scholarly journals The parallel-stranded d(CGA) duplex is a highly predictable structural motif with two conformationally distinct strands

2021 ◽  
Author(s):  
Emily M. Luteran ◽  
Paul J. Paukstelis

ABSTRACTDNA can adopt non-canonical structures that have important biological functions while also providing structural diversity for nanotechnology applications. Here, we describe the crystal structures of two oligonucleotides composed of d(CGA) triplet repeats in the parallel-stranded duplex form. The structure determination of four unique d(CGA)-based parallel-stranded duplexes across two crystal structures has allowed us to characterize and establish structural parameters of d(CGA) triplets in the parallel-stranded duplex form. Our results show that d(CGA) units are highly uniform, but that each strand in the duplex is structurally unique and has a distinct role in accommodating structural asymmetries induced by the C-CH+ base pair.

2020 ◽  
Vol 25 (42) ◽  
pp. 4464-4485 ◽  
Author(s):  
Katarzyna Kluszczyńska ◽  
Liliana Czernek ◽  
Wojciech Cypryk ◽  
Łukasz Pęczek ◽  
Markus Düchler

Background: Exosomes open exciting new opportunities for advanced drug transport and targeted release. Furthermore, exosomes may be used for vaccination, immunosuppression or wound healing. To fully utilize their potential as drug carriers or immune-modulatory agents, the optimal purity of exosome preparations is of crucial importance. Methods: Articles describing the isolation and purification of exosomes were retrieved from the PubMed database. Results: Exosomes are often separated from biological fluids containing high concentrations of proteins, lipids and other molecules that keep vesicle purification challenging. A great number of purification protocols have been published, however, their outcome is difficult to compare because the assessment of purity has not been standardized. In this review, we first give an overview of the generation and composition of exosomes, as well as their multifaceted biological functions that stimulated various medical applications. Finally, we describe various methods that have been used to purify small vesicles and to assess the purity of exosome preparations and critically compare the quality of these evaluation protocols. Conclusion: Combinations of various techniques have to be applied to reach the required purity and quality control of exosome preparations.


Epigenomes ◽  
2021 ◽  
Vol 5 (1) ◽  
pp. 5 ◽  
Author(s):  
Ryohei Wada ◽  
Wataru Yoshida

N6-methyladenine modification (m6dA) has recently been identified in eukaryote genomic DNA. The methylation destabilizes the duplex structure when the adenine forms a Watson–Crick base pair, whereas the methylation on a terminal unpaired adenine stabilizes the duplex structure by increasing the stacking interaction. In this study, the effects of m6dA modification on the thermal stability of four distinct telomeric G-quadruplex (G4) structures were investigated. The m6dA-modified telomeric oligonucleotide d[AGGG(TTAGGG)3] that forms a basket-type G4 in Na+, d[(TTAGGG)4TT] that forms a hybrid-type G4 in K+ (Form-2), d[AAAGGG(TTAGGG)3AA] that forms a hybrid-type G4 in K+ (Form-1), and d[GGG(TTAGGG)3T] that forms a basket-type G4 with two G-tetrads in K+ (Form-3) were analyzed. Circular dichroism melting analysis demonstrated that (1) A7- and A19-methylation destabilized the basket-type G4 structure that formed in Na+, whereas A13-methylation stabilized the structure; (2) A15-methylation stabilized the Form-2 G4 structure; (3) A15- and A21-methylations stabilized the Form-1 G4 structure; and (4) A12-methylation stabilized the Form-3 G4 structure. These results suggest that m6dA modifications may affect the thermal stability of human telomeric G4 structures in regulating the biological functions.


2014 ◽  
Vol 92 (6) ◽  
pp. 496-507 ◽  
Author(s):  
Hans Reuter ◽  
Hilko Wilberts

