1
|
Carrocci TJ, Lohe L, Ashton MJ, Höbartner C, Hoskins AA. Debranchase-resistant labeling of RNA using the 10DM24 deoxyribozyme and fluorescent modified nucleotides. Chem Commun (Camb) 2017; 53:11992-11995. [PMID: 28984884 PMCID: PMC5668183 DOI: 10.1039/c7cc06703h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The 10DM24 deoxyribozyme can site-specifically label RNAs with fluorophore-GTP conjugates; however, the 2',5'-branched RNA linkage is readily cleaved by debranchase. To prevent loss of labels upon cleavage, we synthesized phosphorothioate-modified, fluorescent GTP derivatives and elaborated conditions for their incorporation by 10DM24. RNAs labeled with fluorescent derivatives of Sp-GTPS were found to be resistant to debranchase.
Collapse
Affiliation(s)
- Tucker J Carrocci
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Dr., Madison, WI 53706, USA.
| | - Lea Lohe
- Institute for Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstr. 2, 37077 Göttingen, Germany
| | - Matthew J Ashton
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Dr., Madison, WI 53706, USA.
| | - Claudia Höbartner
- Institute for Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstr. 2, 37077 Göttingen, Germany and Institute for Organic Chemistry, Julius-Maximilians-University Würzburg, Am Hubland, 97074 Würzburg, Germany.
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Dr., Madison, WI 53706, USA.
| |
Collapse
|
2
|
Kato Y, Oka N, Wada T. Highly chemo- and regioselective phosphitylation of unprotected 2′-deoxyribonucleosides. Tetrahedron Lett 2006. [DOI: 10.1016/j.tetlet.2006.02.060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
3
|
Misiura K, Szymanowicz D, Stec WJ. Synthesis of nucleoside alpha-thiotriphosphates via an oxathiaphospholane approach. Org Lett 2006; 7:2217-20. [PMID: 15901173 DOI: 10.1021/ol050617r] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text]. Nucleoside 5'-O-(alpha-thiotriphosphates) were obtained in reactions of the appropriate nucleoside 5'-O-(2-thio-1,3,2-oxathiaphospholanes) with pyrophosphate in the presence of DBU. The presented method allows also for preparation of alpha-seleno congeners and corresponding alpha-modified diphosphates.
Collapse
Affiliation(s)
- Konrad Misiura
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland
| | | | | |
Collapse
|
4
|
Mathew KM, Ravi S, Sontakke CV, Chander H. Synthesis of deoxyadenosine-5?-(35S)-thiomonophosphate [dAMP(35S)] of high specific activity - a key intermediate for the synthesis of Sp-deoxyadenosine-5?-(alpha;-35S)-thiotriphosphate [Sp-dATP (?-35S)]. J Labelled Comp Radiopharm 2002. [DOI: 10.1002/jlcr.531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
5
|
Affiliation(s)
- K Burgess
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842-3012, and ISIS Pharmaceuticals, Carlsbad Research Center, 2292 Faraday Avenue, Carlsbad, California 920088
| | | |
Collapse
|
6
|
Moore BM, Li K, Doughty MB. Deoxyadenosine-based DNA polymerase photoprobes: design, synthesis, and characterization as inhibitors of the Escherichia coli DNA polymerase I Klenow fragment. Biochemistry 1996; 35:11634-41. [PMID: 8794743 DOI: 10.1021/bi952514u] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
DNA polymerase photoprobes 2-[(4-azidophenacyl)thio]-2'-deoxyadenosine 5'-triphosphate (1), 2-[(4-azidophenylsulfenyl)thio]-2'-deoxyadenosine 5'-triphosphate (2), and 2-[(4-azido-2-nitrophenyl)-thio]-2'-deoxyadenosine 5'-triphosphate (3) were designed from a thermodynamic model of DNA polymerase 1-substrate interactions such that the triphosphate would anchor the inhibitor and allow the phenyl azide to interact with the complementary template binding site. Photoprobes 1-3 were synthesized by condensation of 2-thio-2'-deoxyadenosine or its phosphate with p-azidophenacyl bromide, N-(4-azidophenylsulfenyl)phthalimide, and 4-azido-1-fluoro-2-nitrobenzene, respectively, and characterized as reversible and photoinduced irreversible inhibitors of the DNA polymerase I Klenow fragment and HIV I reverse transcriptase. The aryl azides decomposed with irradiation at 300 and 350 nm with half-lives ranging from 0.98 to 2.33 min and 2.15 to 5.38 min, respectively, with quantum efficiencies ranging from 0.29 to 0.55 and no apparent photodecomposition of the 2-thio-2'-deoxyadenosine nucleotide. Photoprobes 1-3 showed mixed noncompetitive inhibition of the Klenow fragment polymerase activity versus poly(dA).(T)10 as variable substrate with apparent competitive inhibition constants of 2.1, 36, and 29 microM, respectively, evidence suggesting that these photoprobes bind to both the free enzyme form and the enzyme-template-primer binary complex. Of the three photoprobes, only nucleotide 1 photoinactivates the Klenow fragment; in the presence of a 200-fold excess of nitrene scavenger, photoprobe 1 inactivates 92% of the Klenow fragment polymerase activity with saturation observed at 9.7 microM and an IC50 of about 2 microM. This evidence demonstrates that photoprobe 1 does bind to the Klenow fragment in the absence of template-primer and that it is an efficient photoprobe.
