Tunable light absorption of graphene using topological interface states.

A tunable light absorption of graphene using topological interface states (TISs) is presented. The monolayer graphene is embedded in the interface of asymmetric topological photonic crystals (ATPCs). A strong absorption phenomenon occurs by the excitation of TISs. It is found that the absorption spectra are intensively dependent on the chemical potential of graphene and the periodic number of the ATPCs. Furthermore, the absorption can be rapidly switched in a slight variation of chemical potential, which is modulated by the applied gate voltage on graphene. This study not only opens up a new approach for enhancing light-monolayer graphene interactions, but also provides for practical applications in high absorption optoelectronic devices. This strong absorption phenomenon is different from those in Fabry-Perot resonators, nano-cavities photonic crystal, and traditional topological photonic crystals (TPCs).

The Future of Neurocritical Care Research: Proceedings and Recommendations from the Fifth Neurocritical Care Research Network Conference.

The Fifth Neurocritical Care Research Network (NCRN) Conference held in Boca Raton, Florida, in September of 2018 was devoted to challenging the current status quo and examining the role of the Neurocritical Care Society (NCS) in driving the science and research of neurocritical care. The aim of this in-person meeting was to set the agenda for the NCS's Neurocritical Care Research Central, which is the overall research arm of the society. Prior to the meeting, all 103 participants received educational content (book and seminar) on the 'Blue Ocean Strategy®,' a concept from the business world which aims to identify undiscovered and uncontested market space, and to brainstorm innovative ideas and methods with which to address current challenges in neurocritical care research. Three five-member working groups met at least four times by teleconference prior to the in-person meeting to prepare answers to a set of questions using the Blue Ocean Strategy concept as a platform. At the Fifth NCRN Conference, these groups presented to a five-member jury and all attendees for open discussion. The jury then developed a set of recommendations for NCS to consider in order to move neurocritical care research forward. We have summarized the topics discussed at the conference and put forward recommendations for the future direction of the NCRN and neurocritical care research in general.

Genetic susceptibility for ischemic infarction and arteriolosclerosis based on neuropathologic evaluations.

BACKGROUND: Recent genetic studies of stroke and related risk factors have identified a growing number of susceptibility loci; however, the relationship of these alleles to ischemic stroke is unknown. The challenge in finding reproducible loci of ischemic stroke susceptibility may be in part related to the etiologic heterogeneity in clinically defined stroke subtypes. In this study, we tested whether known single nucleotide polymorphisms (SNPs) associated with stroke or putative stroke risk factors are associated with neuropathologically defined micro- or macroscopic infarcts and with arteriolosclerosis. METHODS: Measures of neuropathology and genotyping were available from 755 deceased participants from the Religious Orders Study and the Rush Memory and Aging Project. All donated brains were examined by a board-certified neuropathologist using standardized protocol for the presence of microscopic infarct, macroscopic infarct and arteriolosclerosis (lipohyalinosis). In primary analysis, 74 candidate SNPs previously associated (p < 5 × 10(-8)) with ischemic stroke or known risk factors, including atrial fibrillation (AF), hypertension, diabetes, low-density lipoprotein (LDL) level and carotid artery stenosis, were evaluated for association with neuropathologic endpoints. We performed a secondary exploratory analysis to include 93 additional SNPs associated with putative ischemic stroke risk factors including SNPs associated with high-density lipoprotein (HDL), triglyceride serum levels, myocardial infarction (MI), coronary artery disease and cerebral white matter disease. Regression models relating SNPs to cerebrovascular neuropathology were adjusted for age at death, gender and cohort membership. RESULTS: The strongest associations seen for both macroscopic and microscopic infarcts were risk variants associated with diabetes. The diabetes risk variant rs7578326 located near the IRS1 locus was associated with both macroscopic (OR = 0.73, p = 0.011) and microscopic (OR = 0.71, p = 0.009) infarct pathology. Another diabetes susceptibility locus (rs12779790) located between the calcium/calmodulin-dependent protein kinase ID (CAMK1D) and cell division cycle 123 homolog (CDC123) genes is also associated with both macroscopic (OR = 1.40, p = 0.0292) and microscopic infarcts (OR = 1.43, p = 0.0285). The diabetes risk variant rs864745 within JAZF1 was associated with arteriolosclerosis (OR = 0.80, p = 0.014). We observed suggestive associations with the diabetes risk variant rs7961581 (p = 0.038; between TSPAN8 and LGR5) and rs5215 (p = 0.043; KCNJ11), the LDL risk variant rs11206510 (p = 0.045; PCSK9), as well as the AF risk locus ZFHX3. The CDKN2A/B locus (rs2383207, 9p21), identified initially as a susceptibility allele for MI and recently implicated in large vessel stroke, was associated with macroscopic infarct pathology in our autopsy cohort (OR = 1.26, p = 0.031). CONCLUSION: Our results suggest replication of the candidate CDKN2A/B stroke susceptibility locus with directly measured macroscopic stroke neuropathology, and further implicate several diabetes and other risk variants with secondary, pleiotropic associations to stroke-related pathology in our autopsy cohort. When coupled with larger sample sizes, cerebrovascular neuropathologic phenotypes will likely be powerful tools for the genetic dissection of susceptibility for ischemic stroke.

