Lateral Loop Research Articles

Coexistence of two quadruplex-duplex hybrids in the PIM1 gene.

The triple-negative breast cancer (TNBC), a subtype of breast cancer which lacks of targeted therapies, exhibits a poor prognosis. It was shown recently that the PIM1 oncogene is highly related to the proliferation of TNBC cells. A quadruplex–duplex hybrid (QDH) forming sequence was recently found to exist near the transcription start site of PIM1. This structure could be an attractive target for regulation of the PIM1 gene expression and thus the treatment of TNBC. Here, we present the solution structures of two QDHs that could coexist in the human PIM1 gene. Form 1 is a three-G-tetrad-layered (3+1) G-quadruplex containing a propeller loop, a lateral loop and a stem-loop made up of three G•C Watson–Crick base pairs. On the other hand, Form 2 is an anti-parallel G-quadruplex comprising two G-tetrads and a G•C•G•C tetrad; the structure has three lateral loops with the middle stem-loop made up of two Watson-Crick G•C base pairs. These structures provide valuable information for the design of G-quadruplex-specific ligands for PIM1 transcription regulation.

Study of Fingerprints in Relation to Dental Caries

Fingerprints of 40 individuals of age group 4-18 years were sampled from Agyaram Kherbari L.P. School, D. L. P School and J.N. M. E school (Dhubri District) to study the pattern of fingerprints and their relation with dental caries as they may be associated with the disease and serve as a predictor for early detection of it. Analysis was carried out in the affected individuals and it was found that the per centage of ulnar loop is highest (23.75%) in females and also in males (19.7%) and per centage of lateral loop is lowest (1.25% and 1.24%), whereas the control had more per centage of ulnar loop in both males and females. The study shows an association of dermatoglyphic pattern of fingerprints and prevalence of dental caries.

Mapping Lateral Loop Conformational Switching of the Telomeric DNA G-Quadruplex on NMM Prophyrin Binding Using Fluorescent Guanine Analogs

Mapping Lateral Loop Conformational Switching of the Telomeric DNA G-Quadruplex on NMM Prophyrin Binding Using Fluorescent Guanine Analogs

Resolving the cognitive clinico-radiological paradox – Microstructural degeneration of fronto-striatal-thalamic loops in early active multiple sclerosis

BackgroundAssociations between cognitive impairment (CI) and both global and regional brain volumes can be weak in early multiple sclerosis (MS), a dilemma known as cognitive clinico-radiological paradox. We hypothesized that white-matter (WM) integrity within fronto-striatal-thalamic networks may be a sensitive marker for impaired performance in speed-dependent tasks, typical for early MS. MethodsTwenty-seven patients with early active relapsing-remitting MS (RRMS) received comprehensive neuropsychological assessment and underwent structural and diffusion-weighted brain magnetic resonance imaging (MRI). Global and regional brain volumes were obtained using FreeSurfer software. Fractional anisotropy (FA) was computed from diffusion tensor images to assess microstructural alterations within three anatomically predefined fronto-striatal-thalamic loops known to be relevant for speed-dependent attention and executive functions. ResultsOverall cognitive performance (Spearman's ρ = .51) and performance in the domains processing speed (ρ = .44) and executive functions (ρ = .41) were correlated with patients' mean FA within the right dorsolateral-prefrontal loop. In addition, overall cognitive performance correlated with mean FA within the right lateral orbitofrontal loop (ρ = .39) – but only before controlling for WM lesion count. In contrast, regional volumes of grey-matter structures within these fronto-striatal-thalamic loops (including the thalamus) were not significantly related to CI. The total brain volume was associated with performance in the domain verbal memory (ρ = .43) only. ConclusionsMicrostructural degeneration within specific fronto-striatal-thalamic WM networks, previously characterized as crucial for task-monitoring, better accounts for speed-dependent CI in patients with early active RRMS than global or regional brain volumes. Our findings may advance our understanding of the neural substrates underlying CI characteristic for early RRMS.

Study of conformational transitions of i-motif DNA using time-resolved fluorescence and multivariate analysis methods.

