NMR characterization of the structure of the intrinsically disordered region of human origin recognition complex subunit 1, hORC1, and of its interaction with G-quadruplex DNAs

Human origin recognition complex (hORC) binds to the DNA replication origin and then initiates DNA replication. However, hORC does not exhibit DNA sequence-specificity and how hORC recognizes the replication origin on genomic DNA remains elusive. Previously, we found that hORC recognizes G-quadruplex structures potentially formed near the replication origin. Then, we showed that hORC subunit 1 (hORC1) preferentially binds to G-quadruplex DNAs using a hORC1 construct comprising residues 413 to 511 (hORC1413-511). Here, we investigate the structural characteristics of hORC1413-511 in its free and complex forms with G-quadruplex DNAs. Circular dichroism and nuclear magnetic resonance (NMR) spectroscopic studies indicated that hORC1413-511 is disordered except for a short α-helical region in both the free and complex forms. NMR chemical shift perturbation (CSP) analysis suggested that basic residues, arginines and lysines, and polar residues, serines and threonines, are involved in the G-quadruplex DNA binding. Then, this was confirmed by mutation analysis. Interestingly, CSP analysis indicated that hORC1413-511 binds to both parallel- and (3 + 1)-type G-quadruplex DNAs using the same residues, and thereby in the same manner. Our study suggests that hORC1 uses its intrinsically disordered G-quadruplex binding region to recognize parallel-type and (3 + 1)-type G-quadruplex structures at replication origin.

Complex Formation of an RNA Aptamer with a Part of HIV-1 Tat through Induction of Base Triples in Living Human Cells Proven by In-Cell NMR

An RNA aptamer that strongly binds to a target molecule has the potential to be a nucleic acid drug inside living human cells. To investigate and improve this potential, it is critical to elucidate the structure and interaction of RNA aptamers inside living cells. We examined an RNA aptamer for HIV-1 Tat (TA), which had been found to trap Tat and repress its function in living human cells. We first used in vitro NMR to examine the interaction between TA and a part of Tat containing the binding site for trans-activation response element (TAR). It was revealed that two U-A∗U base triples are formed in TA upon binding of Tat. This was assumed to be critical for strong binding. Then, TA in complex with a part of Tat was incorporated into living human cells. The presence of two U-A∗U base triples was also revealed for the complex in living human cells by in-cell NMR. Thus, the activity of TA in living human cells was rationally elucidated by in-cell NMR.

Detection of interaction between an RNA aptamer and its target compound in living human cells using 2D in-cell NMR

We introduced an isotopically labeled RNA aptamer for HIV-1 Tat prepared by E. coli transcription into HeLa cells. We successfully recorded the first heteronuclear 2D in-cell NMR spectra, which makes it possible to study the interaction of the RNA aptamer with argininamide in living human cells with higher resolution.

Detection of parallel and antiparallel DNA triplex structures in living human cells using in-cell NMR

We introduced oligodeoxynucleotides (ODNs) that form parallel and antiparallel triplex structures in vitro into living human cells and recorded their in-cell NMR spectra. Observation of landmark signals for triplex structures proved for the first time that parallel and antiparallel triplex structures are formed in living human cells.

Observation of nucleic acids inside living human cells by in-cell NMR spectroscopy

The intracellular environment is highly crowded with biomacromolecules such as proteins and nucleic acids. Under such conditions, the structural and biophysical features of nucleic acids have been thought to be different from those in vitro. To obtain high-resolution structural information on nucleic acids in living cells, the in-cell NMR method is a unique tool. Following the first in-cell NMR measurement of nucleic acids in 2009, several interesting insights were obtained using Xenopus laevis oocytes. However, the in-cell NMR spectrum of nucleic acids in living human cells was not reported until two years ago due to the technical challenges of delivering exogenous nucleic acids. We reported the first in-cell NMR spectra of nucleic acids in living human cells in 2018, where we applied a pore-forming toxic protein, streptolysin O. The in-cell NMR measurements demonstrated that the hairpin structures of nucleic acids can be detected in living human cells. In this review article, we summarize our recent work and discuss the future prospects of the in-cell NMR technique for nucleic acids.

