| 1. |
- Dutta, Suman, et al.
(författare)
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The R-diastereomer of 6 '-O-toluoyl-carba-LNA modification in the core region of siRNA leads to 24-times improved RNA silencing potency against the HIV-1 compared to its S-counterpart
- 2011
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Ingår i: MedChemComm. - : Royal Society of Chemistry (RSC). - 2040-2503 .- 2040-2511. ; 2:11, s. 1110-1119
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Tidskriftsartikel (refereegranskat)abstract
- The modified siRNA with pure [6'(S)-O-(p-toluoyl)-7'(S)-methyl]-carba-LNA [6'(S)-O-toluoyl-jcLNA] at position T(13) displayed an IC(50) of 79.8 nM, which has been found to be nearly 24-times less potent as a HIV-1 RNAi silencing agent against TAR RNA than that of the corresponding pure [6'(R)-O-(ptoluoyl)-7'(S)-methyl]jcLNA [6'(R)-O-(p-toluoyl)-jcLNA] counterpart [IC(50) 3.3 nM]. The later [6'(R)-O-(p-toluoyl)-jcLNAl-modified siRNAs have been found to be nearly 2-fold more efficient as a silencing agent than the corresponding 6'-deoxy-jcLNA modified siRNA [IC(50) 8.1 nM], and also nearly 3-fold more effective as a silencing agent than that of LNA-modified siRNA [IC(50) 11.7 nM], thereby showing that the 6'-carbon center in the jcLNA-modified siRNA in the core region is relatively more exposed to the Ago protein in the RISC with a clear chirality preference for the siRNA cleavage reaction. It is noteworthy that the IC(50) of jcLNA-modified siRNAs are very comparable to that of the native siRNA [1.8 nM]. The jcLNA derivatized siRNAs, however, have a clear advantage of being, in general, considerably more stable in human serum. The main structural difference in duplexes of the antisense strand of the 6'(R or S)-O-(p-toluoyl)-jcLNA modified siRNA and target RNA duplex is found to be the spatial orientation of the 6'(R)-O-toluoyl group, which is exposed towards the edge of the duplex backbone, while the 6'(S) makes the minor groove relatively inaccessible for the Ago protein in the RISC. Clearly, any further C6'-modification in jcLNA-modified siRNAs with any hydrophobic group for tighter binding and cleavage or for cross-linking in the core region should preferably be done in the 6'(R)-stereochemistry.
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| 2. |
- Forsberg, Mathias
(författare)
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Optical and Structural Characterization of GaN Based Hybrid Structures and Nanorods
- 2015
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- GaN belongs to the group III nitrides and is today the material of choice for efficient blue light emission, enabling solid state white lighting by combining red, blue and green light emitting diodes (LED) or by having a blue LED illuminating a phosphor. By combining GaN quantum well (QW) structures with colloids, nanoparticles or polyfluorene films, LEDs may be fabricate at lower cost. Such hybrid structures are promising for future micro-light sources in full-color displays, sensors and imaging systems. In this work, hybrid structures based on an MOCVD grown GaN QW sandwiched between two layers of AlGaN have been studied. On top of the structure, colloidal ZnO nano-crystals were deposited by spin-coating. Time-resolved photoluminescence was used to investigate the QW exciton dynamics in these hybrids depending on the cap layer thickness. From comparison of the recombination rate in the bare QW structure and the hybrid, the efficiency of the non-radiative resonant energy transfer between the QW and the nano-crystals could be obtained.Bulk GaN of large area is difficult to synthesize. Thus, due to lack of native substrates, GaN-based structures are grown on SiC or sapphire, which results in high threading dislocation density in the active layer of the device. Fabricating GaN nanorods (NR) can be a way to produce GaN with lower defect density since threading dislocations are annihilated toward the NR wall during growth. Here, GaN(0001) NRs grown on Si(111) substrates by magnetron sputter epitaxy using a liquid Ga target have been investigated. Sputter deposition has the advantage of being easy to scale up for depositions on large surfaces. It is also possible to deposit at lower temperatures, which allows the use of substrates with lower decomposition temperature. In the second paper of this thesis, optical and structural properties of sputtered GaN NRs have been studied.
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| 3. |
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| 4. |
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| 5. |
- Isaksson, Johan, et al.