Left endobronchial intubation with a double-lumen tube using direct laryngoscopy or the Trachway® video stylet.

We compared direct laryngoscopy with a Macintosh blade vs indirect bronchoscopy with a Trachway® stylet, for endobronchial intubation with a left-sided double-lumen tube. We allocated participants scheduled for thoracic surgery and who had normal predicted laryngoscopy, 30 to each group. The mean (SD) intubation times with laryngoscope and Trachway were 48 (11) s vs 28 (4) s, respectively, p < 0.001. The rates of hoarseness on the first postoperative day, categorised as none/mild/moderate/severe, were 10/12/7/1 and 22/6/2/0, respectively, p = 0.008, without differences on subsequent days. Left endobronchial intubation with a double-lumen tube is slower using direct laryngoscopy and causes more hoarseness than indirect bronchoscopy with a Trachway stylet.

Comparison of the GlideScope® videolaryngoscope and the Macintosh laryngoscope for double-lumen tube intubation.

Intubation with a double-lumen tube is important for achieving one-lung ventilation and facilitating thoracic surgery. The GlideScope(®) videolaryngoscope (Verathon Inc., Bothell, WA, USA) is designed to assist tracheal intubation for patients with a difficult airway. We wished to compare the GlideScope and direct laryngoscopy for double-lumen tube intubation. Sixty adult patients requiring a double-lumen tube for thoracic surgery and predicted uncomplicated laryngoscopy were randomly assigned to a direct Macintosh laryngoscopy group (n = 30) or a GlideScope group (n = 30). The mean (SD) duration of intubation was longer in the Macintosh group (62.5 (29.7) s) than in the GlideScope group (45.6 (10.7) s; p = 0.007). There was no difference in the success of the first attempt at intubation (26/30 (87%) and 30/30 (100%) for Macintosh and GlideScope groups, respectively; p = 0.112). The incidence of sore throat and hoarseness was higher in the Macintosh group (18 (60%) and 14 (47%), respectively) than in the GlideScope group (6 (20%) and 4 (13%), respectively; p = 0.003 and 0.004). We conclude that double-lumen tube intubation in patients with predicted normal laryngoscopy is easier using the GlideScope videolaryngoscope than the Macintosh laryngoscope.

Effects of supplemental 25-hydroxycholecalciferol on growth performance, small intestinal morphology, and immune response of broiler chickens.

