohexanoyl)-2′-deoxyuridine in a mouse neuroblastoma model shows significant tumor retention of radioactivity. Neuroblastoma xenografts regress in response to the clinically achievable doses of this agent.
- Kortylewicz, Zbigniew P.,Coulter, Donald W.,Han, Guang,Baranowska-Kortylewicz, Janina
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Read Online
- Acrylamide-dT: A polymerisable nucleoside for DNA incorporation
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The synthesis of a novel modified nucleoside phosphoramidite, Acrylamide-dT-CE phosphoramidite, obtained in three steps from commercially available starting materials, is reported. It was readily incorporated into thrombin binding aptamer (TBA) sequences
- Allabush, Francia,Mendes, Paula M.,Tucker, James H. R.
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Read Online
- Development of High-Performance Pyrimidine Nucleoside and Oligonucleotide Diarylethene Photoswitches
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Nucleosidic and oligonucleotidic diarylethenes (DAEs) are an emerging class of photochromes with high application potential. However, their further development is hampered by the poor understanding of how the chemical structure modulates the photochromic properties. Here we synthesized 26 systematically varied deoxyuridine- and deoxycytidine-derived DAEs and analyzed reaction quantum yields, composition of the photostationary states, thermal and photochemical stability, and reversibility. This analysis identified two high-performance photoswitches with near-quantitative, fully reversible back-and-forth switching and no detectable thermal or photochemical deterioration. When incorporated into an oligonucleotide with the sequence of a promotor, the nucleotides maintained their photochromism and allowed the modulation of the transcription activity of T7 RNA polymerase with an up to 2.4-fold turn-off factor, demonstrating the potential for optochemical control of biological processes.
- Kolmar, Theresa,Büllmann, Simon M.,Sarter, Christopher,H?fer, Katharina,J?schke, Andres
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supporting information
p. 8164 - 8173
(2021/03/08)
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- AN ALL-OPTICAL EXCITONIC SWITCH OPERATED IN LIQUID AND SOLID PHASES
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The present disclosure is directed to an all-optical excitonic switch comprising one or two oligonucleotides that comprises in turn donor/acceptor chromophores and photochromic nucleotide and is assembled with nanometer scale precision using DNA nanotechn
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Page/Page column 22
(2020/08/22)
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- EVOLUTION BIOACTIVE SEQUENCE-DEFINED SYNTHETIC POLYMERS USING DNA-TEMPLATED POLYMERIZATION
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The present invention provides methods and compositions for performing ordered multi- step syntheses involving modified nucleic acids by nucleic acid-mediated chemistry. This approach is useful for generating sequence-defined highly functionalized nucleic
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Paragraph 0058; 0072
(2019/01/21)
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- Catalysis of Michael Additions by Covalently Modified G-Quadruplex DNA
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Enantioselective catalysis utilizing G-quadruplex DNA-based artificial metalloenzymes has emerged as a new approach in the field of aqueous-phase homogeneous catalysis. Recently, a catalytic asymmetric Michael addition employing a covalently modified G-quadruplex in combination with CuII ions has been reported. Here we assess, by systematic chemical variation and using various spectrometric techniques, a variety of parameters that govern rate acceleration and stereoselectivity of the reaction, such as the position of modification, the topology of the quadruplex, the nature of the ligand, the length of the linker between ligand and DNA, the chemical identity of monovalent ions and transition metal complexes. The DNA quadruplex modified at position 10 (dU10) with hexynyl-linked bpy ligand showed twice the initial reaction rate as compared with the DNA strand derivatized at position 12 (dU12). The strikingly different dependence of the stereoselectivity on the linker length, and their different spectroscopic properties indicate large differences in the architecture of the catalytic centers between the dU10-derivatized and the dU12-modified quadruplexes. Upon addition of CuII, both types of bpy-derivatized DNA strands form defined 1:1 Cu–DNA complexes stable enough for mass spectrometric analysis, while the underivatized strands exhibit weak and unspecific binding, correlated with much lower catalytic rate acceleration. Both dU10- and dU12-derivatized quadruplexes could be reused ten times without reduction of stereoselectivity.