(författare)
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Oxetane locked thymidine in the Dickerson-Drew dodecamer causes local base pairing distortions : an NMR structure and hydration study
- 2005
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Ingår i: Journal of Biomolecular Structure and Dynamics. - : Informa UK Limited. - 0739-1102 .- 1538-0254. ; 23:3, s. 299-330
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Tidskriftsartikel (refereegranskat)abstract
- The introduction of a North-type sugar conformation constrained oxetane T block, 1-(1',3'-O-anhydro-beta-D-psicofuranosyl) thymine, at the T(7) position of the self-complementary Dickerson-Drew dodecamer, d[(5'-C(1)G(2)C(3)G(4)A(5)A(6)T(7)T(8)C(9)G(10)C(11)G(12)-3')](2), considerably perturbs the conformation of the four central base pairs, reducing the stability of the structure. UV spectroscopy and 1D NMR display a drop in melting temperature of approximately 10 degrees C per modification for the T(7) oxetane modified duplex, where the T(7) block has been introduced in both strands, compared to the native Dickerson-Drew dodecamer. The three dimensional structure has been determined by NMR spectroscopy and has subsequently been compared with the results of 2.4 ns MD simulations of the native and the T(7) oxetane modified duplexes. The modified T(7) residue is found to maintain its constrained sugar- and the related glycosyl torsion conformations in the duplex, resulting in staggered and stretched T(7).A(6) and A(6).T(7) non-linear base pairs. The stacking is less perturbed, but there is an increased roll between the two central residues compared to the native counterpart, which is compensated by tilts of the neighboring base steps. The one dimensional melting profile of base protons of the T(7) and T(8) residues reveals that the introduction of the North-type sugar constrained thymine destabilizes the core of the modified duplex, promoting melting to start simultaneously from the center as well as from the ends. Temperature dependent hydration studies by NMR demonstrate that the central T(7).A(6)/A(6).T(7) base pairs of the T(7) oxetane modified Dickerson-Drew dodecamer have at least one order of magnitude higher water exchange rates (correlated to the opening rate of the base pair) than the corresponding base pairs in the native duplex.
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| 6. |
- Li, Qing, et al.
(författare)
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Free-Radical Ring Closure to Conformationally Locked alpha-L-Carba-LNAs and Synthesis of Their Oligos : Nuclease Stability, Target RNA Specificity, and Elicitation of RNase H
- 2010
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Ingår i: Journal of Organic Chemistry. - : American Chemical Society (ACS). - 0022-3263 .- 1520-6904. ; 75:18, s. 6122-6140
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Tidskriftsartikel (refereegranskat)abstract
- A new class of conformationally constrained nucleosides, alpha-L-ribo-carbocyclic LNA thymidine (alpha-L-carba-LNA-T, LNA is an abbreviation of locked nucleic acid) analogues and a novel "double-locked" alpha-L-ribo-configured tetracyche thymidine (6,7'-methylene-bridged-alpha-L-carba-LNA-T) in which both the sugar puckering and glyeosidic torsion are simultaneously constrained, have been synthesized through a key step involving 5-exo free-radical intramolecular cyclization. These alpha-L-carba-LNA analogues have been subsequently transformed to corresponding phosphoramidites and incorporated into isosequential antisense oligonucleotides (AONs), which have then been examined for the thermal denaturation of their duplexes, nuclease stability, and RNase H recruitment capabilities. Introduction of a single 6',7'-substituted alpha-L-carba-LNA-T modification in the AON strand of AON/RNA heteroduplex led to T-m reduction by 2-3 degrees C as compared to the native heteroduplex, whereas the parent 2'-oxa-alpha-L-LNA-T modification at the identical position in the AON strand has been found to lead to an increase in the T-m by 3-5 degrees C. This suggests that the 6' and 7' substitutions lead to much reduced thermal stability for the modified heteroduplex, especially the hydrophobic 7'-methyl on alpha-L-carba-LNA, which is located in the major groove of the duplex. All of the AONs incorporating 6',7'-substituted alpha-L-earba-LNA-T have, however, showed considerably improved nuclease stability toward 3'-exonuclease (SVPDE) and in human blood serum compared to the 2'-oxa-alpha-L-LNA-T incorporated AONs. The hybrid duplexes that are formed by 6',7'-substituted alpha-L-carba-LNA-T-modified AONs with complementary RNA have been found to recruit RNase H with higher efficiency than those of the beta-D-LNA-T or beta-D-carba-LNA-T-modified counterparts. These greatly improved nuclease resistances and efficient RNasc H recruitment capabilities elevate the alpha-L-carba-LNA-modified nucleotides into a new class of locked nucleic acids for potential RNA targeting therapeutics.
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| 7. |
- Li, Qing, 1981-, et al.