Three experiments were conducted to evaluate the effects of 25-hydroxycholecalciferol (25-OH-D(3)) on the growth performance, small intestinal morphology, and immune response of broiler chickens. In experiment 1, 25-OH-D(3) neither increased nor decreased weight gain and feed efficiency compared with the controls during the 39-d feeding period. Birds fed 25-OH-D(3) exhibited numerically higher phagocytosis (45%) than the controls (35%). In experiment 2, chicks were fed diets similar to those used in experiment 1 and were killed at 7, 14, 21, 28, and 35 d of age to determine the relative weight and histology of the small intestine. The relative weight of the small intestine from birds fed 25-OH-D(3) was numerically lower (P < 0.1) at 7 d of age. It was found that 25-OH-D(3) consistently resulted in longer (P < 0.05) villus length of the duodenum in 21- and 28-d-old birds and of the jejunum in 14- and 28-d-old birds. Shorter (P < 0.05) crypt depth was observed in the duodenum at 14 d of age and in the jejunum at 21 and 28 d of age. A higher (P < 0.05) ratio of villus length to crypt depth was also observed in the duodenum and jejunum at 14, 21, and 28 d of age of birds fed 25-OH-D(3). The thickness of muscle layer increased in the duodenum at 14, 28, and 35 d of age in birds fed 25-OH-D(3). In experiment 3, birds were orally challenged with either Luria-Bertani broth or Salmonella Typhimurium E29 at 7 and 14 d of age. Uninfected birds fed 25-OH-D(3) had lower total serum IgA at 14 d of age and lower total serum IgG at 21 d of age. However, infected birds fed 25-OH-D(3) produced higher (P < 0.1) total serum IgG at 21 d of age. The results of this study suggest that supplemental 25-OH-D(3) improves small intestinal morphology and protective humoral immunity to infection.

Apoptotic effect of Helicobacter pylori on oesophageal squamous-cell carcinoma cells in vitro.

BACKGROUND: The relationship between Helicobacter pylori (Hp) infection and oesophageal squamous-cell carcinoma (ESCC) risk is still inconclusive. Our previous study found an inverse association between the two, but its mechanism is still unknown. Thus, we conducted in vitro studies to clarify the issue. MATERIALS AND METHODS: One ESCC (CE 81T/VGH) cell line was co-cultured with Hp, using one gastric adenocarcinoma (AGS) cell line as the control. Hp-induced cell apoptosis was determined by flow cytometry, terminal transferase-mediated dUTP nick end labelling (TUNEL) assay and staining; caspase-3 protein expressions in cell lysates were detected by Western immunoblot. RESULTS: Increased apoptosis was found in CE 81T/VGH, but not in AGS cells, by flow cytometry and TUNEL assay after being co-cultured with Hp at the multiplicity of infection of 1/100 (but not at 1/400) for 36 h. The amount of activated caspase-3 (17/19 kDa) also increased in CE 81T/VGH, but not in AGS cells, after co-culturing with Hp at MOI of 1/100 for 36 h. The results were confirmed by triplicate experiments in which the different apoptotic assays remained consistent. CONCLUSIONS: Our study provides indirect evidence of the inverse association between Hp infection and ESCC risk, which is possibly due to Hp-induced apoptosis in ESCC cells. A further in vivo study is necessary to confirm our findings.

The importance of classification in sympathetic surgery and a proposed mechanism for compensatory hyperhidrosis: experience with 464 cases.

BACKGROUND: Compensatory hyperhidrosis is the most troublesome side effect and the leading cause of regret with sympathetic surgery. A new classification is proposed to make the procedure more selective and to minimize the side effects and regret rate. Also, a proposed mechanism for compensatory hyperhidrosis is discussed. METHODS: Between January 2002 and July 2003, 464 patients with various sympathetic disorders underwent thoracoscopic sympathectomy/sympathicotomy (ETS) or sympathetic block by clipping (ESB) at various levels according to the authors' classification. The surgery was performed on an outpatient basis. The rates of success, compensatory hyperhidrosis, and regret were recorded. RESULTS: All the patients were followed up for 17 to 35 months. All excessive sweating was effectively stopped to varying degrees. The 25 patients with palmar hyperhidrosis who insisted on receiving ETS of T4 experienced no compensatory hyperhidrosis. Of the 54 patients with facial blushing who received ESB of T2, 23 experienced compensatory hyperhidrosis. Nine patients expressed regret and requested removal of the clips. Of the 33 patients with craniofacial hyperhidrosis who received ESB of T3, 9 experienced compensatory hyperhidrosis. Three expressed regret, and reverse procedures were performed. For 324 patients with palmar hyperhidrosis receiving ESB of T4, no compensatory hyperhidrosis was found. Only two expressed regret because of discomfort. No compensatory hyperhidrosis or regret was noted with 28 patients who received ESB of T5 for axillary sweating. There was no recurrence in the entire series. CONCLUSIONS: Different procedures are recommended for different sympathetic disorders according to the classification. The higher the level of sympathetic ganglion blockade, the higher is the regret rate. Therefore, for T2 and T3 ganglion, endoscopic thoracic sympathetic block by the clipping method is strongly recommended because of its reversibility.