Collapse
Affiliation(s)
- B M Moore
- Department of Medicinal Chemistry, University of Kansas, Lawrence 66045, USA
| | | | | |
Collapse
|
7
|
Gopal D, Pavlov DI, Levitsky DI, Ikebe M, Burke M. Chemomechanical transduction in the actomyosin molecular motor by 2',3'-dideoxydidehydro-ATP and characterization of its interaction with myosin subfragment 1 in the presence and absence of actin. Biochemistry 1996; 35:10149-57. [PMID: 8756479 DOI: 10.1021/bi960597o] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The effect of torsional freedom about the N-glycoside bond of ATP in the ability of the nucleoside triphosphate to support chemomechanical transduction (Takenaka et al., 1978) has been investigated by examining the ability of the nucleotide analogue 2',3'-dideoxy-2',3'-didehydro-ATP (1b, enf-ATP) to act as a substrate for myosin subfragment 1 in the presence and absence of actin and to support actin sliding in the standard in vitro motility assay. By converting the ribosyl ring of the natural substrate to the rigid and almost planar enofuranosyl ring, effects on torsional freedom about the N-glycoside bond due to changes in ribosyl ring pucker and/or by steric interferences of the protons attached to the 2' and 3' carbons are eliminated allowing for increased torsional freedom about the N-glycoside bond. The data indicate that this enofuranosyl analogue is an excellent substrate for subfragment 1 and actosubfragment 1 and produces actin sliding velocities which are twice as fast as those observed with ATP in the standard in vitro motility assay. The analogue diphosphate is trapped in S1 by the common P(i) analogues, but the rate of formation of the ternary complex formed with Vi is very slow compared to that observed with MgADP. Similar conformations of S1 are formed with Mg.enf-ATP and MgATP under steady-state conditions, but S1 with bound Mg.enf-ADP differs significantly from that observed with MgADP.
Collapse
Affiliation(s)
- D Gopal
- Department of Biology, College of Arts and Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | | | | | | | | |
Collapse
|
8
|
Seidel CAM, Schulz A, Sauer MHM. Nucleobase-Specific Quenching of Fluorescent Dyes. 1. Nucleobase One-Electron Redox Potentials and Their Correlation with Static and Dynamic Quenching Efficiencies. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp951507c] [Citation(s) in RCA: 805] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
9
|
Puri N, Hünsch S, Sund C, Ugi I, Chattopadhyaya J. The synthesis and reactivity of new 2-(N,N-diisopropylamino)-3-methylsulfonyl-1,3,2-benzoxazaphospholes. The utility of the 5-chloro analogue in the one-pot synthesis of oligothiophosphates: [ApsppA, ApspppA, ppp5′A2′ps5′A, m7GpsppA, Apspppp, Apspp]. Tetrahedron 1995. [DOI: 10.1016/0040-4020(95)00031-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
10
|
Rensland H, John J, Linke R, Simon I, Schlichting I, Wittinghofer A, Goody RS. Substrate and product structural requirements for binding of nucleotides to H-ras p21: the mechanism of discrimination between guanosine and adenosine nucleotides. Biochemistry 1995; 34:593-9. [PMID: 7819254 DOI: 10.1021/bi00002a026] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The interaction of the protein product of the H-ras oncogene with a series of nucleoside di- and triphosphates has been examined to investigate the tolerance of the active site to departures from the GTP or GDP structures. Nucleotides which bind relatively strongly could be used as competitors of GDP in a simple filter binding assay to give semiquantitave estimates of their affinities. For more weakly binding nucleotides or to obtain quantitative data, a transient kinetic method was used which was based on determination of the association and dissociation rate constants. The results obtained indicate that substantial modification of the sugar or phosphate structure is tolerated with little or moderate loss of affinity, but that large losses in affinity occur on modification of the base structure. In particular, replacing the guanine by an adenine residue leads to a dramatic loss of affinity. Thus, discrimination against ATP and ADP is very high (relative affinities of ATP and GTP 1:10(7)). This is due not only to loss of positive (stabilizing) interactions, but especially to the introduction of negative ones.