Recently, the presence of i-motif structures at C-rich sequences in human cells and their regulatory functions have been demonstrated. Despite numerous steady-state studies on i-motif at neutral and slightly acidic pH, the number and nature of conformation of this biological structure are still controversial. In this work, the fluorescence lifetime of labelled molecular beacon i-motif-forming DNA sequences at different pH values is studied. The influence of the nature of bases at the lateral loops and the presence of a Watson–Crick-stabilized hairpin are studied by means of time-correlated single-photon counting technique. This allows characterizing the existence of several conformers for which the fluorophore has lifetimes ranging from picosecond to nanosecond. The information on the existence of different i-motif structures at different pH values has been obtained by the combination of classical global decay fitting of fluorescence traces, which provides lifetimes associated with the events defined by the decay of each sequence and multivariate analysis, such as principal component analysis or multivariate curve resolution based on alternating least squares. Multivariate analysis, which is seldom used for this kind of data, was crucial to explore similarities and differences of behaviour amongst the different DNA sequences and to model the presence and identity of the conformations involved in the pH range of interest. The results point that, for i-motif, the intrachain contact formation and its dissociation show lifetimes ten times faster than for the open form of DNA sequences. They also highlight that the presence of more than one i-motif species for certain DNA sequences according to the length of the sequence and the composition of the bases in the lateral loop.

Qualitative signs of digital dermatoglyphics as markers of diseases of atopic nature

The lawfulness of the application of the method of dermatoglyphics in the study of atopic diseases is ensured by the polygenic inheritance of signs of dermatoglyphics, on the one hand, and the pathogenetic heterogeneity of these diseases, on the other hand, as well as high informative ability of signs of dermatoglyphics as markers of diseases of hereditary and multifactorial nature. The purpose of the study is to detect differences in qualitative signs of digital dermatoglyphics between patients with atopic dermatitis, allergic rhinitis and bronchial asthma. Primary indicators of digital dermatoglyphics of sick young men and young women of the Podillia region are taken from the data bank of the research center of the National Pirogov Memorial Medical University, Vinnytsya and were used in previous studies when compared with the practically healthy population of this region. Imprints were obtained by the method of “printing ink” by Gladkova T. D. By the method of Cummins H. and Midlo Ch. a dermatological study was performed for 320 young men and young women with allergic rhinitis (n=69), bronchial asthma (n=108) and atopic dermatitis (n=143). The frequency and location of 8 types of finger patterns were subject to analysis. Statistical processing of the obtained results was carried out in the package “Statistica 6.1” using nonparametric methods. The reliability of the difference in values between independent qualitative values was determined by the formula of Weber E. (1961). The specificity of the digital typology of atopic diseases is established, which is based on the differences in the frequency and location of the whorl, central pocket and arches between the young men, except those indicated - a random pattern between young women, patients with atopic dermatitis, bronchial asthma, allergic rhinitis. Additionally, when comparing young men, patients with allergic rhinitis with patients with bronchial asthma and atopic dermatitis - ulnar loop; for bronchial asthma with patients with allergic rhinitis and atopic dermatitis - lateral pocket loop (in young men) and ulnar, lateral pocket and double loops (in young women); when comparing young men, patients with atopic dermatitis with patients with bronchial asthma, and allergic rhinitis - a random pattern.

Major G-Quadruplex Form of HIV-1 LTR Reveals a (3 + 1) Folding Topology Containing a Stem-Loop.

Nucleic acids can form noncanonical four-stranded structures called G-quadruplexes. G-quadruplex-forming sequences are found in several genomes including human and viruses. Previous studies showed that the G-rich sequence located in the U3 promoter region of the HIV-1 long terminal repeat (LTR) folds into a set of dynamically interchangeable G-quadruplex structures. G-quadruplexes formed in the LTR could act as silencer elements to regulate viral transcription. Stabilization of LTR G-quadruplexes by G-quadruplex-specific ligands resulted in decreased viral production, suggesting the possibility of targeting viral G-quadruplex structures for antiviral purposes. Among all the G-quadruplexes formed in the LTR sequence, LTR-III was shown to be the major G-quadruplex conformation in vitro. Here we report the NMR structure of LTR-III in K+ solution, revealing the formation of a unique quadruplex–duplex hybrid consisting of a three-layer (3 + 1) G-quadruplex scaffold, a 12-nt diagonal loop containing a conserved duplex-stem, a 3-nt lateral loop, a 1-nt propeller loop, and a V-shaped loop. Our structure showed several distinct features including a quadruplex–duplex junction, representing an attractive motif for drug targeting. The structure solved in this study may be used as a promising target to selectively impair the viral cycle.