RNA sequence and length contribute to RNA-induced conformational change of TLS/FUS

Translocated in liposarcoma (TLS)/fused in sarcoma (FUS) is a multitasking DNA/RNA binding protein implicated in cancer and neurodegenerative diseases. Upon DNA damage, TLS is recruited to the upstream region of the cyclin D1 gene (CCND1) through binding to the promotor associated non-coding RNA (pncRNA) that is transcribed from and tethered at the upstream region. Binding to pncRNA is hypothesized to cause the conformational change of TLS that enables its inhibitive interaction with histone acetyltransferases and resultant repression of CCND1 expression, although no experimental proof has been obtained. Here, the closed-to-open conformational change of TLS on binding pncRNA was implied by fluorescence resonance energy transfer. A small fragment (31 nucleotides) of the full-length pncRNA (602 nucleotides) was shown to be sufficient for the conformational change of TLS. Dissection of pncRNA identified the G-rich RNA sequence that is critical for the conformational change. The length of RNA was also revealed to be critical for the conformational change. Furthermore, it was demonstrated that the conformational change of TLS is caused by another target DNA and RNA, telomeric DNA and telomeric repeat-containing RNA. The conformational change of TLS on binding target RNA/DNA is suggested to be essential for biological functions.

Selective alkylation of T-T mismatched DNA using vinyldiaminotriazine-acridine conjugate

The alkylation of the specific higher-order nucleic acid structures is of great significance in order to control its function and gene expression. In this report, we have described the T–T mismatch selective alkylation with a vinyldiaminotriazine (VDAT)–acridine conjugate. The alkylation selectively proceeded at the N3 position of thymidine on the T–T mismatch. Interestingly, the alkylated thymidine induced base flipping of the complementary base in the duplex. In a model experiment for the alkylation of the CTG repeats DNA which causes myotonic dystrophy type 1 (DM1), the observed reaction rate for one alkylation increased in proportion to the number of T–T mismatches. In addition, we showed that primer extension reactions with DNA polymerase and transcription with RNA polymerase were stopped by the alkylation. The alkylation of the repeat DNA will efficiently work for the inhibition of replication and transcription reactions. These functions of the VDAT–acridine conjugate would be useful as a new biochemical tool for the study of CTG repeats and may provide a new strategy for the molecular therapy of DM1.

The anti-prion RNA aptamer R12 disrupts the Alzheimer's disease-related complex between prion and amyloid β

The neurodegenerative disorder Alzheimer's disease (AD) is associated with the accumulation of misfolded proteins. Some recent studies suggested that amyloid beta (Aβ) forms soluble oligomers, protofibrils, and fibrils; the Aβ oligomers being more toxic than the fibrils. Surprisingly, these Aβ oligomers reportedly bind to prion protein (PrP), which acts as a receptor on the cell membrane, possibly resulting in AD. Thus, it is thought that compounds that can disrupt the formation of the prion-Aβ oligomer complex may prevent AD. Here, we demonstrate that an anti-prion RNA aptamer, R12, inhibits the interaction of PrP with Aβ. Fluorescence assaying involving thioflavin S showed that wild-type PrP, a mutant of the N-terminal half of PrP, and even fragment peptides of PrP effectively inhibit Aβ fibrillization. Fluorescence anisotropy revealed that R12 is capable of binding to PrP, resulting in dissociation of PrP with Aβ. Consequently, the Aβ that dissociated from PrP was shown to polymerize into fibrils. These spectroscopic observations were visualized by transmission electron microscopy. This is the first demonstration of the PrP-Aβ interaction being disrupted by a nucleic acid. This ability of R12 highlights its therapeutic potential for treating AD pathology.

Analysis of Interactions between Telomeric i-Motif DNA and a Cyclic Tetraoxazole Compound

The interaction of a macrocyclic tetraoxazole compound, L2H2-4OTD (1), with two aminoalkyl side chains and telomeric i-motif, was investigated by means of electrophoretic mobility shift assay, circular dichroism spectroscopy, mass spectrometry and NMR spectroscopy analyses. The results indicate that 1 interacts with the i-motif structure at two preferred binding sites.