Collapse
Affiliation(s)
- H Rensland
- Abetilung Physikalische Biochemie, Max-Planck-Institut für molekulare Physiologie, Dortmund, FRG
| | | | | | | | | | | | | |
Collapse
|
11
|
Ettner N, Haak U, Niederweis M, Hillen W. Synthesis of 8-Bromo- and 8-Azido-2′-deoxyadenosine-5′-O-(1-thiotriphosphate). ACTA ACUST UNITED AC 1993. [DOI: 10.1080/07328319308021508] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
12
|
John J, Rensland H, Schlichting I, Vetter I, Borasio G, Goody R, Wittinghofer A. Kinetic and structural analysis of the Mg(2+)-binding site of the guanine nucleotide-binding protein p21H-ras. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)54022-9] [Citation(s) in RCA: 206] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
|
13
|
Gaur R, Sproat B, Krupp G. Novel solid phase synthesis of 2'-o-methylribonucleoside 5'-triphosphates and their α-thio analogues. Tetrahedron Lett 1992. [DOI: 10.1016/s0040-4039(00)92072-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
14
|
Dahl O. Preparation of Nucleoside Phosphorothioates, Phosphorodithioates and Related Compounds. ACTA ACUST UNITED AC 1991. [DOI: 10.1080/01961779108048765] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
15
|
Hoheisel JD, Lehrach H. Quantitative measurements on the duplex stability of 2,6-diaminopurine and 5-chloro-uracil nucleotides using enzymatically synthesized oligomers. FEBS Lett 1990; 274:103-6. [PMID: 2253762 DOI: 10.1016/0014-5793(90)81340-t] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
2,6-Diaminopurine and 5-chloro-uracil 2'-deoxynucleoside 5'-triphosphates were synthesized from their 2'-deoxynucleosides. Using a method of creating oligonucleotides by enzymatic primer extension, dodecanucleotides representing an XbaI/SalI site and the complementary SalI/XbaI site were generated containing these base modifications. Their duplex stability was quantitatively compared by thin-layer chromatography to oligomers containing 2'-deoxyadenosine and 2'-deoxythymidine. The two unmodified oligomers already showed significant differences in dissociation temperature and binding equilibrium. Substitution with 5-chloro-2'-deoxyuridine did not affect the dissociation temperature of either oligomer, the 2,6-diaminopurine, however, led to an increase of 1.8 degrees C or 1.5 degrees C per modified base, respectively. While in the XbaI/SalI oligomer both base modifications changed the binding equilibrium, the 2,6-diaminopurine by a factor of 1.32, the 5-chloro-uracil by 0.65, no such effect was found with the complementary oligomer.
Collapse
|
16
|
Blackburn G, Guo MJ. Chemical synthesis, separation, and identification of diastereoisomers of P1,P4-dithio-5′,5‴-diadenosyl P1,P4-tetraphosphate and its P2,P3-methylene analogues. Tetrahedron Lett 1990. [DOI: 10.1016/s0040-4039(00)97625-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
17
|
John J, Schlichting I, Schiltz E, Rösch P, Wittinghofer A. C-terminal Truncation of p21H Preserves Crucial Kinetic and Structural Properties. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)51599-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
18
|
John J, Frech M, Wittinghofer A. Biochemical properties of Ha-ras encoded p21 mutants and mechanism of the autophosphorylation reaction. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)37854-2] [Citation(s) in RCA: 84] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
19
|
|
20
|
|