- Dey, Surjendu,Rühl, Carmen L.,J?schke, Andres
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supporting information
p. 12162 - 12170
(2017/09/14)
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- Deoxynucleoside triphosphates bearing histamine, carboxylic acid, and hydroxyl residues-synthesis and biochemical characterization
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Modified nucleoside triphosphates (dAHsTP, dUPOHTP, and dCValTP) bearing imidazole, hydroxyl, and carboxylic acid residues connected to the purine and pyrimidine bases through alkyne linkers were prepared. These modified d
- Hollenstein, Marcel
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supporting information
p. 5162 - 5172
(2013/08/23)
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- Detection of mRNA of the cyclin D1 breast cancer marker by a novel duplex-DNA probe
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Previously, we have described 5-((4-methoxy-phenyl)-trans-vinyl)-2′- deoxy-uridine, 6, as a fluorescent uridine analogue exhibiting a 3000-fold higher quantum yield (Φ 0.12) and maximum emission (478 nm) which is 170 nm red-shifted as compared to uridine.
- Segal, Meirav,Yavin, Eylon,Kafri, Pinhas,Shav-Tal, Yaron,Fischer, Bilha
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p. 4860 - 4869
(2013/07/26)
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- OLIGONUCLEOTIDE LIGATION
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A method for joining oligonucleotides. The method includes joining together one or more oligonucleotides by reacting an alkyne group lined to an oligonucleotide with an azide group linked to an oligonucleotide to form a triazole linkage. The alkyne group is a strained alkyne group. The method can include ligating together ends of one or more oligonucleotides or cross-linking strands of an oligonucleotide duplex. The methods described allow oligonucleotide strands to be ligated together without the need for a ligase enzyme.
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Paragraph 0174-0178
(2013/09/12)
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- Radiolabeled cyclosaligenyl monophosphates of 5-iodo-2′-deoxyuridine, 5-iodo-3′-fluoro-2′,3′-dideoxyuridine, and 3′-fluorothymidine for molecular radiotherapy of cancer: Synthesis and biological evaluation
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Targeted molecular radiotherapy opens unprecedented opportunities to eradicate cancer cells with minimal irradiation of normal tissues. Described in this study are radioactive cyclosaligenyl monophosphates designed to deliver lethal doses of radiation to cancer cells. These compounds can be radiolabeled with SPECT- and PET-compatible radionuclides as well as radionuclides suitable for Auger electron therapies. This characteristic provides an avenue for the personalized and comprehensive treatment strategy that comprises diagnostic imaging to identify sites of disease, followed by the targeted molecular radiotherapy based on the imaging results. The developed radiosynthetic methods produce no-carrier-added products with high radiochemical yield and purity. The interaction of these compounds with their target, butyrylcholinesterase, depends on the stereochemistry around the P atom. IC50 values are in the nanomolar range. In vitro studies indicate that radiation doses delivered to the cell nucleus are sufficient to kill cells of several difficult to treat malignancies including glioblastoma and ovarian and colorectal cancers.
- Kortylewicz, Zbigniew P.,Kimura, Yu,Inoue, Kotaro,MacK, Elizabeth,Baranowska-Kortylewicz, Janina
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scheme or table
p. 2649 - 2671
(2012/06/16)
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- The effects of the 4-(4-methylpiperazine)phenyl group on nucleosides and oligonucleotides: Cellular delivery, detection, and stability
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As drug candidates, one promising way to improve the cellular delivery efficacy of oligonucleotides is to introduce a cationic group. By introducing a cationic moiety into the oligonucleotide structure, they become capable of approaching the cell surface
- Park, Sun Min,Nam, Su-Jin,Jeong, Hyun Seok,Kim, Won Jong,Kim, Byeang Hyean
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scheme or table
p. 487 - 492
(2011/10/03)
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- Synthesis and evaluation of 5-substituted 2′-deoxyuridine monophosphate analogues as inhibitors of flavin-dependent thymidylate synthase in mycobacterium tuberculosis
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A series of 5-substituted 2′-deoxyuridine monophosphate analogues has been synthesized and evaluated as potential inhibitors of mycobacterial ThyX, a novel flavin-dependent thymidylate synthase in Mycobacterium tuberculosis. A systematic SAR study led to the identification of compound 5a, displaying an IC50 value against mycobacterial ThyX of 0.91 μM. This derivative lacks activity against the classical mycobacterial thymidylate synthase ThyA (IC50 > 50 μM) and represents the first example of a selective mycobacterial FDTS inhibitor.
