Investigation of B-Z transitions with DNA oligonucleotides containing 8-methylguanine

Chen, Frederic Y.-H.; Park, Soyoung; Otomo, Haruka; Sakashita, Sohei; Sugiyama, Hiroshi

doi:10.4161/adna.28226

Cited by 15 publications

(7 citation statements)

References 18 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In contrast to the right-handed structure of the B-DNA, the Z-DNA has a left-handed structure 10 . The structures and biological functions of the Z-DNA have been studied for several decades 3,4,11 since the discovery of the Z-DNA by Rich in 1979 4 . Recently the fine structures of the B–Z junction, a junction of the B-form and Z-form DNAs coexisting in a single dsDNA, was revealed by atomic-resolution X-ray crystallography 12 .…”

Section: Introductionmentioning

confidence: 99%

Molecular-scale visualization and surface charge density measurement of Z-DNA in aqueous solution

Kominami

Kobayashi

Yamada

2019

Sci Rep

View full text Add to dashboard Cite

The DNA in the left-handed conformation (Z-conformation) was first discovered by A. Rich, who revealed the crystalline structure of a DNA oligomer d(GC) 3 by X-ray diffraction method. Later it was also found that DNA molecules change their conformations from typical right-handed form (B-DNA) to the left-handed form (Z-DNA) under specific conditions (B–Z transition). Furthermore, the detailed structures of the interface between B- and Z-DNAs, B-Z junction, was also determined with an atomic resolution. Recently it was found that some proteins have the Z-DNA binding domains, but the biological functions of Z-DNA are not well understood yet. Therefore the investigation of Z-DNA under physiological conditions is highly essential. In this study, we demonstrated the high-resolution real-space imaging of DNA molecules having the Z- and B-form conformations by frequency-modulation atomic force microscopy (FM-AFM), that has made a great progress in recent years, in an aqueous solution. The major and minor grooves of both DNA conformations were clearly visualized. Furthermore, the surface charge density was measured by three-dimensional (3D) force mapping method. We found that Z-form region was less negatively charged than the B-form region.

show abstract

Section: Introductionmentioning

confidence: 99%

Molecular-scale visualization and surface charge density measurement of Z-DNA in aqueous solution

Kominami

Kobayashi

Yamada

2019

Sci Rep

View full text Add to dashboard Cite

show abstract

“…These biological structures can also undergo conformational changes under different physiological conditions. Although the canonical DNA structure is a right‐handed duplex (B‐DNA), B‐DNA with alternating purine–pyrimidine sequences can conformationally change to a left‐handed duplex (Z‐DNA) due to various factors, such as high ionic strength, protein binding, small molecule binding, and chemical modifications . The B‐ to Z‐DNA transition, which plays a crucial role in biological systems, has been utilized for nanomechanical devices and nanosensors .…”

Section: Introductionmentioning

confidence: 99%

Controlling Pyrene Association in DNA Duplexes by B‐ to Z‐DNA Transitions

2019

View full text Add to dashboard Cite

B‐ to Z‐DNA transitions play a crucial role in biological systems and have attracted the interest of researchers for their applications in DNA nanotechnology. DNA and DNA analogues have also been used as templates to construct helical chromophore associations with π interactions. In this work, the B‐ to Z‐DNA transition‐induced switching of pyrene in an association manner was evaluated using DNA duplexes with non‐nucleosidic pyrene residues in the middle of d(CG) repeat sequences. One of the pyrene‐labeled DNAs was shown to exhibit inverted exciton coupled circular dichroism signals upon pyrene association through a B‐ to Z‐DNA transition. This observation indicates that pyrene association switches the DNA conformation from right‐ to left‐handed. Interestingly, the fluorescence of the pyrene‐labeled DNA duplex also dynamically changed upon switching of the pyrene in an association‐based manner. Taken together, these studies demonstrate that pyrene‐labeled DNA shows promise as a chiroptical molecular switch.

show abstract

“…Several studies have been reported on incorporating modified nucleic acid residues for the stabilization of Z-DNA [ 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 ]. Notably modified guanine residues highly favor the formation of Z-DNA.…”

Section: Introductionmentioning

confidence: 99%

2′-O-Methyl-8-methylguanosine as a Z-Form RNA Stabilizer for Structural and Functional Study of Z-RNA

et al. 2018

View full text Add to dashboard Cite

In contrast to Z-DNA that was stabilized and well-studied for its structure by chemical approaches, the stabilization and structural study of Z-RNA remains a challenge. In this study, we developed a Z-form RNA stabilizer m8Gm, and demonstrated that incorporation of m8Gm into RNA can markedly stabilize the Z-RNA at low salt conditions. Using the m8Gm-contained Z-RNA, we determined the structure of Z-RNA and investigated the interaction of protein and Z-RNA.

show abstract

Investigation of B-Z transitions with DNA oligonucleotides containing 8-methylguanine

Cited by 15 publications

References 18 publications

Molecular-scale visualization and surface charge density measurement of Z-DNA in aqueous solution

Molecular-scale visualization and surface charge density measurement of Z-DNA in aqueous solution

Controlling Pyrene Association in DNA Duplexes by B‐ to Z‐DNA Transitions

2′-O-Methyl-8-methylguanosine as a Z-Form RNA Stabilizer for Structural and Functional Study of Z-RNA

Contact Info

Product

Resources

About