Abstract 685: Structural study of the 3'-end G-quadruplex formed in the human PDGFR-β promoter: Insight into a transcriptional inhibitor element

Abstract Aberrant expression of PDGFR-β promotes multiple hallmarks of cancer, and its transcriptional regulation provides an attractive means to inhibit the PDGFR-β signaling pathway. The human PDGFR-β promoter nuclease hypersensitive element (NHE) can form multiple G-quadruplexes. While the most stable G-quadruplex formed in the human PDGFR-β promoter NHE region is the 5'-mid G-quadruplex, the 3'-end sequence that contains a 3'-GGA run forms a less stable G-quadruplex. Interestingly, the G-quadruplex formed in the 3'-end region of the NHE is recently found to be a transcriptional repressor of PDGFR-β, and a small molecule ellipticine, GSA1129, is shown to selectively stabilize the 3'-end G-quadruplex and repress PDGFR-β activity in cancer cell lines and in a preclinical animal model. Therefore, understanding the molecular structure of the 3'-end G-quadruplex is important for small molecule targeting in PDGFR-β gene regulation. Using Nuclear Magnetic Resonance (NMR) spectroscopy, we found that the 3'-end G-quadruplex formed in the extended PDGFR-β NHE 3'-end sequence consists of two novel intramolecular end-insertion G-quadruplexes, one with a 3'-non-adjacent flanking guanine inserted into the 3'-external tetrad (3'-insertion-G4), and another with a 5'-non-adjacent flanking guanine inserted into the 5'-external tetrad (5'-insertion-G4), respectively. The two guanines in the GGA-run move up or down within the G-quadruplex to accommodate the inserted guanine. The two end-insertion G-quadruplexes co-exist in equilibrium under physiological salt conditions. In the 3'-insertion-G4, the 3' non-adjacent guanine G20 is involved in the formation of the 3'-external G-tetrad, with the two guanines from the GGA-run involved in the formation of the 5'-external and middle G-tetrads, thereby inducing the formation of a bulge loop structure from the 3'-flanking strand. In the 5'-insertion-G4, the 5'-non-adjacent flanking guanine G0 is involved in the formation of the 5'-external G-tetrad, with the two guanines from the GGA-run involved in the formation of the middle and 3'-external G-tetrads, thereby inducing the formation of a lateral loop from the 5'-flanking residues on top of the 5'-external tetrad. The loop interactions and capping structures of the two end-insertion G-quadruplexes appear to be different. For the 3'-insertion-G4, only the 5'-flanking bases stabilize the structure. For the 5'-insertion-G4, the flanking residues at both the 5'- and 3'-ends stabilize the structure, and a favorable capping structure appears to be adopted by the 5'-lateral loop. Significantly, the formation of two equilibrating end-insertion G-quadruplexes appears to depend on the GGA-run and the guanine-containing flanking sequences. The unique end-insertion structures and capping conformations may provide a specific platform for small molecule targeting. Citation Format: Buket Onel, Clement Lin, Danzhou Yang. Structural study of the 3'-end G-quadruplex formed in the human PDGFR-β promoter: Insight into a transcriptional inhibitor element [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 685.

Abstract 687: A dGMP fill-in G-quadruplex forms in the PDGFR-β promoter that serves as a unique target for drug design

