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.

scholarly journals Conformational and structural stability of the single molecule and hydrogen bonded clusters of para aminobenzoic acid in the gas and solution phases

CrystEngComm ◽  
2018 ◽  
Vol 20 (46) ◽  
pp. 7543-7555 ◽  
Author(s):  
Ian Rosbottom ◽  
Dimitrios Toroz ◽  
Robert B. Hammond ◽  
Kevin J. Roberts
Keyword(s):  
Hydrogen Bonding ◽  
Ab Initio ◽  
Structural Stability ◽  
Single Molecule ◽  
Building Blocks ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Aminobenzoic Acid ◽  
Cluster Stability ◽  
Hydrogen Bonded

The structures of α- and β-para aminobenzoic acid are deconstructed into their hydrogen bonding molecular structural building blocks, where they are analysed usingab initioquantum mechanical calculations of their conformation and cluster stability in solution.

Evaluation of the 2 NH2A—T Pair in Hybridization, I Synthesis of the DNA/RNA Hybrid Oligomers Containing 2-Aminoadenosines

1988 ◽  
Vol 43 (5) ◽  
pp. 623-630 ◽  
Author(s):  
Kaeko Kikuchi ◽  
Yoshio Taniyama ◽  
Ryuji Marumoto
Keyword(s):  
Hydrogen Bonding ◽  
Dna Structure ◽  
Dna Duplexes ◽  
Cd Spectra ◽  
Base Pairing ◽  
Base Stacking ◽  
Base Pairs ◽  
Nuclease P1 ◽  
Rna Duplexes

Abstract DNA decamers containing 2-aminoadenosine were synthesized. Oligonucleotide duplexes including the 2 NH2A-T base pairs were prepared and their Tm profile examined. Contrary to expectation, elevation of the Tm value by the 2 NH2 group is very small in DNA/RNA duplexes. From the CD spectra measurement, we assume that the distortion of the B-DNA structure caused by scattered DNA/RNA base pairing diminishes the efficient hydrogen bonding and base stacking of the duplexes. It was also found that the DNA duplexes containing 2-aminoadenosine hybrids are considerably resistant to ribonuclease T2 or nuclease P1 digestion.

scholarly journals Hydrophobic catalysis and a potential biological role of DNA unstacking induced by environment effects

2019 ◽  
Vol 116 (35) ◽  
pp. 17169-17174 ◽  
Author(s):  
Bobo Feng ◽  
Robert P. Sosa ◽  
Anna K. F. Mårtensson ◽  
Kai Jiang ◽  
Alex Tong ◽  
...  
Keyword(s):  
Ethylene Glycol ◽  
Optical Tweezers ◽  
Single Molecule ◽  
Hydrophobic Interactions ◽  
Persistence Length ◽  
Poly Ethylene Glycol ◽  
Glycol Ethers ◽  
Base Stacking ◽  
Poly Ethylene ◽  
Dna Double Helix

Hydrophobic base stacking is a major contributor to DNA double-helix stability. We report the discovery of specific unstacking effects in certain semihydrophobic environments. Water-miscible ethylene glycol ethers are found to modify structure, dynamics, and reactivity of DNA by mechanisms possibly related to a biologically relevant hydrophobic catalysis. Spectroscopic data and optical tweezers experiments show that base-stacking energies are reduced while base-pair hydrogen bonds are strengthened. We propose that a modulated chemical potential of water can promote “longitudinal breathing” and the formation of unstacked holes while base unpairing is suppressed. Flow linear dichroism in 20% diglyme indicates a 20 to 30% decrease in persistence length of DNA, supported by an increased flexibility in single-molecule nanochannel experiments in poly(ethylene glycol). A limited (3 to 6%) hyperchromicity but unaffected circular dichroism is consistent with transient unstacking events while maintaining an overall average B-DNA conformation. Further information about unstacking dynamics is obtained from the binding kinetics of large thread-intercalating ruthenium complexes, indicating that the hydrophobic effect provides a 10 to 100 times increased DNA unstacking frequency and an “open hole” population on the order of 10−2 compared to 10−4 in normal aqueous solution. Spontaneous DNA strand exchange catalyzed by poly(ethylene glycol) makes us propose that hydrophobic residues in the L2 loop of recombination enzymes RecA and Rad51 may assist gene recombination via modulation of water activity near the DNA helix by hydrophobic interactions, in the manner described here. We speculate that such hydrophobic interactions may have catalytic roles also in other biological contexts, such as in polymerases.

Geometric, electronic and magnetic structures of S = 19/2 and S = 20/2 thiophene-2-carboxylate functionalized Mn12 single molecule magnets

2015 ◽  
Vol 44 (1) ◽  
pp. 167-175 ◽  
Author(s):  
Jorge H. Rodriguez ◽  
Christopher J. Ziegler
Keyword(s):  
Hydrogen Bonding ◽  
Single Molecule ◽  
Magnetic Moment ◽  
Water Molecules ◽  
Single Molecule Magnets ◽  
Magnetic Structures ◽  
Electronic And Magnetic Structures ◽  
Hydrogen Bonded

Hydrogen bonding of water molecules to Mn4O4 inner cubane of S = 19/2 Mn12 SMM gives rise to geometric and magnetic asymmetries. Two Mn ions hydrogen bonded to water molecules depart from their Mn4+(S = 3/2) states and acquire an incipient Mn3+(S = 4/2) character. The magnetic moment vectors of the cubane Mn ions are inequivalent.