(författare)
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Free-Radical Ring Closure to Conformationally Locked α-l-Carba-LNAs and Synthesis of Their Oligos: : Nuclease Stability, Target RNA Specificity, and Elicitation of RNase H
- 2010
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Ingår i: Journal of Organic Chemistry. - U. S. A : American Chemical Society (ACS). - 0022-3263 .- 1520-6904. ; 75:18, s. 6122-6140
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Tidskriftsartikel (refereegranskat)abstract
- A new class of conformationally constrained nucleosides, α-L-ribo-carbocyclic LNA thymidine (α-L-carba-LNA-T, LNA is an abbreviation of locked nucleic acid) analogues and a novel "double-locked" α-L-ribo-configured tetracyclic thymidine (6,7'-methylene-bridged-α-L-carba-LNA-T) in which both the sugar puckering and glycosidic torsion are simultaneously constrained, have been synthesized through a key step involving 5-exo free-radical intramolecular cyclization. These α-L-carba-LNA analogues have been subsequently transformed to corresponding phosphoramidites and incorporated into isosequential antisense oligonucleotides (AONs), which have then been examined for the thermal denaturation of their duplexes, nuclease stability, and RNase H recruitment capabilities. Introduction of a single 6',7'-substituted α-L-carba-LNA-T modification in the AON strand of AON/RNA heteroduplex led to T(m) reduction by 2-3 °C as compared to the native heteroduplex, whereas the parent 2'-oxa-α-L-LNA-T modification at the identical position in the AON strand has been found to lead to an increase in the T(m) by 3-5 °C. This suggests that the 6' and 7' substitutions lead to much reduced thermal stability for the modified heteroduplex, especially the hydrophobic 7'-methyl on α-L-carba-LNA, which is located in the major groove of the duplex. All of the AONs incorporating 6',7'-substituted α-L-carba-LNA-T have, however, showed considerably improved nuclease stability toward 3'-exonuclease (SVPDE) and in human blood serum compared to the 2'-oxa-α-L-LNA-T incorporated AONs. The hybrid duplexes that are formed by 6',7'-substituted α-L-carba-LNA-T-modified AONs with complementary RNA have been found to recruit RNase H with higher efficiency than those of the β-D-LNA-T or β-D-carba-LNA-T-modified counterparts. These greatly improved nuclease resistances and efficient RNase H recruitment capabilities elevate the α-L-carba-LNA-modified nucleotides into a new class of locked nucleic acids for potential RNA targeting therapeutics.
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| 8. |
- Li, Qing, 1981-, et al.
(författare)
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The Physicochemical Properties of DNA-RNA Duplexes Containing Pure 7′R-Me- or 7′S-Me-Carba-LNA Derivatives of A, G, 5-MeC or T in the DNA Strand: Diastereomer Specific Comparison of The 3′-Exonuclease Stability and RNase H Elicitation
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Tidskriftsartikel (refereegranskat)abstract
- Recently, the intramolecular 5-exo-5-hexenyl free-radical cyclization gave access to 2′, 4′-locked carba-LNAs with different nucleobase moieties, i.e. 7′S- and 7′R-Me-cLNA-A, -G, -MeC and -T nucleosides (J. Am. Chem. Soc. 2007, 129, 8362-8379; J. Org. Chem. 2011, 76, 4408-4431). In these studies, diastereomeric mixtures of 7′S/R-Me-cLNA-MeC and -T and diastereomerically pure 7′R-Me-cLNA-A and -G have been incorporated into antisense oligonucleotides (AONs) for biological evaluations. These cLNA modified oligos have shown to have comparable RNA affinity and highly improved nuclease and blood serum stabilities relative to that of their LNA modified counterparts. In order to fully understand the spatial effect of diastereomeric orientation of 7′-methyl group in cLNA-A/G/MeC/T on the RNA affinity, nuclease stability and RNase H elicitation efficiency, we have synthesized and preparatively HPLC separated and tested each of the 7′S- (minor) and 7′R- (major) pure diastereomer of 7′S/R-Me-cLNA-A/G/MeC/T nucleosides. Incorporation into oligos of each pure diastereomer of cLNA led to higher RNA affinity (1-4°C/mod). Tm increase was found to be dependent both on the modification site in the AON as well as whether it is 7′S or 7′R modified cLNA is incorporated. RNA selectivity (DDTm) was found to be in the range of 3.1-6.7°C compared to DDTm of 2.7°C for the native counterpart. The Tm variations modulated by 7′S- and 7′R-Me-cLNAs in the AON have been found to be sequence and position-dependent. Molecular dynamics (MD) simulations of DNA-RNA duplexes with AON2 and AON5, with pure diastereomer incorporated at the 7th position of the AON strand from 3′-end, revealed that both 7′S- and 7′R-Me-cLNA-A modifications have only small local effect on stacking and hydrogen bonding within the duplexes, with Watson-Crick base-pairing remained intact during 98-100% duration of the