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| 2. |
- Nordén, Bengt, 1945
(författare)
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Editorial
- 2024
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Ingår i: QRB Discovery. - 2633-2892. ; 5
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 3. |
- Nordén, Bengt, 1945
(författare)
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Editorial QRB Discovery
- 2020
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Ingår i: QRB Discovery. - : Cambridge University Press (CUP). - 2633-2892. ; 1, s. 1-1
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 4. |
- Nordén, Bengt, 1945, et al.
(författare)
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Mismatch detection in homologous strand exchange amplified by hydrophobic effects
- 2021
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Ingår i: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 112:4
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Tidskriftsartikel (refereegranskat)abstract
- In contrast to DNA replication and transcription where nucleotides are added and matched one by one, homologous recombination by DNA strand exchange tests whole sequences for complementarity, which requires elimination of mismatched yet thermodynamically stable intermediates. To understand the remarkable sequence specificity of homologous recombination, we have studied strand exchange between a 20-mer duplex containing one single mismatch (placed at varied positions) with the matching single strand in presence of poly(ethylene glycol) representing a semi-hydrophobic environment. A FRET-based assay shows that rates and yields of strand exchange from mismatched to matched strands rapidly increase with semi-hydrophobic co-solute concentration, contrasting previously observed general strand exchange accelerating effect of ethyl glycol ethers. We argue that this effect is not caused simply by DNA melting or solvent-induced changes of DNA conformation but is more complex involving several mechanisms. The catalytic effects, we propose, involve strand invasion facilitated by reduced duplex stability due to weakened base stacking (“longitudinal breathing”). Secondly, decreased water activity makes base-pair hydrogen bonds stronger, increasing the relative energy penalty per mismatch. Finally, unstacked mismatched bases (gaps) are stabilized through partly intercalated hydrophobic co-solvent molecules, assisting nucleation of strand invasion at the point of mismatch. We speculate that nature long ago discovered, and now exploits in various enzymes, that sequence recognition power of nucleic acids may be modulated in a hydrophobic environment.
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| 5. |
- Nordén, Bengt, 1945
(författare)
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Mitigating Climate Changes: A Global Approach
- 2022
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Ingår i: Molecular Frontiers Journal. - 2529-7333 .- 2529-7325. ; 6, s. 1-23
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Tidskriftsartikel (refereegranskat)abstract
- While the diagnosis of emergent climate change problems and their mechanistic origins are today generally accepted, and the principles understood—in fact since very long, main-ly thanks to two Nobel Laureates (Figure 1), a strategic and globally coherent pathway how to mitigate the development and restore a stable climate is not fully agreed upon. As a matter of fact, there is no consensus about the priority of possible actions for getting a complete and satisfactory solution.
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| 8. |
- Nordén, Bengt, 1945
(författare)
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The Mole, Avogadro’s Number and Albert Einstein
- 2021
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Ingår i: Molecular Frontiers Journal. - 2529-7333 .- 2529-7325. ; In press
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Tidskriftsartikel (refereegranskat)abstract
- The molea concept and Avogadro’s number are discussed as sought by Albert Einstein in his PhD thesis of 1905. Einstein would probably have regarded the metric system of units based on centimetre-gram-second (cgs) preferable to today’s SI system and specifically he would have rejected a recent SI suggestion to redefine Avogadro’s constant as based on a nonatomistic continuum description of matter. He would probably also have preferred keeping a dualistic definition of mole able of bookkeeping both mass and number of particles: we advocate that here and call it the ‘Einstein Definition’ and as Avogadro’s number we shall adopt an integer, the cube of 84446888 as suggested by Fox and Hill, providing also a definition of the kilogram based on the atomic mass of the carbon 12 isotope. Einstein was the first to explain the microscopic movements of pollen grains reported by Robert Brown in 1828 and his explanation that the particles move as a result of an unequal number of water molecules bumping into them from opposite sides was what finally made the scientific world accept the atom theory in its modern shape. In a cosmic diffusion analogy, pollen or bacterial spores moving randomly in outer space driven by the solar winds between solar systems can be envisaged. Applying Einstein’s diffusion theory, one can argue that life might have emerged from far outside of our planet from billions of solar systems, though not from outside of our Milky Way galaxy. As a curiosity we note that the number of solar systems (stars) in the Universe has been estimated to be of the order of Avogadro’s number.
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| 9. |
- Nordén, Bengt, 1945, et al.
(författare)
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Understanding Rad51 function is a prerequisite for progress in cancer research
- 2020
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Ingår i: QRB Discovery. - : Cambridge University Press (CUP). - 2633-2892. ; 1
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Tidskriftsartikel (refereegranskat)abstract
- The human protein Rad51 is double-edged in cancer contexts: on one hand, preventing tumourigenesis by eliminating potentially carcinogenic DNA damage and, on the other, promoting tumours by introducing new mutations. Understanding mechanistic details of Rad51 in homologous recombination (HR) and repair could facilitate design of novel methods, including CRISPR, for Rad51-targeted cancer treatment. Despite extensive research, however, we do not yet understand the mechanism of HR in sufficient detail, partly due to complexity, a large number of Rad51 protein units being involved in the exchange of long DNA segments. Another reason for lack of understanding could be that current recognition models of DNA interactions focus only on hydrogen bond-directed base pair formation. A more complete model may need to include, for example, the kinetic effects of DNA base stacking and unstacking ('longitudinal breathing'). These might explain how Rad51 can recognize sequence identity of DNA over several bases long stretches with high accuracy, despite the fact that a single base mismatch could be tolerated if we consider only the hydrogen bond energy. We here propose that certain specific hydrophobic effects, recently discovered destabilizing stacking of nucleobases, may play a central role in this context for the function of Rad51.
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