Single molecule optical diffraction: A tool for understanding the structure of triple stranded left-hand helical cellulose

1989 ◽  
Vol 47 ◽  
pp. 1024-1025
Author(s):  
George C. Ruben ◽  
William Krakow
Keyword(s):  
Single Molecule ◽  
Helical Structure ◽  
Optical Diffraction ◽  
Maximum Diameter ◽  
Primary Cell Wall ◽  
Cellulose Synthesis ◽  
Left Hand ◽  
Left Handed ◽  
Freeze Dried ◽  
Diffraction Patterns

Tobacco primary cell wall and normal bacterial Acetobacter xylinum cellulose formation produced a 36.8±3Å triple-stranded left-hand helical microfibril in freeze-dried Pt-C replicas and in negatively stained preparations for TEM. As three submicrofibril strands exit the wall of Axylinum , they twist together to form a left-hand helical microfibril. This process is driven by the left-hand helical structure of the submicrofibril and by cellulose synthesis. That is, as the submicrofibril is elongating at the wall, it is also being left-hand twisted and twisted together with two other submicrofibrils. The submicrofibril appears to have the dimensions of a nine (l-4)-ß-D-glucan parallel chain crystalline unit whose long, 23Å, and short, 19Å, diagonals form major and minor left-handed axial surface ridges every 36Å.The computer generated optical diffraction of this model and its corresponding image have been compared. The submicrofibril model was used to construct a microfibril model. This model and corresponding microfibril images have also been optically diffracted and comparedIn this paper we compare two less complex microfibril models. The first model (Fig. 1a) is constructed with cylindrical submicrofibrils. The second model (Fig. 2a) is also constructed with three submicrofibrils but with a single 23 Å diagonal, projecting from a rounded cross section and left-hand helically twisted, with a 36Å repeat, similar to the original model (45°±10° crossover angle). The submicrofibrils cross the microfibril axis at roughly a 45°±10° angle, the same crossover angle observed in microflbril TEM images. These models were constructed so that the maximum diameter of the submicrofibrils was 23Å and the overall microfibril diameters were similar to Pt-C coated image diameters of ∼50Å and not the actual diameter of 36.5Å. The methods for computing optical diffraction patterns have been published before.

Monitoring the Structural Dynamics of U2 snRNA Via Single-Molecule Förster Resonance Energy Transfer

2018 ◽  
Author(s):  
Alexander Carl DeHaven
Keyword(s):  
Energy Transfer ◽  
Structural Dynamics ◽  
Single Molecule ◽  
Conformational Dynamics ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Förster Resonance Energy Transfer ◽  
U2 Snrna ◽  
Folding Dynamics ◽  
The Impact

This thesis contains four topic areas: a review of single-molecule microscropy methods and splicing, conformational dynamics of stem II of the U2 snRNA, the impact of post-transcriptional modifications on U2 snRNA folding dynamics, and preliminary findings on Mango aptamer folding dynamics.

Theoretical study of hydrogen bonding interactions in substituted nitroxide radicals

2021 ◽  
Author(s):  
Thufail M. Ismail ◽  
Neetha Mohan ◽  
P. K. Sajith
Keyword(s):  
Hydrogen Bonding ◽  
Interaction Energy ◽  
Electrostatic Potential ◽  
Molecular Electrostatic Potential ◽  
Theoretical Study ◽  
Nitroxide Radicals ◽  
Hydrogen Bonding Interactions ◽  
Bonded Complexes ◽  
Hydrogen Bonded

Interaction energy (Eint) of hydrogen bonded complexes of nitroxide radicals can be assessed in terms of the deepest minimum of molecular electrostatic potential (Vmin).

scholarly journals Spontaneous and frequent conformational dynamics induced by A…A mismatch in d(CAA)·d(TAG) duplex

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yogeeshwar Ajjugal ◽  
Kripi Tomar ◽  
D. Krishna Rao ◽  
Thenmalarchelvi Rathinavelan
Keyword(s):  
Mismatch Repair ◽  
Conformational Dynamics ◽  
Md Simulations ◽  
Umbrella Sampling ◽  
Base Flipping ◽  
Base Pairs ◽  
2D Noesy ◽  
Junction Formation ◽  
Nmr Techniques ◽  
Transient Events

AbstractBase pair mismatches in DNA can erroneously be incorporated during replication, recombination, etc. Here, the influence of A…A mismatch in the context of 5′CAA·5′TAG sequence is explored using molecular dynamics (MD) simulation, umbrella sampling MD, circular dichroism (CD), microscale thermophoresis (MST) and NMR techniques. MD simulations reveal that the A…A mismatch experiences several transient events such as base flipping, base extrusion, etc. facilitating B–Z junction formation. A…A mismatch may assume such conformational transitions to circumvent the effect of nonisostericity with the flanking canonical base pairs so as to get accommodated in the DNA. CD and 1D proton NMR experiments further reveal that the extent of B–Z junction increases when the number of A…A mismatch in d(CAA)·d(T(A/T)G) increases (1–5). CD titration studies of d(CAA)·d(TAG)n=5 with the hZαADAR1 show the passive binding between the two, wherein, the binding of protein commences with B–Z junction recognition. Umbrella sampling simulation indicates that the mismatch samples anti…+ syn/+ syn…anti, anti…anti & + syn…+ syn glycosyl conformations. The concomitant spontaneous transitions are: a variety of hydrogen bonding patterns, stacking and minor or major groove extrahelical movements (with and without the engagement of hydrogen bonds) involving the mismatch adenines. These transitions frequently happen in anti…anti conformational region compared with the other three regions as revealed from the lifetime of these states. Further, 2D-NOESY experiments indicate that the number of cross-peaks diminishes with the increasing number of A…A mismatches implicating its dynamic nature. The spontaneous extrahelical movement seen in A…A mismatch may be a key pre-trapping event in the mismatch repair due to the accessibility of the base(s) to the sophisticated mismatch repair machinery.

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