- K?gler, Martin,Vanderhoydonck, Bart,De Jonghe, Steven,Rozenski, Jef,Van Belle, Kristien,Herman, Jean,Louat, Thierry,Parchina, Anastasia,Sibley, Carol,Lescrinier, Eveline,Herdewijn, Piet
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supporting information; experimental part
p. 4847 - 4862
(2011/09/19)
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- Improved synthesis of 5-hydroxymethyl-2′-deoxycytidine phosphoramidite using a 2′-deoxyuridine to 2′-deoxycytidine conversion without temporary protecting groups
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5-Hydroxymethylcytosine has recently been characterized as the 'sixth base' in human DNA. To enable research on this DNA modification, we report an improved method for the synthesis of 5-hydroxymethyl-2′-deoxycytidine (5-HOMedC) phosphoramidite for site-specific incorporation into oligonucleotides. To minimize manipulations we employed a temporary protecting group-free 2′-deoxyuridine to 2′-deoxycytidine conversion procedure that utilizes phase transfer catalysis. The desired 5-HOMedC phosphoramidite is obtained in six steps and 24% overall yield from 2′-deoxyuridine.
- Hansen, Anders S.,Thalhammer, Armin,El-Sagheer, Afaf H.,Brown, Tom,Schofield, Christopher J.
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p. 1181 - 1184
(2011/04/16)
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- Virus-like particles templated by DNA micelles: A general method for loading virus nanocarriers
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DNA amphiphile particles template formation of virus capsids and enable their loading.
- Kwak, Minseok,Minten, Inge J.,Anaya, Diana-Milena,Musser, Andrew J.,Brasch, Melanie,Nolte, Roeland J. M.,Muellen, Klaus,Cornelissen, Jeroen J. L. M.,Herrmann, Andreas
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supporting information; experimental part
p. 7834 - 7835
(2010/08/04)
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- Expanding the chemistry of DNA for in vitro selection
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Six new 5-posltlon modified dUTP derivatives connected by a unique amide linkage were synthesized and tested for compatibility with the enzymatic steps of In vitro selection. Six commercially available DNA polymerases were tested for their ability to effi
- Vaught, Jonathan D.,Bock, Chris,Carter, Jeff,Fitzwater, Tim,Otis, Matt,Schneider, Dan,Rolando, Justin,Waugh, Sheela,Wilcox, Sheri K.,Eaton, Bruce E.
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scheme or table
p. 4141 - 4151
(2010/05/15)
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- REAGENTS FOR REVERSIBLY TERMINATING PRIMER EXTENSION
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This invention relates to the field of nucleic acid chemistry, more specifically to the field of compositions of matter that comprise triphosphates of modified 2'-deoxynucleosides and oligonucleotides that are formed when these are appended to the 3'-end of a primer, wherein said modifications comprise NH2 moiety attached to their 3'-hydroxyl group and a fluorescent species in a form of a tag affixed to the nucleobase via a linker that can be cleaved. Such compositions and their associated processes enable and improve the sequencing of oligonucleotides using a strategy of cyclic reversible termination, as outlined in US Patent 6,664,079. Most specifically, the invention concerns compositions of matter that are 5'-triphosphates of ribo- and 2'- deoxyribonucleosides carrying detectable tags and oligonucleotides that might be derived from them. The invention also concerns processes wherein a DNA polymerase, RNA polymerase, or reverse transcriptase synthesizes said oligonucleotides via addition of said triphosphates to a primer.