Abstract Platelet-derived growth factor receptor beta (PDGFR-β) is a cell-surface-receptor tyrosine kinase implicated in platelet-derived growth factor (PDGF) signaling pathways, and overexpression of PDGFR-β is associated with tumor growth, angiogenesis, and migration, making PDGFR-β an attractive target for cancer therapy. The formation of DNA G-quadruplexes in the GC-rich nuclease hypersensitivity element of the human PDGFR-β gene promoter has been found to inhibit PDGFR-β transcriptional activity. We previously determined the major G-quadruplex structure formed in the PDGFR-β promoter using a 22-mer sequence of pu22m1, which adopts a folding pattern containing a unique broken G-strand with the 3' tetrad-guanine coming from a distant site connected by a five nucleotide lateral loop. However, extension of the 3' end flanking segment of pu22m1 results in destabilization of the G-quadruplex, suggesting that this structure may be unstable in vivo. Recently, it has been reported that a unique type of intramolecular G-vacancy-bearing G-quadruplex (GVBQ) can be formed with three G3 tracts and one G2 tract and has an incomplete G-tetrad with a G-vacancy. A guanine derivative, such as GMP or GTP, can fill the G-vacancy with Hoogsteen hydrogen bonding and complete the G-tetrad, resulting in G-quadruplex stabilization. The unique broken-strand structure of PDGFR-β pu22m1 suggests a possibility of the formation of a GVBQ structure in this sequence, which can be completed and stabilized by guanine and guanine derivatives. To test this hypothesis, we examined the formation and stability of G-quadruplex formed in pu22m1 variants and the potential of guanine derivatives to fill in the incomplete G-tetrad and stabilize the overall G-quadruplex, using nuclear magnetic resonance spectroscopy, circular dichroism spectroscopy and DMS footprinting experiments. Our results showed that a GVBQ could form in in the PDGFR-β promoter sequence and that dGMP could insert and complete the incomplete G-tetrad to induce the formation of a stable and well-defined dGMP-fill-in-GVBQ in potassium solution. In addition, we discovered two natural plant alkaloids, berberine and chelerythrine, which could stabilize this dGMP-fill-in-GVBQ, with an increase in melting temperature by more than 10 °C. Therefore, it appears that dGMP could interact and stabilize the broken-stranded PDGFR-β promoter G-quadruplex, which may play a role in PDGFR-β transcriptional regulation. Elevated levels of guanine and guanine derivatives/metabolites are found in tumor cells, suggesting that the GVBQs may play important regulatory roles in tumor cell pathological processes, such as PDGFR-β transcriptional regulation. Furthermore, our results suggest that this unique dGMP-fill-in G-quadruplex in the PDGFR-β promoter may serve as a novel anticancer drug target for modulating PDGFR-β gene regulation. Citation Format: Kaibo Wang, Clement Lin, Guanhui Wu, Danzhou Yang. A dGMP fill-in G-quadruplex forms in the PDGFR-β promoter that serves as a unique target for drug design [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 687.

Fluorine-Mediated Editing of a G-Quadruplex Folding Pathway.

A (3+1)-hybrid-type G-quadruplex was substituted within its central tetrad by a single 2'-fluoro-modified guanosine. Driven by the anti-favoring nucleoside analogue, a novel quadruplex fold with inversion of a single G-tract and conversion of a propeller loop into a lateral loop emerges. In addition, scalar couplings across hydrogen bonds demonstrate the formation of intra- and inter-residual F⋅⋅⋅H8-C8 pseudo-hydrogen bonds within the modified quadruplexes. Alternative folding can be rationalized by the impact of fluorine on intermediate species on the basis of a kinetic partitioning mechanism. Apparently, chemical or other environmental perturbations are able to redirect folding of a quadruplex, possibly modulating its regulatory role in physiological processes.

Evidence for Reverse Hoogsteen Hairpin Intermediates in the Photocrosslinking of Human Telomeric DNA Sequences.

UVB irradiation of human telomeric d(GGGTTA)3 GGG sequences in potassium ion solution crosslinks the first and third TTA segments through anti cyclobutane pyrimidine dimer (CPD) formation. The photocrosslinking reaction was first proposed to occur through a form 3 two-tetrad G-quadruplex in which the lateral four-nucleotide GTTA loop can interact with an adjacent TTA loop. Curiously, the reaction does not occur with sodium ion, which was explained by the formation of a basket structure which only has three-nucleotide TTA loops that cannot interact. Sequences known or expected to favor the two-tetrad basket did not show enhanced photocrosslinking, suggesting that some other structure was the reactive intermediate. Herein, we report that anti CPDs form in human telomeric DNA sequences with lithium ion that is known to disfavor G-quadruplex formation, as well as with potassium ion when the bases are modified to interfere with G-quartet formation. We also show that anti CPDs form in sequences containing A's in place of G's that cannot form Hoogsteen hairpins, but can form reverse Hoogsteen hairpins. These results suggest that reverse Hoogsteen hairpins may play a hitherto unrecognized role in the biology and photoreactivity of DNA in telomeres, and possibly in other purine-rich sequences found in regulatory regions.

