5-(1-propargylamino)-2'-deoxyuridine (UP): A novel thymidine analogue for generating DNA triplexes with increased stability

Two phosphate modifications were introduced into the DNA backbone using the Staudinger reaction between the 3’,5’-dinucleoside β-cyanoethyl phosphite triester formed during DNA synthesis and sulfonyl azides, 4-(azidosulfonyl)-N,N,N-trimethylbutan-1-aminium iodide (N+ azide) or p-toluenesulfonyl (tosyl or Ts) azide, to provide either a zwitterionic phosphoramidate with N+ modification or a negatively charged phosphoramidate for Ts modification in the DNA sequence. The incorporation of these N+ and Ts modifications led to the formation of thermally stable parallel DNA triplexes, regardless of the number of modifications incorporated into the oligodeoxynucleotides (ONs). For both N+ and Ts-modified ONs, the antiparallel duplexes formed with complementary RNA were more stable than those formed with complementary DNA (except for ONs with modification in the middle of the sequence). Additionally, the incorporation of N+ modifications led to the formation of duplexes with a thermal stability that was less dependent on the ionic strength than native DNA duplexes. The thermodynamic analysis of the melting curves revealed that it is the reduction in unfavourable entropy, despite the decrease in favourable enthalpy, which is responsible for the stabilisation of duplexes with N+ modification. N+ONs also demonstrated greater resistance to nuclease digestion by snake venom phosphodiesterase I than the corresponding Ts-ONs. Cell uptake studies showed that Ts-ONs can enter the nucleus of mouse fibroblast NIH3T3 cells without any transfection reagent, whereas, N+ONs remain concentrated in vesicles within the cytoplasm. These results indicate that both N+ and Ts-modified ONs are promising for various in vivo applications.

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The binding of analogues of coralyne and related heterocyclics to DNA triplexes

Biochemistry and Cell Biology ◽

10.1139/o95-002 ◽

1995 ◽

Vol 73 (1-2) ◽

pp. 11-18 ◽

Cited By ~ 25

Author(s):

Laura J. P. Latimer ◽

Natasha Payton ◽

Gavin Forsyth ◽

Jeremy S. Lee

Keyword(s):

Thermal Denaturation ◽

Positive Charge ◽

Triplex Dna ◽

Alkyl Chains ◽

Dna Triplexes ◽

Weak Binding ◽

Related Alkaloid ◽

General Preference ◽

Nitrogen Ring ◽

Derivatives Of

Coralyne has been shown previously to bind well to both T∙A∙T- and C∙G∙C+-containing triplexes. Derivatives of coralyne were prepared and their binding to poly(dT)∙poly(dA)∙poly(dT) and poly[d(TC)]∙poly[d(GA)]∙poly[d(C+T)] was assessed from thermal denaturation profiles. A tetraethoxy derivative showed only weak binding to both types of triplex. Analogues with extended 8-alkyl chains showed good binding to poly(dT)∙poly(dA)∙poly(dT), but the preference for triplex poly[d(TC)]∙poly[d(GA)]∙poly[d(C+T)] was decreased compared with the duplex. Sanguinarine, a related alkaloid, bound well to poly(dT)∙poly(dA)∙poly(dT) but only weakly to the protonated triplex. It is hypothesized that the position of the protonated nitrogen ring is important for binding to poly[d(TC)]∙poly[d(GA)]∙poly[d(C+T)]. A series of other chromophores was studied and only those with a positive charge bound to triplexes. All of these bound well to poly(dT)∙poly(dA)∙poly(dT) but only weakly if at all to the duplex poly(dA)∙poly(dT). In contrast, most of them did not bind well to the triplex poly[d(TC)]∙poly[d(GA)]∙poly[d(C+T)] and those that did still showed a preference for duplex poly[d(TC)]∙poly[d(GA)]. In general, preference for triplex poly(dT)∙poly(dA)∙poly(dT) compared with the duplex is a common feature of intercalating drugs. On the other hand, specificity for protonated triplexes may be very difficult to achieve.Key words: triplex DNA, DNA-binding drugs, intercalation.

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NMR structural studies of intramolecular (Y+)n.cntdot.(R+)n(Y-)n DNA triplexes in solution: imino and amino proton and nitrogen markers of G.cntdot.AT base triple formation

Biochemistry ◽

10.1021/bi00101a016 ◽

1991 ◽

Vol 30 (37) ◽

pp. 9022-9030 ◽

Cited By ~ 47

Author(s):

Ishwar Radhakrishnan ◽

Xiaolian Gao ◽

Carlos De los Santos ◽

David Live ◽

Dinshaw J. Patel

Keyword(s):

Structural Studies ◽

Dna Triplexes

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Physico-chemical studies on DNA triplexes containing an alternate third strand with a non-nucleotide linker

International Journal of Biological Macromolecules ◽

10.1016/s0141-8130(01)00136-2 ◽

2001 ◽

Vol 28 (5) ◽

pp. 387-394 ◽

Cited By ~ 4

Author(s):

Concetta Giancola ◽

Luigi Petraccone ◽

Maria Pieri ◽

Lorenzo De Napoli ◽

Daniela Montesarchio ◽

...

Keyword(s):

Dna Triplexes ◽

Physico Chemical ◽

Chemical Studies

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DNA triplex structure, thermodynamics, and destabilisation: insight from molecular simulations

Physical Chemistry Chemical Physics ◽

10.1039/c8cp02385a ◽

2018 ◽

Vol 20 (20) ◽

pp. 14013-14023 ◽

Cited By ~ 6

Author(s):

Belinda J. Boehm ◽

Charles Whidborne ◽

Alexander L. Button ◽

Tara L. Pukala ◽

David M. Huang

Keyword(s):

Molecular Dynamics ◽

Neurodegenerative Disease ◽

Molecular Dynamics Simulations ◽

Small Molecule ◽

Molecular Simulations ◽

Friedreich’S Ataxia ◽

Dna Triplexes ◽

Dna Triplex ◽

Triplex Structure ◽

Dynamics Simulations

Molecular dynamics simulations are used to elucidate the structure and thermodynamics of DNA triplexes associated with the neurodegenerative disease Friedreich's ataxia (FRDA), as well as complexes of these triplexes with the small molecule netropsin, which is known to destabilise triplexes.

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Cell proliferation in the repairing adult insect central nervous system: incorporation of the thymidine analogue 5-bromo-2-deoxyuridine in vivo

Journal of Cell Science ◽

10.1242/jcs.95.4.599 ◽

1990 ◽

Vol 95 (4) ◽

pp. 599-604

Author(s):

P.J. Smith ◽

E.A. Howes ◽

J.E. Treherne

Keyword(s):

Central Nervous System ◽

Cell Proliferation ◽

Nervous System ◽

Blood Brain Barrier ◽

Glial Cells ◽

Past Research ◽

Thymidine Analogue ◽

Adult Insect ◽

Insect Central Nervous System

Uptake of the thymidine analogue 5-bromo-2-deoxyuridine into non-neuronal cells of the insect central nervous system has been examined following a controlled lesioning of the glial elements. The pattern of BUdR labelling along the penultimate abdominal connective was examined over a period of 17 days. Cell proliferation occurred in and immediately around the site of damage in both perineurial and subperineurial glial cells but at different times post-lesion for the two regions. Proliferation in the perineurial zone was maximal at 6–8 days post-lesion but continued for at least 17 days. Subperineurial proliferation was less dramatic and peaked between days 8–11 post-lesion. In both areas division appears to be confined to the reactive glial cells. These results are discussed in the context of past research on this system, particularly with regard to the restoration of the blood-brain barrier.

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