| 1. |
- Börjesson, Karl, 1982, et al.
(författare)
-
A membrane anchored DNA-based energy/electron transfer assembly
- 2008
-
Ingår i: Nucleic acids symposium series (2004). - 1746-8272. ; :52, s. 691-691
-
Tidskriftsartikel (refereegranskat)abstract
- In this work the trapping and conversion of visible light energy into chemical energy is examined using a supramolecular assembly. This consists of a light absorbing antenna and a porphyrin redox centre both covalently attached to a DNA strand, which in turn is bound to a lipid membrane. The excitation energy is finally trapped as a benzoquinone radical anion that could potentially be used in subsequent chemical reactions.
|
|
| 2. |
- Börjesson, Karl, 1982, et al.
(författare)
-
Characterization and use of tricyclic fluorescent nucleic acid base analogues
- 2008
-
Ingår i: Nucleic acids symposium series (2004). - 1746-8272. ; :52, s. 3-4
-
Tidskriftsartikel (refereegranskat)abstract
- The two recently developed nucleic acid probe molecules tC and tC(O) both have unique properties compared to other molecules in the family of fluorescent base analogues.(1-5) These tricyclic base analogues both form very stable base pairs with guanine and give minimal perturbations to the native structure of DNA.(2) We have found that tC(O) is the brightest fluorescent base analogue reported(4) and that tC also is very bright and has a fluorescence quantum yield that is virtually insensitive to its surrounding microenvironment within the nucleic acid(3). These base analogues have so far been used in FRET-studies of a DNA-polymerase system(6) and in initial anisotropy-studies of DNA-containing systems(4).
|
|
| 3. |
- Engman, Cecilia, 1974, et al.
(författare)
-
DNA adopts normal B-form upon incorporation of highly fluorescent DNA base analogue tC: NMR structure and UV-Vis spectroscopy characterization
- 2004
-
Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 1362-4962 .- 0305-1048. ; 32:17, s. 5087-95
-
Tidskriftsartikel (refereegranskat)abstract
- The influence of the highly fluorescent tricyclic cytosine base analogue (tC) on duplex DNA conformation is investigated. The duplex properties are characterized by absorbance and circular dichroism (CD) for all combinations of neighbouring bases to tC, and an NMR structure is determined for one tC-containing sequence. For the oligonucleotides with one tC incorporated instead of cytosine, the melting temperature is increased on average by 2.7 degrees C above that for the unmodified ones. CD spectra are practically identical for modified and unmodified sequences, indicating an unperturbed B-DNA conformation. The NMR structure determination of the self-complementary sequence 5'-CTC(tC)ACGTGGAG shows a DNA conformation consistent with B-form for the whole duplex. The root-mean-square distance for the nucleotides of the eight central base pairs between the 10 structures with lowest CYANA target functions and a mean structure is 0.45 +/- 0.17 A. The NMR data confirm correct base pairing for tC by the observation of both intrastrand and interstrand imino proton NOEs. Altogether, this suggests that tC works well as a cytosine analogue, i.e. it is situated in the base stack, forming hydrogen bonds with G in the complementary strand, without distorting the DNA backbone conformation. This first example of an artificial, highly fluorescent DNA base that does not perturb the DNA conformation could have valuable applications for the study of the structure and dynamics of nucleic acid systems.
|
|
| 4. |
- Lawson, Christopher, 1968, et al.
(författare)
-
Synthesis, oligonucleotide incorporation and fluorescence properties in DNA of a bicyclic thymine analogue
- 2018
-
Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8
-
Tidskriftsartikel (refereegranskat)abstract
- Fluorescent base analogues (FBAs) have emerged as a powerful class of molecular reporters of location and environment for nucleic acids. In our overall mission to develop bright and useful FBAs for all natural nucleobases, herein we describe the synthesis and thorough characterization of bicyclic thymidine (bT), both as a monomer and when incorporated into DNA. We have developed a robust synthetic route for the preparation of the bT DNA monomer and the corresponding protected phosphoramidite for solid-phase DNA synthesis. The bT deoxyribonucleoside has a brightness value of 790 M(-1)cm(-1) in water, which is comparable or higher than most fluorescent thymine analogues reported. When incorporated into DNA, bT pairs selectively with adenine without perturbing the B-form structure, keeping the melting thermodynamics of the B-form duplex DNA virtually unchanged. As for most fluorescent base analogues, the emission of bT is reduced inside DNA (4.5- and 13-fold in single- and double-stranded DNA, respectively). Overall, these properties make bT an interesting thymine analogue for studying DNA and an excellent starting point for the development of brighter bT derivatives.
|
|
| 5. |
- Lundberg, Erik, 1981, et al.
(författare)
-
A new fixation strategy for addressable nano-network building blocks
- 2010
-
Ingår i: Chemical Communications. - 1364-548X .- 1359-7345. ; 46:21, s. 3714-3716
-
Tidskriftsartikel (refereegranskat)abstract
- Rapid controlled self-assembly makes DNA ideal for building nanostructures. A problem using hybridized intermediates in hierarchic assembly is their thermodynamic lability. We demonstrate a click-fixation technology by which robust hexagonal DNA modules can be made. This principle is applicable to a wide variety of DNA nanoconstructs.
|
|
| 6. |
- Lundberg, Erik, 1981, et al.