MD simulations. It has been however found that the Tm of each of the modified heteroduplex is dictated by the individual solvation energy (CPCM) of the 7′S- or 7′R-Me-cLNA diastereomer of A, G, MeC or T nucleobase. This demonstrates that the major factor behind variation in the thermal stabilities of the 7′R- or 7′S-Me-cLNA modified AON-RNA duplexes lies in the intrinsic hydrophobicity, hence its relative solvation energy, inherent in the 7′R- vis-a-vis 7′S-Me-cLNA modified monomer blocks, compared to those of the native and LNA counterparts. We have also found that AONs containing 7′S- and 7′R-Me-cLNA-MeC modifications exhibited unprecedented nuclease stabilities: the most stable AON is the one that contains 7′S-Me-cLNA-MeC, which is ~40 times more stable towards 3′-exonuclease (SVPDE) than 7′S- and 7′R-Me-cLNA-T modified AONs, which was in turn much more stable than 7′S- and 7′R-Me-cLNA-A and G modified counterparts. It is noteworthy that 7′S-methyl group of cLNAs endows the AON strand with more nuclease stability than that of 7′R configured counterpart when compared within the same nucleobase. Thus the carba-LNA modified AONs show nucleobase-dependent activity in the following order: MeC > T > A > G, regardless of 7′S- or 7′R-configurations in the carba-LNA. All of the cLNA and LNA modified AON/RNA hybrids can elicit RNase H activity with similar or even more enhanced rates of digestion by E. coli RNase H1 compared to that of the native AON/RNA. The cleavage rates and patterns of modified AON/RNA hybrids by E. coli RNase H1 are only correlated with the modification site in AON sequence of AON/RNA hybrids, but irrelevant to the structural features of incorporated modifications.
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| 9. |
- Moriou, Céline, et al.
(författare)
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C2 '-F Stereoconfiguration As a Puckering Switch for Base Stacking at the Dinucleotide Level
- 2018
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Ingår i: Journal of Organic Chemistry. - : AMER CHEMICAL SOC. - 0022-3263 .- 1520-6904. ; 83:4, s. 2473-2478
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Tidskriftsartikel (refereegranskat)abstract
- Fluorine configuration at C2′ of the bis(2′-fluorothymidine) dinucleotide is demonstrated to drive intramolecular base stacking. 2′-β F-Configuration drastically reduces stacking compared to the 2′-α series. Hence, base stacking emerges as being tunable by the C2′-F stereoconfiguration through dramatic puckering variations scrutinized by NMR and natural bond orbital analysis. Accordingly, 2′-β F-isomer photoreactivity is significantly reduced compared to that of the 2′-α F-isomer.
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| 10. |
- Plashkevych, Oleksandr, et al.
(författare)
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Chemical and Structural Implications of 1‘,2‘- versus 2‘,4‘- Conformational Constraints in the Sugar Moiety of Modified Thymine Nucleosides
- 2007
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Ingår i: Journal of Organic Chemistry. - : American Chemical Society (ACS). - 0022-3263 .- 1520-6904. ; 72:13, s. 4716-4726
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Tidskriftsartikel (refereegranskat)abstract
- In order to understand how the chemical nature of the conformational constraint of the sugar moiety in ON/RNA(DNA) dictates the duplex structure and reactivity, we have determined molecular structures and dynamics of the conformationally constrained 1‘,2‘-azetidine- and 1‘,2‘-oxetane-fused thymidines, as well as their 2‘,4‘-fused thymine (T) counterparts such as LNA-T, 2‘-amino LNA-T, ENA-T, and aza-ENA-T by NMR, ab initio (HF/6-31G** and B3LYP/6-31++G**), and molecular dynamics simulations (2 ns in the explicit aqueous medium). It has been found that, depending upon whether the modification leads to a bicyclic 1‘,2‘-fused or a tricyclic 2‘,4‘-fused system, they fall into two distinct categories characterized by their respective internal dynamics of the glycosidic and the backbone torsions as well as by characteristic North-East type sugar conformation (P = 37° ± 27°, φm = 25° ± 18°) of the 1‘,2‘-fused systems, and (ii) pure North type (P = 19° ± 8°, φm = 48° ± 4°) for the 2‘,4‘-fused nucleosides. Each group has different conformational hyperspace accessible, despite the overall similarity of the North-type conformational constraints imposed by the 1‘,2‘- or 2‘,4‘-linked modification. The comparison of pKas of the 1-thyminyl aglycon as well as that of endocyclic sugar-nitrogen obtained by theoretical and experimental measurements showed that the nature of the sugar conformational constraints steer the physicochemical property (pKa) of the constituent 1-thyminyl moiety, which in turn can play a part in tuning the strength of hydrogen bonding in the basepairing.
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