A modified Arg-Asp-Val (RDV) peptide derived during the synthesis of Arg-Glu-Asp-Val (REDV), a tetrapeptide derived from an alternatively spliced site in fibronectin, inhibits the binding of fibrinogen, fibronectin, von Willebrand factor and vitronectin to activated platelets.

Characterization of a side-product obtained during the synthesis of Arg-Glu-Asp-Val (REDV) with inhibitory activity in thrombin-activated platelet aggregation was carried out. The semipreparative column fractionation of REDV peptide was rechromatographed on an analytical HPLC column and revealed two peaks which were re-tested for inhibitory activity. Using amino acid analysis with sequencing and fast atom bombardment mass spectrometry (FABMS), the first peak was determined to be REDV with molecular mass of 517 Da, and the second peak was determined to be a modified RDV with a mass of 608 Da. The modified RDV peptide inhibited thrombin-induced platelet aggregation with an IC50 of 200 microM, and complete inhibition occurred at 600 microM. However, the REDV peptide did not inhibit platelet aggregation up to 1 mM concentration. The modified RDV peptide eluted platelet glycoprotein IIb-IIIa complex that had been bound to GRGDSP-agarose. These studies show that the modified RDV peptide interacts with the platelet glycoprotein IIb-IIIa complex. Based on the collision-induced dissociation (CID) mass spectral data analysis, the modified RDV peptide has been characterized to contain an N-terminus blocking group on the Arg residue. The origin of this blocking group is presumed to have originated from decomposition products of the phenylacetamidomethyl (PAM) resin used in the solid-phase synthesis of the target peptide Arg-Glu-Asp-Val.

Conformation of the propeptide domain of factor IX.

The propeptide domain in the precursor forms of blood clotting proteins contains the recognition sequences for gamma-carboxylase. In hemophilia B, several point mutations in this propeptide domain are responsible for the inherited disease. A peptide containing the propeptide sequence of factor IX was synthesized by solid phase methods. Two dimensional 1H-NMR and CD studies indicate that this peptide motif adopts an alpha-helical structure in a 40% trifluoroethanol-containing aqueous solution. The results suggest that the amphipathic alpha-helix within the propeptide domain of factor IX could create a recognition surface for gamma-carboxylase. The influences of mutations and their relationship with the alpha-helical structure are discussed.

Cross-strand purine-pyrimidine stack and sheared purine.pyrimidine pairing in the human HIV-1 reverse transcriptase inhibitors.

Cross-strand homo purine-purine (G-G or A-A) stacks and sheared purine.purine pairing have been found to be important motifs in nucleic acid duplex structures. We now report novel cross-strand purine-pyrimidine (A-C) and hetero purine-purine (G-A) stacks that are established from a sheared purine.pyrimidine (A.C) pair adjacent to a sheared G.A pair in the 5'-AA/GC-3' sequence. This "internal loop" sequence is conserved in two families of single-stranded DNA inhibitors of the reverse transcriptase of type 1 human immunodeficiency virus. The distorted backbone of these inhibitors, resulting from the unique helical twists and kinks in the 5'-AA/GC-3' sequence, may be responsible for the increased affinities of these single-stranded DNA inhibitors as compared with other regular B-form duplex substrates. Two simple rules have been generalized to account for all reported cross-strand stacks.