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Page/Page column 19-20; 24
(2010/11/04)
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- Selective fluorometric detection of guanosine-containing sequences by 6-phenylpyrrolocytidine in DNA
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The intrinsically fluorescent nucleoside 2′-deoxy-6- phenylpyrrolocytidine, when incorporated into an oligonucleotide, is selectively quenched by hybridization with match DNA vs. mismatched sequences. Georg Thieme Verlag Stuttgart.
- Hudson, Robert H. E.,Ghorbani-Choghamarani, Arash
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p. 870 - 873
(2008/02/03)
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- The 6-methoxymethyl derivative of pyrrolo-dC for selective fluorometric detection of guanosine-containing sequences
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The β-cyanoethyl phosphosphoramidite derivatives of 6-methyl- and 6-methoxymethyl-3-(2-deoxy-β-D-ribofuranosyl)-3H-pyrrolo[2,3-d] pyrimidin-2-one have been synthesized. These monomers have been employed for oligodeoxynucleotide synthesis to evaluate their
- Hudson, Robert H. E.,Choghamarani, Arash Ghorbani
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p. 533 - 537
(2008/09/17)
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- 2′-O-dimethylaminoethoxyuridine and 5-dimethylaminopropargyl deoxyuridine for at base pair recognition in triple helices
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The nucleoside analogues 2′-O-dimethylaminoethoxy uridine and 5-dimethylaminopropargyl deoxyuridine have been synthesised and incorporated into oligonucleotides. Their triplex-stabilising properties have been determined in fluorescence melting experiments
- Brennan, Lavinia,Peng, Guomei,Srinivasan, Natarajan,Fox, Keith R.,Brown, Tom
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p. 1283 - 1286
(2008/09/18)
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- SYNTHESIS OF FOUR COLOR 3'-O-ALLYL MODIFIED PHOTOCLEAVABLE FLUORESCENT NUCLEOTIDES AND RELATED METHODS
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This invention provides a process for making 3'-O- allyl-dGTP-PC-Biodopy-FL-51O, 3' -0-allyl-dATP-PC-ROX, 3'-O-allyl-dCTP-PC-Bodipy-650 and 3' -O-allyl-dUTP-PC- R6G, and related methods.
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Page/Page column Sheet 2/22; 23
(2010/11/27)
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- Cancer specific radiolabeled conjugates regulated by the cell cycle for the treatment and diagnosis of cancer
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Radiolabeled conjugates are disclosed which have a component that is effective to target tumor cells, which cells selectively take up and degrade the conjugate, thereby delivering to the tumor cell nucleus a radioisotope capable of being incorporated into
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Page/Page column 4
(2008/06/13)
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- Pyrrolo-dC and pyrrolo-C: Fluorescent analogs of cytidine and 2′-deoxycytidine for the study of oligonucleotides
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Pyrrolo-dC (1a, 6-methyl-3-(2-deoxy-β-D-ribofuranosyl)-3H-pyrrolo[2,3- d]pyrimidin-2-one) and its cyanoethyl phosphoramidite 2a were synthesized. The latter was incorporated into oligodeoxyribonucleotides by standard automated synthesis techniques, where
- Berry, David A.,Jung, Kee-Yong,Wise, Dean S.,Sercel, Anthony D.,Pearson, William H.,Mackie, Hugh,Randolph, John B.,Somers, Robert L.