The first successful observation of in-cell NMR signals of DNA and RNA in living human cells

In order to understand intracellular biological events, information on the structure, dynamics and interaction of proteins and nucleic acids in living cells is of crucial importance. In-cell NMR is a promising method to obtain this information. Although NMR signals of proteins in human cells have been reported, those of nucleic acids were reported only in Xenopus laevis oocytes, i.e., not in human cells. Here, DNA and RNA were introduced into human cells by means of pore formation by bacterial toxin streptolysin O and subsequent resealing. Then, NMR signals of DNA and RNA were successfully observed for the first time in living human cells. The observed signals directly suggested the formation of DNA and RNA hairpin structures in living human cells.

Development of an RNA aptamer that acquires binding capacity against HIV-1 Tat protein via G-quadruplex formation in response to potassium ions

For the development of K⁺-responsive RNA aptamers, we proposed a new general strategy that makes use of a G-quadruplex formation in response to K⁺. This is the first report of developing an RNA aptamer that demonstrates ON/OFF switching of its target-binding activity by sensing the addition/removal of K⁺.

Boosting of activity enhancement of K+-responsive quadruplex hammerhead ribozyme

Second-generation quadruplex hammerhead ribozymes, whose activity enhances in response to K⁺, were developed. New strategies suppressed the basal activity and boosted the activity enhancement upon the addition of K⁺ to 21-fold.

An FT-IR study on packing defects in mixed β-aggregates of poly(L-glutamic acid) and poly(D-glutamic acid): a high-pressure rescue from a kinetic trap

Under favorable conditions of pH and temperature, poly(L-glutamic acid) (PLGA) adopts different types of secondary and quaternary structures, which include spiral assemblies of amyloid-like fibrils. Heating of acidified solutions of PLGA (or PDGA) triggers formation of β(2)-type aggregates with morphological and tinctorial properties typical for amyloid fibrils. In contrast to regular antiparallel β-sheet (β(1)), the amide I' vibrational band of β(2)-fibrils is unusually red-shifted below 1600 cm(-1), which has been attributed to bifurcated hydrogen bonds coupling C═O and N-D groups of the main chains to glutamic acid side chains. However, unlike for pure PLGA, the amide I' band of aggregates precipitating from racemic mixtures of PLGA and PDGA (β(1)) is dominated by components at 1613 and 1685 cm(-1)-typically associated with intermolecular antiparallel β-sheets. The coaggregation of PLGA and PDGA chains is slower and biphasic and leads to less-structured assemblies of fibrils, which is reflected in scanning electron microscopy images, sedimentation properties, and fluorescence intensity after staining with thioflavin T. The β(1)-type aggregates are metastable, and they slowly convert to fibrils with the infrared characteristics of β(2)-type fibrils. The process is dramatically accelerated under high pressure. This implies the presence of void volumes within structural defects in racemic aggregates, preventing the precise alignment of main and side chains necessary to zip up ladders of bifurcated hydrogen bonds. As thermodynamic costs associated with maintaining void volumes within the racemic aggregate increase under high pressure, a hyperbaric treatment of misaligned chains leads to rectifying the packing defects and formation of the more compact form of fibrils.

De novo formation of adipose tissue by controlled release of basic fibroblast growth factor

De novo adipogenesis at the implanted site of a basement membrane extract (Matrigel) was induced through controlled release of basic fibroblast growth factor (bFGF). bFGF was incorporated into biodegradable gelatin microspheres for its controlled release. When the mixture of Matrigel and bFGF-incorporated gelatin microspheres was implanted subcutaneously into the back of mice, a clearly visible fat pad was formed at the implanted site 6 weeks later. Histologic examination revealed that the de novo formation of adipose tissue accompanied with angiogenesis was observed in the implanted Matrigel at bFGF doses of 0.01, 0.1, and 1 microg/site, the lower and higher doses being less effective. The de novo formation induced by the bFGF-incorporated microspheres was significantly higher than that induced by free bFGF of the same dose. The mRNA of a lipogenesis marker protein, glycerophosphate dehydrogenase, was detected in the formed adipose tissues, biochemically indicating de novo adipogenesis. Free bFGF, the bFGF-incorporated gelatin microspheres, or Marigel alone and bFGF-free gelatin microspheres with or without Matrigel did not induce formation of adipose tissue. This de novo adipogenesis by mixture of Matrigel and the bFGF-incorporated gelatin microspheres will provide a new idea for tissue engineering of adipose tissue.