Zipper-like Watson-Crick base-pairs.

A series of DNA heptadecamers containing the DNA analogues of RNA E-like 5'-d(GXA)/(AYG)-5' motifs (X/Y is complementary T/A, A/T, C/G, or G/C pair) were studied using nuclear magnetic resonance (NMR) methodology and distance geometry (DG)/molecular dynamics (MD) approaches. Such oligomers reveal excellent resolution in NMR spectra and exhibit many unusual nuclear Overhauser effects (NOEs) that allow for good characterization of an unusual zipper-like conformation with zipper-like Watson-Crick base-pairs; the potential canonical X.Y H-bonding is not present, and the central X/Y pairs are transformed instead into inter-strand stacks that are bracketed by sheared G.A base-pairs. Such phenomenal structural change is brought about mainly through two backbone torsional angle adjustments, i.e. delta from C2'-endo to C3'-endo for the sugar puckers of unpaired residues and gamma from gauche(+) to trans for the following 3'-adenosine residues. Such motifs are analogous to the previously studied (GGA)(2) motif presumably present in the human centromeric (TGGAA)(n) tandem repeat sequence. The novel zipper-like motifs are only 4-7 deg. C less stable than the (GGA)(2) motif, suggesting that inter-strand base stacking plays an important role in stabilizing unusual nucleic acid structures. The discovery that canonical Watson-Crick G.C or A.T hydrogen-bonded pairs can be transformed into stacking pairs greatly increases the repertoire for unusual nucleic acid structural motifs.

Solution structure of a DNA double helix incorporating four consecutive non-Watson-Crick base-pairs.

A series of DNA 21-mers containing a variety of the 4 x 4 internal loop sequence 5'-CAAG-3'/3'-ACGT-5' were studied using nuclear magnetic resonance (NMR) methodology and distance geometry (DG)/molecular dynamics (MD) approaches. Such oligomers exhibit excellent resolution in the NMR spectra and reveal many unusual NOEs (nuclear Overhauser effect) that allow for the detailed characterization of a DNA hairpin incorporating a track of four different non-Watson-Crick base-pairs in the stem. These include a wobble C.A base-pair, a sheared A.C base-pair, a sheared A.G base-pair, and a wobble G.T base-pair. Significantly different twisting angles were observed between the base-pairs in internal loop that results with excellent intra-strand and inter-strand base stacking within the four consecutive mismatches and the surrounding canonical base-pairs. This explains why it melts at 52 degrees C even though five out of ten base-pairs in the stem adopt non-Watson-Crick pairs. However, the 4 x 4 internal loop still fits into a B-DNA double helix very well without significant change in the backbone torsion angles; only zeta torsion angles between the tandem sheared base-pairs are changed to a great extent from the gauche(-) domain to the trans domain to accommodate the cross-strand base stacking in the internal loop. The observation that several consecutive non-canonical base-pairs can stably co-exist with Watson-Crick base-pairs greatly increases the limited repertoire of irregular DNA folds and reveals the possibility for unusual structural formation in the functionally important genomic regions that have potential to become single-stranded.

Quadruple intercalated G-6 stack: a possible motif in the fold-back structure of the Drosophila centromeric dodeca-satellite?

The purine-rich strand d(GTACGGGACCGA)(n) of the Drosophila centromeric dodeca-satellite sequence is highly conserved and was found to form stable fold-back structures in which the homopurine 5'-GGGA-3' sequence was determined to play a crucial role. Here, we report the stable formation of the d(GGGA)(2) motif in the stem of a DNA hairpin closed by a single-residue d(ACC) loop. Similar to the zipper-like d(GGA)(2) motif observed in the human centromeric (TGGAA)(n) sequence, the central four guanosine bases in the d(GGGA)(2) motif do not pair, but interdigitate to form an elongated zipper-like quadruple-intercalated G-6 stack bracketed by sheared G.A base-pairs. Comparison between the current d(GGGA)(2) structure and the published crystal d(GAAA)(2) structure implies that the alignment of the unpaired purine bases plays an important role in determining the minor groove width of the purine-rich d(GPuPuA)(2) motif. Similarity between the zipper-like motifs possibly present in the Drosophila centromeric dodeca-satellite sequence and in the human centromeric (TGGAA)(n) sequence led us to propose that these special zipper-like motifs may constitute common cores in organizing eukaryotic centromeres.

