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Thermodynamics and ...
Thermodynamics and kinetics of the B-S transition in base-modified DNA
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- Sundar Rajan, Vinoth, 1987 (författare)
- Chalmers tekniska högskola,Chalmers University of Technology
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- Levin, Sune, 1991 (författare)
- Chalmers tekniska högskola,Chalmers University of Technology
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- McCauley, M. J. (författare)
- Northeastern University
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- Williams, Mark C. (författare)
- Northeastern University
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- Rouzina, I. (författare)
- Ohio State University
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- Wilhelmsson, Marcus, 1974 (författare)
- Chalmers tekniska högskola,Chalmers University of Technology
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- Westerlund, Fredrik, 1978 (författare)
- Chalmers tekniska högskola,Chalmers University of Technology
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(creator_code:org_t)
- Elsevier BV, 2023
- 2023
- Engelska.
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 122:3S1
- Relaterad länk:
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https://doi.org/10.1...
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https://research.cha...
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Abstract
Ämnesord
Stäng
- Understanding changes in the mechanical properties of nucleic acids is important to understand many biological processes. DNA exhibits a conformational change from canonical B- to overstretched S-form, characterized by 70% elongation, at ∼60–70 pN. The structure of S-form DNA is still debated and also difficult to distinguish from force-induced melting and peeling of DNA. Here, we characterized the kinetics and thermodynamics of the B-S transition and also investigated the effect of base modifications on the transition using tricyclic cytosine tC, which forms hydrogen bonds with guanine and changes the base stacking properties of B-DNA. The B-S transition in 60 bp DNA occurs at ∼63.5 pN (at 1 M salt) and fraying of ∼20 bp precedes the cooperative B-to-S transition of the remaining ∼40 bp. The B-S transition force increases gradually with tC incorporation, whereas the extension and free energy of the transition decrease. We conclude that fewer bp undergo the cooperative B-S transition in tC-stabilized duplexes, due to more fraying of B-DNA at higher transition forces, consistent with the transition becoming faster. For the first time we characterize the kinetics of the cooperative B-to-S transition and it occurs significantly faster than the alternative melting transition, while the extension of B-DNA at the B-to-S transition barrier is almost half-way between B- and S-DNA, suggesting an elastic nature of this transition. By characterizing the free energies of tC-modified relative to unmodified oligos, we estimated that each tC stabilizes the duplex by ∼3 kBT. The approach of studying short synthetic oligonucleotides with modified bases opens up new opportunities for understanding the local structure of nucleic acids with base-pair resolution.
Ämnesord
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Fysiologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Physiology (hsv//eng)
- NATURVETENSKAP -- Fysik -- Annan fysik (hsv//swe)
- NATURAL SCIENCES -- Physical Sciences -- Other Physics Topics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Biofysik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biophysics (hsv//eng)
Nyckelord
- Kinetics
- Nucleic acids
- Thermodynamics
- B-S transition
Publikations- och innehållstyp
- art (ämneskategori)
- ref (ämneskategori)
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