The syntheses and crystal structures of [(t-Bu2Sn)3O(OH)2]CO3·3MeOH, 1a, [(t-Bu2Sn)3O(OH)2]CO3·3H2O·acetone, 1b, [(t-Bu2Sn)3O(OH)2][I]2·[(t-Bu2Sn(OH)I]2·2DMSO, 1c, and [(Cy2Sn)3O(OH)2][I]2·2DMSO, 2a, all containing the trinuclear [(R2Sn)3O(OH)2]2+ ion have been described. The butterfly shape of this cation is derived from two annulated, four-membered tin–oxygen rings with a central μ3-oxygen atom and trigonal-bipyramidally coordinated tin atom both belonging to both rings and two μ2-hydroxyl groups and two outer, four-fold coordinated tin atoms. In 1a and 1b, the carbonate anions interact with the outer tin atoms of the cations as bidentate chelating ligands in the classical syn–syn coordination mode, and vice versa. In this way, both outer tin atoms expand their coordination sphere from four to five, with the consequence that bond angles and lengths within the cation are determined by the axial and equatorial position of the oxygen atoms within the trigonal-bipyramidal coordination on all three tin atoms. 1c consists of two different building units, an up to now unknown hydroxide iodide of composition [(t-Bu2Sn(OH)I]2 with hydrogen-bonded DMSO molecules and a [(t-Bu2Sn)3O(OH)2]2+ cation with one coordinated and one isolated, via hydrogen bonds connected iodine ion. The hydroxide iodine is built up of two five-fold coordinated tin atoms linked via two hydroxyl groups with exocyclic iodine atoms occupying axial positions at the trigonal-biypramidally coordinated tin atoms. The unprecedented coordination of the iodine ion to the [(t-Bu2Sn)3O(OH)2]2+ cation takes place between both outer tin atoms, resulting in a five-fold, trigonal-bipyramidal coordination at these tin atoms, too. Structural parameters within the so-formed [(t-Bu2Sn)3O(OH)2I]+ complex are very similar to those of 1a and 1b, with the exception of a significant lengthening of the tin–oxygen bonds opposite to the bridging iodine atom. 2a represents the first example of the [(R2Sn)3O(OH)2]2+ cation without R = t-butyl, so far. In the solid, it consists of two crystallographic independent [(Cy2Sn)3O(OH)2][I]2 building units, each connected to two DMSO molecules via hydrogen bonds. Both building units are very similar with respect to their conformation. Each of the iodine anions coordinates with only one of the two outer tin atoms, one in an inwards, one in an outwards to the tin-oxygen framework directed position. These tin atoms are therefore also trigonal-bipyramidally coordinated as in 1a−1c, but because of steric reasons one of the trigonal-bipyramids has changed its orientation within the tin–oxygen framework, accompanied by enormous changes of bond lengths and angles therein.


Biochemistry ◽  
1982 ◽  
Vol 21 (14) ◽  
pp. 3352-3358 ◽  
Author(s):  
Jay Newman ◽  
Loren A. Day ◽  
Gregory W. Dalack ◽  
Don Eden

Author(s):  
Zhigang Xie ◽  
Lei Wang ◽  
YiTe Li ◽  
Junli Zhou

Photoactive MOFs-based delivery systems are highly attractive for photodynamic therapy (PDT), but the fundamental interplay among structural parameters and photoactivity and biological properties of those MOFs remains unclear. Herein, porphyrinic...


2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Satoko Inagaki ◽  
Kazuyo Fujita ◽  
Yukiko Takashima ◽  
Kayoko Nagayama ◽  
Arifah C. Ardin ◽  
...  

Streptococcus mutansproduces 3 types of glucosyltransferases (GTFs), whose cooperative action is essential for cellular adhesion. The recombinase A (RecA) protein is required for homologous recombination. In our previous study, we isolated several strains with a smooth colony morphology and low GTF activity, characteristics speculated to be derived from the GTF fusions. The purpose of the present study was to investigate the mechanism of those fusions.S. mutansstrain MT8148 was grown in the presence of recombinant RecA (rRecA) protein, after which smooth colonies were isolated. The biological functions and sequences of thegtfBandgtfCgenes of this as well as other clinical strains were determined. The sucrose-dependent adherence rates of those strains were reduced as compared to that of MT8148. Determination of the sequences of thegtfBandgtfCgenes showed that an approximately 3500 bp region was deleted from the area between them. Furthermore, expression of therecAgene was elevated in those strains as compared to MT8148. These results suggest that RecA has an important role in fusions ofgtfBandgtfCgenes, leading to alteration of colony morphology and reduction in sucrose-dependent adhesion.


1999 ◽  
Vol 55 (12) ◽  
pp. 2005-2012 ◽  
Author(s):  
Anirban Ghosh ◽  
Manju Bansal

AA·TT and GA·TC dinucleotide steps in B-DNA-type oligomeric crystal structures and in protein-bound DNA fragments (solved using data with resolution <2.6 Å) show very small variations in their local dinucleotide geometries. A detailed analysis of these crystal structures reveals that in AA·TT and GA·TC steps the electropositive C2—H2 group of adenine is in very close proximity to the keto O atoms of both the pyrimidine bases in the antiparallel strand of the duplex structure, suggesting the possibility of intra-base pair as well as cross-strand inter-base pair C—H...O hydrogen bonds in the DNA minor groove. The C2—H2...O2 hydrogen bonds in the A·T base pairs could be a natural consequence of Watson–Crick pairing. However, the cross-strand interactions between the bases at the 3′-end of the AA·TT and GA·TC steps obviously arise owing to specific local geometry of these steps, since a majority of the H2...O2 distances in both data sets are considerably shorter than their values in the uniform fibre model (3.3 Å) and many are even smaller than the sum of the van der Waals radii. The analysis suggests that in addition to already documented features such as the large propeller twist of A·T base pairs and the hydration of the minor groove, these C2—H2...O2 cross-strand interactions may also play a role in the narrowing of the minor groove in A-tract regions of DNA and help explain the high structural rigidity and stability observed for poly(dA)·poly(dT).


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