Distribution of heterochromatin markers in lampbrush chromosomes in birds

Changes in functional gene activity not affecting primary DNA structure can be inherited by a cell and in total represent epigenetic mechanisms of the genome expression regulation. Epigenetic genome modifications include DNA methylation, histone modifications, and binding of the proteins and noncoding RNA. The distribution of heterochromatin markers (such as methylated cytosine, HP1 heterochromatin protein, and modifications of H3, H4, and H2A histones) was analyzed by example of lampbrush chromosomes typical for growing bird oocytes. On the lampbrush chromosomes of domesticated chicken (Gallus gallus domesticus), Japanese quail (Coturnix japonica), and chaffinch (Fringilla coelebs), methylated cytosine was mainly detected in chromomeres, as well as in unextended regions of lateral loop axes. The largest accumulation of methylated cytosine was demonstrated by chromosome W and dense chromomeres of macro- and microchromosomes. The HP1β protein distribution in the lampbrush chromosomes corresponded in general to the distribution of methylated cytosine. Chromomeres of chromosome W as well as centromeric and terminal chromomeres of macro- and microchromosomes accumulated the highest amount of the HP1β protein as compared with the remaining chromomeres. The character of distribution of the H3K9 me3 and H3K27 me3 histone modifications, as well as phosphorylated H4 and H2A histones, was different. Phosphorylated H4 and H2A histones were distributed proportionally to the staining by DNA specific dyes and were accumulated in all chromosomes, while trimethylated H3K9 histone was enriched in the regions of constitutive heterochromatin. We assume that the HP1β heterochromatin protein is involved in compaction and transcriptional inactivation of the chromatin in chromomeres of the lampbrush chromosomes.

Abstract 5232: The molecular basis for specific recognition of the biologically relevant hybrid-2 type human telomeric G-quadruplex by epiberberine

Abstract G-quadruplex structures have been shown to form in human telomeres, and the formation of G-quadruplexes can inhibit telomerase, which plays a key role in cancers by stabilizing telomere length and integrity thereby granting limitless replicative potential. The human telomeric G-quadruplex is thus considered to be a potential target for cancer therapeutics. In physiologically relevant potassium solution, human telomeric DNA sequences form two equilibrating hybrid-type G-quadruplex structures, with the hybrid-2 structure being the predominant form in extended sequences. We discovered that epiberberine (EPI), a naturally occurring protoberberine alkaloid, can specifically bind the hybrid-2 human telomeric G-quadruplex and can induce the conversion to the hybrid-2 structure. Using nuclear magnetic resonance (NMR) spectroscopy, we determined the solution structure of the 1:1 complex of EPI and hybrid-2 human telomeric G-quadruplex. Our NMR structure shows EPI bound at the 5’ end of the hybrid-2 telomeric quadruplex with an unexpectedly large drug-induced conformational change in the flanking and loop regions, creating a very well-defined drug binding pocket with extensive capping structures. The EPI molecule and 5’ flanking adenine form an induced quasi-triad plane which is intercalated between the external 5’ tetrad and capping structures. Two layers of new capping structures are formed with the 5’ flanking segment and the second TTA lateral loop to cover the “intercalated quasi-triad”. Notably, the well-defined EPI-induced multi-layer binding-site arrangement is only possible in the hybrid-2 folding topology of telomeric DNA. Our results provide important insights into specific targeting of the physiologically relevant hybrid-2 human telomeric G-quadruplex by a small molecule compound; EPI’s asymmetric crescent-shape and the positioning of its dioxolane moiety, as well as the hybrid-2 folding and the loop and flanking bases in the human telomeric DNA sequence, all contribute toward the specific recognition of EPI. In addition, we have conducted polymerase stop assays, which confirmed that EPI can stabilize the human telomeric G-quadruplex to inhibit polymerase activity. Citation Format: Clement Lin, Guanhui Wu, Yong Shao, Danzhou Yang. The molecular basis for specific recognition of the biologically relevant hybrid-2 type human telomeric G-quadruplex by epiberberine [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5232. doi:10.1158/1538-7445.AM2017-5232

Chicken Microchromosomes in the Lampbrush Phase: A Cytogenetic Description

Lampbrush chromosomes are giant, transcriptionally active, meiotic chromosomes found in oocytes of all vertebrates with the exception of mammals. Lampbrush chromosomes offer a convenient tool for cytogenetic mapping and, in particular, have been instrumental in mapping genes and linkage groups on chicken (GGA) chromosomes. Whereas cytogenetic maps of macrochromosome GGA1-10 and microchromosome GGA11-16 lampbrush bivalents have been established, identification and description of smaller microchromosome bivalents are still missing. In this work, we used specific FISH probes for the identification of 12 chicken lampbrush chromosomes formed by GGA17-28. Our observations on chromomere and lateral loop arrangement and chiasma position allowed us to construct the respective cytogenetic maps for these microchromosomes. For the 10 smallest chicken microchromosomes, GGA29-38, no individual molecular tags are available, yet they can be collectively marked using the PO41 repeat. The reported results contribute to building of working cytogenetic maps of the chicken karyotype.