On the relative ability of centromeric GNA triplets to form hairpins versus self-paired duplexes.

While tandem repeats of the human centromere DNA pentamer sequence TGRAA form stable "self-complementary" [TGRAATGRAA]2 duplexes (R = G or A) containing the GA-bracketed unpaired purine stack motif, their phase-shifted variants NAATGNAATG (N = A, G, C, T) were found to exist in solution as an equilibrium mixture of a duplex containing the GA-bracketed unpaired stack motif and a hairpin containing a single-residue loop closed by a sheared G x A pair. The stability of the hairpin form relative to duplex form of GNA triplets was found to be GCA>GAA/GTA>>GGA, with the CAATGCAATG sequence mostly in the hairpin form and the GAATGGAATG sequence mostly in the [GAATGGAATG]2 duplex form. The chemical shifts of the H1' and H4' protons of the central N residue in GNA triplets were found to differ markedly in the duplex and hairpin forms and are diagnostic indicators of which conformation the oligonucleotide adopts. Comparison between the structures of the G x A-closed C loop motif and the G x A-bracketed unpaired G-stack [GGA]2 motif reveals remarkably similar stacking by the loop C residue and the intercalated G residue on the adjacent sheared G x A pair. The anomalous upfield chemical shifts of the H1' and H4' protons in [GGA]2 motifs and the H4' proton in GCA loops, and the different sugar conformations in these two motifs, can be explained by interstrand versus intrastrand stacking of the central (G or C) deoxyribose with the adenine base. Based on these studies, a DNA sequence GTGGAATGGAATGGAAC was designed and shown to form a duplex containing three [GGA]2 motifs, while its 9G-->9C analog GTGGAATGCAATGGAAC was found to adopt a stable hairpin containing a (GGA)2 motif in the stem and a G x A-closed single C-loop.

The structure of a novel DNA duplex formed by human centromere d(TGGAA) repeats with possible implications for chromosome attachment during mitosis.

The solution structure of the DNA duplex [GTGGAATGGAAC]2 containing a tandem repeat of the human centromere (TGGAA)n unit has been determined by two-dimensional nuclear magnetic resonance (2D-NMR), distance geometry (DG) and molecular dynamics/energy minimization (MD/EM) methods. This remarkably stable "self-complementary" antiparallel duplex contains a tandem repeated motif in which unpaired guanine residues from opposite strands intercalate and costack between sheared G.A pairs. Twelve independent refined structures were determined from the NMR data and found to converge to a single family of closely related structures with pair-wise r.m.s.d. values of 0.55 +/- 0.25 Angstrum. All sugar residues are in the normal C2'-endo conformation except for the unpaired guanosines, which are in the unusual C3'-endo conformation. The guanosine residues of the bracketing G.A pairs have high-antiglycosidic torsion angles and zeta backbone torsion angles close to the trans domain. The structure exhibits many unusual interstrand interactions, including base-sugar stacking, base-phosphate hydrogen bonding and cross-strand base stacking. The [GGA]2 unit contains a stack of four contiguous guanine residues, all of which have their hydrogen-bonding surface (N2H-N1H-O6-N7) exposed to solvent and available for interaction with other bases or ligands. This unexpected property may explain the unique morphology and function of the human centromere in mitosis.

Sheared purine x purine pairing in biology.

