- Ultrafast Vibrational Dynamics of Hydrogen-Bonded Dimers and Base Pairs

2013 ◽  
pp. 48-85
Keyword(s):  
Base Pairs ◽  
Vibrational Dynamics ◽  
Hydrogen Bonded

Vibrational Dynamics of Hydrogen Bonded Solids: Phonons and Optical Damage

1988 ◽  
pp. 165-169
Author(s):  
Thomas J. Kosic ◽  
Jeffrey R. Hill ◽  
Dana D. Dlott
Keyword(s):  
Vibrational Dynamics ◽  
Optical Damage ◽  
Hydrogen Bonded

scholarly journals Nanomechanics of negatively supercoiled diaminopurine-substituted DNA

2021 ◽  
Author(s):  
Domenico Salerno ◽  
Francesco Mantegazza ◽  
Valeria Cassina ◽  
Matteo Cristofalo ◽  
Qing Shao ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Single Molecule ◽  
Conformational Dynamics ◽  
Persistence Length ◽  
Base Stacking ◽  
Base Pairs ◽  
Left Handed ◽  
Negative Supercoiling ◽  
Mechanical Dynamics ◽  
Hydrogen Bonded

ABSTRACTSingle molecule experiments have demonstrated a progressive transition from a B- to an L-form helix as DNA is gently stretched and progressively unwound. Since the particular sequence of a DNA segment influences both base stacking and hydrogen bonding, the conformational dynamics of B-to-L transitions should be tunable. To test this idea, DNA with diaminopurine replacing adenine was synthesized to produce linear fragments with triply hydrogen-bonded A:T base pairs. Triple hydrogen bonding stiffened the DNA by 30% flexurally. In addition, DAP-substituted DNA formed plectonemes with larger gyres for both B- and L-form helices. Both unmodified and DAP-substituted DNA transitioned from a B- to an L-helix under physiological conditions of mild tension and unwinding. This transition avoids writhing by DNA stretched and unwound by enzymatic activity. The intramolecular nature and ease of this transition likely prevent cumbersome topological rearrangements in genomic DNA that would require topoisomerase activity to resolve. L-DNA displayed about tenfold lower persistence length indicating it is much more contractile and prone to sharp bends and kinks. However, left-handed DAP DNA was twice as stiff as unmodified L-DNA. Thus, significantly doubly and triply hydrogen bonded segments have very distinct mechanical dynamics at physiological levels of negative supercoiling and tension.

Vibrational dynamics in hydrogen bonded systems

2003 ◽  
Vol 103-104 ◽  
pp. 173-176 ◽  
Author(s):  
C. Branca ◽  
S. Magazù ◽  
F. Migliardo ◽  
G. Romeo
Keyword(s):  
Vibrational Dynamics ◽  
Hydrogen Bonded Systems ◽  
Hydrogen Bonded

Towards A DNA-Like Duplex without Hydrogen-Bonded Base Pairs

2002 ◽  
Vol 41 (17) ◽  
pp. 3203-3205 ◽  
Author(s):  
G��rald Mathis ◽  
J��rg Hunziker
Keyword(s):  
Base Pairs ◽  
Hydrogen Bonded

Structural similarity of hydrogen-bonded and metal-coordinated abiotic base pairs allows oligonucleotide-like mutual stacking,

CrystEngComm ◽  
2009 ◽  
Vol 11 (1) ◽  
pp. 118-121 ◽  
Author(s):  
Marc-Oliver M. Piepenbrock ◽  
Kirsty M. Anderson ◽  
Benedict C. R. Sansam ◽  
Nigel Clarke ◽  
Jonathan W. Steed
Keyword(s):  
Structural Similarity ◽  
Base Pairs ◽  
Hydrogen Bonded
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