This work examined the kinetics for the B→Z-DNA transition of tandem d(CG) repeat sequences induced by NaCl, KCl, MgCl2, and spermine. While d(CG)3 undergoes an incomplete transition, d(CG)6, d(CG)9, and d(CG)18 transition fully in appropriate concentrations of salts or spermine. The transition proceeds more slowly with increasing DNA lengths. Furthermore, d(CG)18 displays complex behavior in the presence of MgCl2. While d(CG)18 fully transitions to Z-DNA in the presence of 2.5 M MgCl2, the process is complicated, likely by condensation. Kinetics of the B-/Z-DNA transition is an important aspect of Z-DNA's roles in biological systems. The knowledge of how this transition is affected by sequence lengths and salts helps define the DNA's conformational plasticity in response to environmental shifts in cells.

This work studied the structure and hybridization properties of DNA in simulated crowded media containing polyethylene glycol 10,000 and sucrose. Synchrotron radiation circular dichroism revealed that the overall CD profiles of a 21-mer and a d(CG)9 duplex remain similar in the simulated crowded fluids compared with those in Tris buffer, but the amplitude ratios of individual maxima and minima vary with the concentration of DNA and the media, suggesting possible conformational changes. Using fluorescence resonance energy transfer, this work confirmed that hairpin and duplex formations are not affected by the crowding condition. On the other hand, the duplex dynamics is affected by the crowding condition, where strand exchanges were promoted by the presence of PEG, but unaffected by sucrose.

Synchrotron radiation circular dichroism spectra of 2'-deoxyribonucleosides, as well as a few guanine nucleosides were recorded between 170-330 nm. The CD profile of each nucleoside is unique, and there is a general similarity in the SRCD patterns of deoxyribonucleosides and those recorded by a benchtop CD as previously reported. Furthermore, the locked nucleic acid derivative of guanine nucleoside (LNA-G) showed opposite CD profiles to the rest of the guanine nucleoside derivatives. The conformational parameters of the nucleosides were analyzed against the crystal structures available in the Cambridge Crystallographic Data Center. The pseudorotational phase angles of the guanine nucleoside derivatives in solution were also determined based on NMR coupling constants. Analyses showed no apparent correlation between pseudorotational phase angles and CD patterns.

Examination of structures of DNA duplexes (A-, B-, and Z-DNA) showed a positive correlation between the pseudorotational phase angle P and the torsion angle δH (H4'-C4'-C3'-H3'). Such a P - δH plot reflects the structural features of the three types of DNA duplexes. Since the δH torsion angle can be measured by nuclear magnetic resonance, the linear correlation between P and δH provides a useful method for predicting the sugar pucker of nucleosides and nucleic acids.

Circular dichroism spectroscopy of nucleic acids has been traditionally performed at sample concentrations orders of magnitude lower than what occur in biological systems. While recent work from us demonstrated the flexibility of an adjustable sample cell that allowed for successful recording of CD spectra of an 18- and a 21-mer double stranded DNA sequences at around 1 mM, sample concentrations beyond 1 mM present a challenge for standard benchtop CD spectrometers. In the present work, the synchrotron radiation circular dichroism (SRCD) spectra were recorded for d(CG)9 and a mixed 18-mer double stranded DNA at 1, 5, and 10 mM in 100 mM or 4 M NaCl. SRCD of low molecular weight salmon DNA was also measured at a 10 mg/ml concentration. These results represent the first report of CD spectra of DNA samples measured at concentrations comparable to those found in the nucleus. The results suggest that dsDNA maintain very similar structures at concentrations up to tens of mg/ml, as evident by the very similar CD patterns in this concentration range. Furthermore, the SRCD allowed for the recording of CD patterns of DNA in the far UV region, which is not readily accessible by standard benchtop CD spectropolarimeters. These far UV signals appear to be quite characteristic of DNA structures and are sensitive to sample conditions.

Circular dichroism (CD) of nucleic acids has been typically carried out at sample concentrations below 10 μM, which is far lower than nucleic acid concentrations in biological systems. Attempts to study nucleic acid conformations by CD at higher concentrations using 10 and 1 mm pathlength cuvettes led to instrument artifacts. By shortening the light pathlength to around 0.1 mm, we herein report the first CD profiles of nucleic acids at sub-mM concentrations, which are relevant to nucleic acid concentrations in cellular cytoplasm and nucleus. These CD experimental conditions will allow future conformational studies of nucleic acids under biologically relevant conditions.

Anion-exchange chromatography carried out under non-denaturing conditions is a versatile tool to differentiate DNA conformations. In this work, the utility of this form of HPLC was demonstrated in four examples. The hairpin and duplex forms of d(CG)9 were readily resolved, which allowed for the studies of the influence of salt on the equilibrium of these two forms of secondary structures. Similarly, the minimum size of Tn in the loop region required for the sequence 5'-d(CCCAA-(T)n-TTGGG)-3' to form hairpin was established to be two nucleotides using anion-exchange HPLC and fluorescence resonance energy transfer. Furthermore, the efficiency of hybridization of partially self-complementary sequences d[(CG)6Nx] was readily monitored by non-denaturing anion-exchange HPLC. Finally, different structures adopted by quadruplex-forming sequences were resolved in the same manner.

We report herein that exposure of DNA to microwave irradiation at constant temperature leads to faster strand exchange, as compared with same experiments carried out in a water bath at the same temperature. Furthermore, polymerase chain reactions carried out under microwave irradiation were faster than those in a water bath at the same temperature as well. While the causes of these differences are unclear at this time, this research suggests that microwave irradiation can lead to subtle changes in DNA structural dynamics and functions. (C) 2019 Elsevier Ltd. All rights reserved.

The photoisomerization properties of a series of cyclic azobenzene (cAb) analogs, including non-substituted, Br-, CN-, carboxyl-, and amino cAb, were compared. While the trans-form of these analogs show different degrees of thermal stability, no spectral changes in the absorption wavelengths were observed for amino cAb upon exposure to purple light. The (NNMR)-N-15 chemical shifts of cAb in both cis- and trans-forms were found to show a large difference from those of aromatic azobenzene; however, the trend of difference in chemical shift is in agreement with that obtained from quantum chemical calculations. More importantly, the structure of the photoisomerization product from cis-cAb was confirmed to be, indeed, the trans-cAb by X-ray diffraction experiments. The (NMR)-N-15 data of the cAb isomers and confirmation of trans-cAb through crystal structure will be of importance for future studies in the design and applications of cAb as a photoswitch.