(författare)
-
Addressable molecular node assembly - high information density DNA nanostructures
- 2008
-
Ingår i: Nucleic acids symposium series (2004). - 1746-8272. ; :52, s. 683-684
-
Tidskriftsartikel (refereegranskat)abstract
- The inherent self-assembly properties of DNA make it ideal in nanotechnology. We present a fully addressable DNA nanostructure with the smallest possible unit cell, a hexagon with a side-length of only 3.4 nm.(2,3) Using novel three-way oligonucleotides, where each side has a unique double-stranded DNA sequence that can be assigned a specific address, we will build a non-repetitive two-dimensional grid.
|
|
| 7. |
- Sandin, Peter, 1977, et al.
(författare)
-
Characterization and Use of an Unprecedentedly Bright and Structurally Non-Perturbing Fluorescent DNA Base Analogue
- 2008
-
Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 36:1, s. 157-167
-
Tidskriftsartikel (refereegranskat)abstract
- This article presents the first evidence that the DNA base analogue 1,3-diaza-2-oxophenoxazine, tC(O), is highly fluorescent, both as free nucleoside and incorporated in an arbitrary DNA structure. tC(O) is thoroughly characterized with respect to its photophysical properties and structural performance in single- and double-stranded oligonucleotides. The lowest energy absorption band at 360 nm (epsilon = 9000 M-1 cm(1)) is dominated by a single in-plane polarized electronic transition and the fluorescence, centred at 465 nm, has a quantum yield of 0.3. When incorporated into double-stranded DNA, tC(O) shows only minor variations in fluorescence intensity and lifetime with neighbouring bases, and the average quantum yield is 0.22. These features make tC(O), on average, the brightest DNA-incorporated base analogue so far reported. Furthermore, it base pairs exclusively with guanine and causes minimal perturbations to the native structure of DNA. These properties make tC(O) a promising base analogue that is perfectly suited for e.g. photophysical studies of DNA interacting with macromolecules (proteins) or for determining size and shape of DNA tertiary structures using techniques such as fluorescence anisotropy and fluorescence resonance energy transfer (FRET).
|
|
| 8. |
- Sandin, Peter, 1977, et al.
(författare)
-
Fluorescent Properties of DNA Base Analogue tC upon Incorporation into DNA - Negligible Influence of Neighboring Bases on Fluorescence Quantum Yield
- 2005
-
Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 33:16, s. 5019-5025
-
Tidskriftsartikel (refereegranskat)abstract
- The quantum yield of the fluorescent tricyclic cytosine analogue, 1,3-diaza-2-oxophenothiazine, tC, is high and virtually unaffected by incorporation into both single- and double-stranded DNA irrespective of neighbouring bases (0.17-0.24 and 0.16-0.21, respectively) and the corresponding fluorescence decay curves are all mono-exponential, properties that are unmatched by any base analogue so far. The fluorescence lifetimes increase when going from tC free in solution (3.2 ns) to single- and double-stranded DNA (on average 5.7 and 6.3 ns, respectively). The mono-exponential decays further support previous NMR results where it was found that tC has a well-defined position and geometry within the DNA helix. Furthermore, we find that the oxidation potential of tC is 0.4 V lower than for deoxyguanosine, the natural base with the lowest oxidation potential. This suggests that tC may be of interest in charge transfer studies in DNA as an electron hole acceptor. We also present a novel synthetic route to the phosphoramidite form of tC. The results presented here together with previous work show that tC is a very good C-analogue that induces minimal perturbation to the native structure of DNA. This makes tC unique as a fluorescent base analogue and is thus highly interesting in a range of applications for studying e.g. structure, dynamics and kinetics in nucleic acid systems.
|
|
| 9. |
- Sandin, Peter, 1977, et al.
(författare)
-
Synthesis and Oligonucleotide Incorporation of Fluorescent Cytosine Analogue tC: a Promising Nucleic Acid Probe
- 2007
-
Ingår i: Nature Protocols. - : Springer Science and Business Media LLC. - 1754-2189 .- 1750-2799. ; 2:3, s. 615-623
-
Tidskriftsartikel (refereegranskat)abstract
- The tricyclic cytosine, tC, is a fluorescent base analogue with excellent properties for investigating intrinsic characteristics of nucleic acid as well as interactions between nucleic acids and other molecules. Its unique fluorescence properties and insignificant influence on overall structure and dynamics of nucleic acid after incorporation makes tC particularly interesting in fluorescence resonance energy transfer and anisotropy measurements. We here describe a straightforward synthesis of the standard monomer form of tC for DNA solid-phase synthesis, the tC phosphoramidite, and its subsequent incorporation into oligonucleotides. The total synthesis of the tC phosphoramidite takes approximately 8 days and its incorporation and the subsequent oligonucleotide purification an additional day.
|
|
| 10. |
- Tumpane, John, 1983, et al.
(författare)
-
Addressable molecular node assembly--functional DNA nanostructures.
- 2008
-
Ingår i: Nucleic acids symposium series (2004). - 1746-8272. ; :52, s. 97-98
-
Tidskriftsartikel (refereegranskat)abstract
- The use of nucleic acids as a nanomaterial is becoming increasingly widespread due to the suitability of the hydrogen-bonding patterns and sequence specificity inherent to the double-helix. As minimisation of size becomes ever more important it is imperative to employ nucleic acids in the most efficient and functional manner possible. To this end we have constructed DNA nanostructures on what may be the smallest possible scale (basic components of just 10 bp) that not only reliably self-assemble but also where each unit of a 2-dimensional DNA network can be uniquely identified and selectively functionalized.(1,2.3) On this length scale and using full addressability of the network to engrave specific pathways on the scaffold, energy and electron transfer become efficient for potential information storage applications.(4).
|
|