New Photomechanical Molecular Switch Based on a Linear π-Conjugated System

We report the electronic transport properties of a new photo-addressable molecular switch. The switching process relies on a new concept based on linear {\pi}-conjugated dynamic systems, in which the geometry and hence the electronic properties of an oligothiophene chain can be reversibly modified by the photochemical trans-cis isomerization of an azobenzene unit fixed in a lateral loop. Electron transport measurements through self-assembled monolayers on gold, contacted with eGaIn top contact, show switching with a conductance ratio up to 1E3. Ab initio calculations have been used to identify the most energetically stable conformations of the molecular switch, the corresponding calculated conductances qualitatively explain the trend observed in the photo-switching experiments.

Abstract 3090: Molecular structure of the major G-quadruplex formed in the PDGFR-β promoter nuclease hypersensitivity element and its binding with small molecules

Abstract Overexpression of platelet-derived growth factor receptor β (PDGFR-β) is associated with multiple cancers, making PDGFR-β an attractive target for anticancer drugs. Few strategies other than molecular targeting of the PDGFR-β protein or its cognate ligand have been reported for developing inhibitors for the PDGFR-β signaling pathway. DNA G-quadruplexes (G4s) formed in the GC-rich nuclease hypersensitivity element of the human PDGFR-β gene promoter have been found to inhibit PDGFR-β transcriptional activity, and stabilization of these G4s by small-molecule compounds could serve as a mechanism for cancer therapeutics. We have shown that the major G4 formed in the PDGFR-β promoter is from the central four G-runs, adopting an intramolecular parallel-stranded structure with a broken G-strand and contains three 1-nucleotide (nt) chain-reversal loops and one lateral loop. The novel folding of the PDGFR-β G4 highlights the inherent stability of the 1-nt loops in parallel-stranded G4 structures. Elucidating the structure of the major PDGFR-β promoter G4 is important for designing small-molecule drugs to specifically target this structure to inhibit gene transcription. Using nuclear magnetic resonance (NMR) spectroscopy, we have determined the potassium solution structure of this major G4 formed in the PDGFR-β promoter. Our structure showed a unique 3’ capping structure involving three guanine nucleotides in the lateral loop. This novel capping structure is determined by the specific loop sequence as well as the broken-stranded PDGFR-β G4 folding pattern. The unique 3’ capping structure could be specifically recognized by proteins and small molecule ligands. Unrestrained molecular dynamic calculations showed that this major PDGFR-β G4 and its 3’ capping structure are stable in aqueous environment on the ns time-scale. We also investigated the binding of small-molecules to the PDGFR-β G4 using a combination of NMR, circular dichroism (CD), and fluorescence based methods to identify compounds that can selectively bind the PDGFR-β G4 over other classic parallel-stranded G-quadruplexes, such as the c-MYC promoter G4. Our study demonstrates the structural diversity in promoter G4s which may enable specific recognition and the modulation of gene expression by small-molecule drugs. Citation Format: Clement Lin, Prashansa Agrawal, Yuwei Chen, Salil Kalarn, Nanjie Deng, Laurence Hurley, Danzhou Yang. Molecular structure of the major G-quadruplex formed in the PDGFR-β promoter nuclease hypersensitivity element and its binding with small molecules. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3090.

Convergent strabismus fixus without high myopia

A 37-year-old woman presented with progressive large-angle esotropia (>140(Δ)) since childhood. Her best-corrected visual acuity was 20/80 in right eye and unrecordable in the left eye because of severe esotropia and limitation of abduction. Computed tomography of the orbits showed presence of nasal displacement of the superior rectus muscle and inferior displacement of the lateral rectus muscle in the left eye, which was confirmed intraoperatively. Intraoperatively, axial length was 23mm in the right eye and 24.6mm in the left eye. Diagnosed with convergent strabismus fixus without high myopia, she underwent medial rectus recession of 8.0mm and superior rectus-lateral rectus loop myopexy. Postoperatively, she had an exotropia of about 8(Δ). This case highlights the possibility of progressive esotropia similar to "heavy eye syndrome" in the absence of high myopia.

Alk1 and Alk5 inhibition by Nrp1 controls vascular sprouting downstream of Notch.