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p. 2457 - 2461
(2007/10/03)
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- Fluorescent 1,10-phenanthroline-containing oligonucleotides distinguish between perfect and mismatched base pairing
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(Matrix Presented) A fluorescent deoxyuridine analogue is sensitive to the polarity of its environment and exhibits a distinct emission profile in single-vs double-stranded oligonucleotides. Emission-monitored denaturation curves of internally modified dU
- Hurley, Dennis J.,Seaman, Susan E.,Mazura, Jan C.,Yitzhak, Tor
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p. 2305 - 2308
(2007/10/03)
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- Internal labeling of oligonucleotide probes by Diels-Alder cycloaddition
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A new method of adding fluorescent labels to the middle of oligonucleotides is reported. Diels-Alder cycloaddition was used to add five fluorescent maleimides to an oligonucleotide containing a 2′-deoxyuridine modified at the 5-position with a spaced fura
- Graham, Duncan,Grondin, Antonio,McHugh, Callum,Fruk, Ljiljana,Smith, W.Ewen
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p. 4785 - 4788
(2007/10/03)
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- New oligoethylene ester derivatives of 5-iodo-2′-deoxyuridine as dermal prodrugs: Synthesis, physicochemical properties, and skin permeation studies
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Five new oligoethylene ester derivatives (9-13) of 5-iodo-2′-deoxyuridine (IDU) were synthesized and assayed to determine their lipophilicity by both experimental lipophilicity indices (log K′) and calculated partition coefficients (CLOGP). In vitro exper
- Bonina, Francesco Paolo,Rimoli, Maria Grazia,Avallone, Lucia,Barbato, Francesco,Amato, Marzia,Puglia, Carmelo,Ricci, Maurizio,De Caprariis, Paolo
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p. 171 - 179
(2007/10/03)
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- Methods of synthesis of halogen base-modified oligonucleotides and subsequent labeling with a metal-catalyzed reaction
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The present invention provides metal-containing purines, pyrimidines, nucleosides, nucleotides and oligonucleotides; including phosphoramidite and photolabile derivatives thereof, including methods of making and method of using same. The present invention provides a method for detection of nucleic acid sequences via electrochemical or photochemical means.
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- Synthesis of a modified thymidine monomer for site-specific incorporation of reporter groups into oligonucleotides
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The efficient incorporation of reporter groups into oligonucleotides at specific sites has been facilitated by the synthesis of a novel modified thymidine monomer with an FMOC-protected hydroxyl group on a linker. The primary hydroxyl group can be deprotected during or after solid-phase oligonucleotide synthesis and reacted with any reporter phosphoramidite.
- Brown, Lynda J.,May, Jonathan P.,Brown, Tom
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p. 2587 - 2591
(2007/10/03)
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- Phosphoramidites and oligonucleotides containing 7-deazapurines and pyrimidines carrying aminopropargyl side chains
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The synthesis of phosphoramidites containing 7-deazaguanine, 7-deazaadenine, uracil and cytosine carrying aminopropargyl chains is described. The corresponding oligonucleotides are stabilized in duplexes thermally as well as against degradation by exonucl
- Seela,Ramzaeva,Leonard,Chen,Debelak,Feiling,Kroeschel,Zulauf,Wenzel,Froehlich,Kostrzewa
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p. 1421 - 1424
(2007/10/03)
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- DNA duplexes stabilized by modified monomer residues: Synthesis and stability
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The synthesis of a series of 2′-deoxyuridine analogues modified at the 5-position and a series of 2′-deoxypurines modified at the 8-position is described. Ultraviolet melting studies have been used to assess the stability of DNA duplexes 12- and 8-residue
- Graham, Duncan,Parkinson, John A.,Brown, Tom
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p. 1131 - 1138
(2007/10/03)
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- Nucleosides and nucleotides. 162. Facile synthesis of 5'-5'-linked oligodeoxyribonucleotides with the potential for triple-helix formation
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The facile synthesis of 5'-5'-linked oligodeoxyribonucleotides (ODNs) with the potential for triple-helix formation is described. ODNs containing 5-trifluoroethoxycarbonyl-2'-deoxyuridine were treated with several diaminoalkanes to give ODNs carrying amin
- Ueno, Yoshihito,Ogawa, Akira,Nakagawa, Aiko,Matsuda, Akira
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p. 2817 - 2822
(2007/10/03)
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