Org Lett
Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka, 8-1, Ibaraki, Osaka 567-0047, Japan.
Published: July 2016
A fluorescent molecule DANP that binds to cytosine bulge DNA and emits characteristic fluorescence was conjugated to pyrene to give a new fluorescence probe PyDANP. Temperature- and solvent-dependent absorption changes showed that DANP and pyrene chromophores stacked at room temperature in an aqueous buffer solution and quenched fluorescence. Upon binding of DANP moiety in PyDANP to cytosine bulge DNA, the fluorescence from DANP bound to C-bulge increased by ∼12-fold, showing that PyDANP is a turn-ON probe for the detection of C-bulge DNA.
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http://dx.doi.org/10.1021/acs.orglett.6b01378 | DOI Listing |
Proc Natl Acad Sci U S A
January 2025
Program in Genetics, Molecular, and Cellular Biology, Tufts University Graduate School of Biomedical Sciences, Boston, MA 02111.
CAG/CTG repeats are prone to expansion, causing several inherited human diseases. The initiating sources of DNA damage which lead to inaccurate repair of the repeat tract to cause expansions are not fully understood. Expansion-prone CAG/CTG repeats are actively transcribed and prone to forming stable R-loops with hairpin structures forming on the displaced single-stranded DNA (S-loops).
View Article and Find Full Text PDFViruses
June 2024
Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
genomic replication initiates at a predicted RNA cloverleaf (5'CL) at the 5' end of the RNA genome. The 5'CL contains one stem (SA) and three stem-loops (SLB, SLC, SLD). Here, we present an analysis of 5'CL conservation and divergence for 209 human health-related serotypes from the genus, including enterovirus and rhinovirus species.
View Article and Find Full Text PDFAm J Ophthalmol
December 2023
From the State Key Laboratory of Ophthalmology (M.F., X.Z., Z-L.C.), Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China; National Clinical Research Center for Ocular Diseases (M.F., X.Z., Z-L.C.), Eye Hospital, Wenzhou Medical University, Wenzhou, China. Electronic address:
Purpose: To investigate the gene mutations and relationship of clinical manifestation in a Chinese family with familial lattice corneal dystrophy (LCD).
Design: Single-family case-control study.
Methods: A family with familial LCD was recruited for this study.
Anal Chem
July 2023
Graduate School of Engineering, Osaka University, A907, 2-8 Yamadaoka, Suita, Osaka 565-0871, Japan.
We have developed a DNA sensor that can be finalized to detect a specific target on demand. The electrode surface was modified with 2,7-diamino-1,8-naphthyridine (DANP), a small molecule with nanomolar affinity for the cytosine bulge structure. The electrode was immersed in a solution of synthetic probe-DNA that had a cytosine bulge structure at one end and a complementary sequence to the target DNA at the other end.
View Article and Find Full Text PDFBiophys Rep (N Y)
December 2021
School of Chemistry, Faculty of Exact Sciences.
RNA is a polymer with pivotal functions in many biological processes. RNA structure determination is thus a vital step toward understanding its function. The secondary structure of RNA is stabilized by hydrogen bonds formed between nucleotide basepairs, and it defines the positions and shapes of functional stem-loops, internal loops, bulges, and other functional and structural elements.
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