Sprouting angiogenesis drives blood vessel growth in healthy and diseased tissues. Vegf and Dll4/Notch signalling cooperate in a negative feedback loop that specifies endothelial tip and stalk cells to ensure adequate vessel branching and function. Current concepts posit that endothelial cells default to the tip-cell phenotype when Notch is inactive. Here we identify instead that the stalk-cell phenotype needs to be actively repressed to allow tip-cell formation. We show this is a key endothelial function of neuropilin-1 (Nrp1), which suppresses the stalk-cell phenotype by limiting Smad2/3 activation through Alk1 and Alk5. Notch downregulates Nrp1, thus relieving the inhibition of Alk1 and Alk5, thereby driving stalk-cell behaviour. Conceptually, our work shows that the heterogeneity between neighbouring endothelial cells established by the lateral feedback loop of Dll4/Notch utilizes Nrp1 levels as the pivot, which in turn establishes differential responsiveness to TGF-β/BMP signalling.

Dopaminergic modulation of motor network dynamics in Parkinson's disease.

Although characteristic motor symptoms of Parkinson's disease such as bradykinesia typically improve under dopaminergic medication, deficits in higher motor control are less responsive. We here investigated the dopaminergic modulation of network dynamics underlying basic motor performance, i.e. finger tapping, and higher motor control, i.e. internally and externally cued movement preparation and selection. Twelve patients, assessed ON and OFF medication, and 12 age-matched healthy subjects underwent functional magnetic resonance imaging. Dynamic causal modelling was used to assess effective connectivity in a motor network comprising cortical and subcortical regions. In particular, we investigated whether impairments in basic and higher motor control, and the effects induced by dopaminergic treatment are due to connectivity changes in (i) the mesial premotor loop comprising the supplementary motor area; (ii) the lateral premotor loop comprising lateral premotor cortex; and (iii) cortico-subcortical interactions. At the behavioural level, we observed a marked slowing of movement preparation and selection when patients were internally as opposed to externally cued. Preserved performance during external cueing was associated with enhanced connectivity between prefrontal cortex and lateral premotor cortex OFF medication, compatible with a context-dependent compensatory role of the lateral premotor loop in the hypodopaminergic state. Dopaminergic medication significantly improved finger tapping speed in patients, which correlated with a drug-induced coupling increase of prefrontal cortex with the supplementary motor area, i.e. the mesial premotor loop. In addition, only in the finger tapping condition, patients ON medication showed enhanced excitatory influences exerted by cortical premotor regions and the thalamus upon the putamen. In conclusion, the amelioration of bradykinesia by dopaminergic medication seems to be driven by enhanced connectivity within the mesial premotor loop and cortico-striatal interactions. In contrast, medication did not improve internal motor control deficits concurrent to missing effects at the connectivity level. This differential effect of dopaminergic medication on the network dynamics underlying motor control provides new insights into the clinical finding that in Parkinson's disease dopaminergic drugs especially impact on bradykinesia but less on executive functions.

Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations.

We have carried out extended set of μs-scale explicit solvent MD simulations of all possible G-triplexes which can participate in folding pathways of the human telomeric quadruplex. Our study accumulates almost 60μs of simulation data, which is by about three orders of magnitude larger sampling compared to the earlier simulations of human telomeric G-DNA triplexes. Starting structures were obtained from experimental quadruplex structures by deleting either the first or the last strand. The life-times of antiparallel triplexes with lateral and diagonal loops are at least on μs-scale, which should be sufficient to contribute to the folding pathways. However, the triplex states may involve structures with various local deviations from the ideal triplexes, such as strand tilting and various alternative and incomplete triads. The simulations reveal easy rearrangements between lateral and diagonal loop triplex topologies. Propeller loops of antiparallel triplexes may to certain extent interfere with the G-triplexes but these structures are still viable candidates to participate in the folding. In contrast, all-parallel all-anti triplexes are very unstable and are unlikely to contribute to the folding. Although our simulations demonstrate that antiparallel G-triplexes, if folded, would have life-times sufficient to participate in the quadruplex folding, the results do not rule out the possibility that the G-triplexes are out-competed by other structures not included in our study. Among them, numerous possible misfolded structures containing guanine quartets can act as off-path intermediates with longer life-times than the triplexes. Besides analyzing the structural dynamics of a diverse set of G-DNA triplexes, we also provide a brief discussion of the limitations of the simulation methodology, which is necessary for proper understanding of the simulation data.