The Watson-Crick G x C and A x T base-paired DNA duplex has been the single most important milestone in modem molecular biology. However, it is possible that other types of stable DNA structures besides the double helix might exist, since only about 5% of the human chromosome is transcribed and expressed. Stable, four-stranded G-tetraplex DNA structures occur in the extensive tandem repeated sequences at the telomeres of chromosome. Formation of stable triplexes of the Py x Pu x Py or Pu x Pu x Py type have been implicated at the control regions of certain human genes. We review and discuss the various types of DNA duplex structures containing stable sheared base-pairs and compare their structural characteristics with that of B-DNA. Pu x Pu structural motifs are found in the highly conserved sequences at the replication origins of several single-stranded DNA viruses and in the peri-centromeric regions of human chromosomes, and may be involved in important biological functions, such as viral DNA replication and centromere formation.

The unusual structure of the human centromere (GGA)2 motif. Unpaired guanosine residues stacked between sheared G.A pairs.

The centromere of human chromosomes contains multiple repeats of the DNA sequence d(TGGAA)n. This sequence has the interesting property of pairing with itself to form stable duplexes. We have determined the solution structure of the unusual DNA duplex 5'-TGGAATGGAA:TGGAATGGAA-3' at atomic resolution. The duplex contains unpaired staggered guanosine residues, which co-stack by intercalation between sheared G.A and A.G base-pairs to form an interesting new structural motif, the GA-bracketed G-stack. The TGGAA repeat unit contains six "steps", four of which are not Watson-Crick base-pairs.

Centromeric pyrimidine strands fold into an intercalated motif by forming a double hairpin with a novel T:G:G:T tetrad: solution structure of the d(TCCCGTTTCCA) dimer.

The solution structures of the oligodeoxynucleotides d(CCCGTTTCC) and d(TCCCGTTTCCA) have been determined by two-dimensional NMR spectroscopy. These oligomers are part of a DNA box in human centromeric alpha satellite targeted by the centromere protein B (CENP-B). Both CENP-B and its recognition box in alphoid DNA are conserved in mammals, suggesting an important biological role. At acidic pH, d(CCCGTTTCC), d(TCCCGTTTCCA) and the full d(TCCCGTTTCCAACGAAG) CENP-B box strand all fold and dimerize in solution forming a stable bimolecular structure containing two GTTT hairpin loops that interact through a novel T : G : G : T tetrad. The stem region of the dimer is a four-stranded intercalated motif in which the hairpin monomers are parallel and held together by C : C+ hydrogen-bonding and intercalation. The loops are at the same end of the dimer and lie across the narrow grooves of the tetraplex. They are remarkably structured and stabilized by base-base cross-stacking, sugar-base stacking, and parallel G:G and antiparallel G:T pairing. In the d(TCCCGTTTCCA)2 structure, the intercalated motif is continued at the other end of the dimer with unpaired but stacked adenine and thymine bases. The possible biological implications of these structures are discussed.

DNA sequence GCGAATGAGC containing the human centromere core sequence GAAT forms a self-complementary duplex with sheared G.A pairs in solution.

The DNA sequence dGCGAATGAGC has a well-resolved, two-dimensional nuclear Overhauser (NOESY) spectrum that is suitable for high quality solution structure determination by NMR methods; in solution this sequence forms a stable self-complementary duplex containing sheared G.A base-pairs. A total of 220 distance constraints derived from time-dependent NOE measurements were collected and refined by repeated back-calculation of the NOESY spectra. Distance information from imino proton studies and from exclusive two-dimensional correlated spectroscopy (E. COSY) and/or linewidth analysis was included in the structure calculation using the program DSPACE 4.2, followed by restrained energy minimization with the program DISCOVER using the AMBER force field. The energies of the distance geometry (DG) structures decreased rapidly in the first few cycles and approached -510 +/- 3 kcal after 1000 cycles of conjugate gradient minimization (about 540 kcal lower than in the initial DG structures). All 15 final DG structures converged to a single family of closely related structures with pair-wise r.m.s.d. values of 0.96 +/- 0.34 A, which was further reduced by energy minimization to 0.70 +/- 0.35 A. Rather unusual structural features of the duplex are revealed in the final structures. The results indicate that, in addition to normal sequences with standard base-pairing, unusual nucleic acid structures can also be determined in solution with quite high precision by NMR/distance geometry methods.