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Oligo Synthesis

Oligo Synthesis : CEPs

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Ribo-tC° Phosphoramidite

Ribo-tC° Phosphoramidite

Glen Research

Catalogue No.DescriptionPack SizePriceQty
10-3517-02Ribo-tC° Phosphoramidite 0.25 grams £1,350.00 Quantity Add to Order
10-3517-90Ribo-tC° Phosphoramidite 100 umoles £518.00 Quantity Add to Order
10-3517-95Ribo-tC° Phosphoramidite 50 umoles £273.00 Quantity Add to Order

Description

Ribo-tC° Phosphoramidite

FLUORESCENT NUCLEOSIDES (Part 3)

The tricyclic fluorescent nucleoside analogues, 1,3-diaza-2-oxophenothiazine, tC, and 1,3-diaza-2-oxophenoxazine, tCo, are deoxycytidine analogs that have been shown to base pair faithfully with dG with virtually no disruption of the normal duplex structure.3-5 This means that the stability of the DNA duplex is not compromised as compared to the control regardless of DNA sequence. The fluorescence quantum yield of tC is essentially unchanged between single stranded and double stranded DNA - 0.21 for single stranded DNA and 0.19 for duplex DNA. Also, the fluorescence characteristics of tC are not sensitive to neighboring base combinations. tCo has been shown to be the brightest fluorescent nucleoside analogue in duplex context reported so far and even retains the majority of its fluorescence when surrounded by guanine residues. Indeed, tCo has been reported to be 25-50 times brighter than 2-aminopurine.

The base analogue tCnitro is a FRET-acceptor together with tCO (or tC) as the donor molecule. This constitutes the first ever description of a nucleobase FRET-pair. This novel FRET-pair provides a unique tool for investigations of nucleic acid containing systems. tCnitro is virtually non-fluorescent under normal conditions.

Glen Report 30.1

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References

References

1. A Highly Fluorescent DNA Base Analogue that Forms floatLefttson-Crick Base Pairs with Guanine. Wilhelmsson L.M., Holmén, A., Lincoln, P., Nielsen, P.E., Nordén, B.. J. Am. Chem. Soc.; 2001, 123(10); 2434-2435.

2. Fluorescent Properties of DNA Base Analogue tC upon Incorporation into DNA – Negligible Influence of Neighboring Bases on Fluorescence Quantum Yield. Sandin, P., Wilhelmsson, L.M., Lincoln, P., Powers, V.E.C., Brown, T., Albinsson, B.. Nucleic Acids Res.; 2005, 33(16); 5019-5025.

3. Characterisation and Use of an Unprecedentedly Bright and Structurally Non-perturbing Fluorescent DNA Base Analogue. Sandin, P., Börjesson, K., Li, H., Mårtensson, J., Brown, T., Wilhelmsson, L.M., Albinsson, B.. Nucleic Acids Res.; 2008, 36(1); 157-167.

4. A Nucleic Acid Base Analog FRET-pair Facilitating Detailed Structural Measurements in Nucleic Acid Containing Systems. Börjesson, K., Preus, S., El-Sagheer, A.H., Brown, T., Albinsson, B., Wilhelmsson, L.M.. J. Am. Chem. Soc.; 2009, 131; 4288-4293.

5. Highly Efficient Incorporation of the Fluorescent Nucleotide Analogues tC and tCO by Klenow Fragment. Sandin, P., Stengel, G., Ljungdahl, T., Börjesson, K., Macao, B., Wilhelmsson, L.M.. Nucleic Acids Res.; 2009, 37(12); 3924-3933.

6. Ambivalent Incorporation of the Fluorescent Cytosine Analogues tC and tCO by Human DNA Polymerase α and Klenow Fragment. Stengel, G., Purse, B.W., Wilhelmsson, L.M., Urban, M., Kuchta, R.D.. Biochemistry; 2009, 48(31); 7547-7555.

7. Discrimination against the Cytosine Analog tC by Escherichia coli DNA Polymerase IV DinB. Walsh, J.M., Bouamaied, I., Brown, T., Wilhelmsson, L.M., Beuning, P.J.. J. Mol. Biol.; 2011, 409; 89-100.

8. Mammalian Transcription Factor A is a Core Component of the Mitochondrial Transcription Machinery. Shi, Y., Dierckx, A., Wanrooij, P.H., Larsson, N-G., Wilhelmsson, L.M., Falkenberg, M., Gustafsson, C.M..Proc. Natl. Acad. Sci. U.S.A.; 2012, 109(41), 16510-16515.

9. FRETmatrix: A General Methodology for the Simulation and Analysis of FRET in Nucleic Acids. Preus, S., Kilså, K., Miannay, F-A., Albinsson, B., Wilhelmsson, L.M.. Nucleic Acids Res.; 2013, 41(1), e18.

10. Studying Z-DNA and B- to Z-DNA transitions using a cytosine analogue FRET-pair. Dumat, B., Larsen, A.F., Wilhelmsson, L.M.. Nucleic Acids Res.; 2016, 44, e101.

11. Twist-open mechanism of DNA damage recognition by the Rad4/XPC nucleotide excision repair complex. Velmurugu, Y. Chen, X.J., Sevilla, P.S., Min, J.H., Ansari, A.. Proc. Natl. Acad. Sci. U.S.A.; 2016, 113, E2296-E2305.

12. In Vitro Fluorogenic Real-Time Assay of the Repair of Oxidative DNA Damage. Edwards S.K., Ono T., Wang S., Jiang W., Franzini R.M., Jung J.W., Chan K.M., Kool E.T.. ChemBioChem; 2015, 16, 1637-1646.

13. Fluorescent RNA cytosine analogue – an internal probe for detailed structure and dynamics investigations. Füchtbauer, A.F., Preus, S., Börjesson, K., McPhee, S.A., Lilley D.M.J., Wilhelmsson, L.M.. Sci. Rep.; 2017, 7, 2393.

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Notes

Absorption and emisssion data for tC and tCo are collected below:

tCQY  
      (L/mol.cm)
single-
stranded		 0.21 385nm 4000
double-
stranded		 0.19    
tCoQY   
      (L/mol.cm)
single-
stranded		 0.30 360nm 9000
double-
stranded		 0.21    

(QY determined relative to quinine sulfate in 0.5M H2SO4)

Intellectual Property

These products are offered in collaboration with ModyBase HB.

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