Structure and stability of human telomeric sequence

Telomeric DNA of a variety of vertebrates including humans contains the tandem repeat d(TTAGGG)n. We have investigated the structural properties of the human telomeric repeat oligonucleotide models d(T2AG3)4, d(G3T2A)3G3, and d(G3T2AG3) using CD, gel electrophoresis, and chemical probing techniques. The sequences d(G3T2A)3G3 and d(T2AG3)4 assume an antiparallel G quartet structure by intramolecular folding, while the sequence d(G3T2AG3) also adopts an antiparallel G quartet structure but by dimerization of hairpins. In all the above cases, adenines are in the loop. The TTA loops are oriented at the same end of the G tetrad stem in the case of hairpin dimer. Further, the oligonucleotide d(G3T2AG3) forms a higher order structure by the association of two hairpin dimers via stacking of G tetrad planes. Here we show that N-7 of adenine in the hairpin dimer is Hoogsteen hydrogen-bonded. The partial reactivity of loop adenines with DEPC in d(T2AG3)4 suggests that the intramolecular G quartet structure is highly polymorphic and structures with different loop orientations and topologies are formed in solution. Intra- and interloop hydrogen bonding schemes for the TTA loops are proposed to account for the observed diethyl pyrocarbonate reactivities of adenines. Sodium-induced G quartet structures differ from their potassium-induced counterparts not only in stability but also in loop conformation and interactions. Thus, the overall structure and stability of telomeric sequences are modulated by the cation present, loop sequence, and the number of G tracts, which might be important for the telomere function

Recent direct measurement of the Top quark mass and quasi-infrared fixed point

We note that the recent direct measurement of the top quark mass at $173.3 \pm 5.6 (stat) \pm 6.2 (syst)$ by D0 collaboration severely constrains the theoretically attractive infra-red fixed point scenario of the top quark Yukawa coupling in supersymmetric GUTs. For one-step unified models the above mentioned measurement bounds the arbitrary but experimentally determinable parameter $\tan \beta$ to the range $1.3 \le \tan \beta \le 2.1$. Further crunch on the top quark mass may determine $\tan \beta$ even more accurately within the fixed point scenario. On the other hand an experimental value of $\tan \beta > 2.1$ will rule out the fixed point scenario bounding $h^2_t(M_X)/4 \pi$ to 0.022 from above.Comment: 7 pages, Latex with epsf style, 1 figure, captions.st

Structural organization of the meiotic prophase chromatin in the rat testis

Pachytene nuclei were isolated from rat testes by the unit gravity sedimentation technique and contained histone variants H1a, H1t, TH2A, TH2B, and X2 in addition to the somatic histones H1bde, H1c, H2A, H2B, H3, and H4. The basic organization of the pachytene chromatin namely the nucleosome repeat length and the accessibility to micrococcal nuclease, was similar to that of rat liver interphase chromatin. However, when digested by DNase I, the susceptibility of pachytene chromatin was 25% more than liver chromatin under identical conditions. Nucleosome core particles were isolated from both liver and pachytene nuclei and were characterized for their DNA length and integrity of the nucleoprotein on low ionic strength nucleoprotein gels. While liver core particles contained all the somatic histones H2A, H2B, H3, and H4, in the pachytene core particles, histone variants TH2A, X2, and TH2B had replaced nearly 60% of the respective somatic histones. A comparison of the circular dichroism spectra obtained for pachytene and liver core particles indicated that the pachytene core particles were less compact than the liver core particles. Studies on the thermal denaturation properties of the two types of core particles revealed that the fraction of the pachytene core DNA melting at the premelting temperature region of 55-60 degrees C was significantly higher than that of the liver core DNA

Synthesis of a novel polynucleotide: potential R-L model

Synthesis of a novel polynucleotide with potential alternating B and Z segments is described. This is the first report of a polynucleotide where the double helix undergoes change in handedness after every half a turn

Synthesis of a novel polynucleotide: potential R-L model

Synthesis of a novel polynucleotide alternating B and Z segments is described. This is the first report of a polynucleotide where the double helix undergoes change in handedness after every half a turn

Asymmetric neutrino Yukawa matrices and neutrino mixing

We study leptonic CKM mixing matrices when the neutrino Yukawa matrices are antisymmetric which gives rise to mass patterns suitable to explain solar, atmospheric and LSND neutrino oscillation experiments. Taking diagonal leptonic matrices which can give rise to hierarchical lepton masses, we compute the leptonic CKM matrix.Comment: version to appear in Phys. Rev.

Left handed DNA in synthetic and topologically constrained form V DNA and its implications in protein recognition

We have investigated structural transitions in Poly(dG-dC) and Poly(dG-Me5dC) in order to understand the exact role of cations in stabilizing left-handed helical structures in specific sequences and the biological role, if any, of these structures. From a novel temperature dependent Z⇌B transition it has been shown that a minor fluctuation in Na+ concentration at ambient temperature can bring about B to Z transition. For the first time, we have observed a novel Z⇌B⇌Zuble transition in poly(dG-Me5dC) as the Na+ concentration is gradually increased. This suggests that a minor fluctuation in Na+ concentration in conjunction with methylation may transform small stretches of CG sequences from one conformational state to another. These stretches could probably serve as sites for regulation. Supercoiled form V DNA reconstituted from pBR322 and pβG plasmids have been studied as model systems, in order to understand the nature and role of left-handed helical conformation in natural sequences. A large portion of DNA in form V, obtained by reannealing the two complementary singlestranded circles is forced to adopt left-handed double helical structure due to topological constraints (Lk=0). Binding studies with Z-DNA specific antibody and spectroscopic studies confirm the presence of left-handed Z-structure in the pβG and pβR322 form V DNA. Cobalt hexamine chloride, which induces Z-form in Poly(dG-dC) stabilizes the Z-conformation in form V DNA even in the non-alternating purine-pyrimidine sequences. A reverse effect is observed with ethidium bromide. Interestingly, both topoisomerase I and II (from wheat germ) act effectively on form V DNA to give rise to a species having an electrophoretic mobility on agarose gel similar to that of open circular (form II) DNA. Whether this molecule is formed as a result of the left-handed helical segments of form V DNA undergoing a transition to the right-handed B-form during the topoisomerase action remains to be solved

Constrained analytical interrelations in neutrino mixing

Hermitian squared mass matrices of charged leptons and light neutrinos in the flavor basis are studied under general additive lowest order perturbations away from the tribimaximal (TBM) limit in which a weak basis with mass diagonal charged leptons is chosen. Simple analytical expressions are found for the three measurable TBM-deviants in terms of perturbation parameters appearing in the neutrino and charged lepton eigenstates in the flavor basis. Taking unnatural cancellations to be absent and charged lepton perturbation parameters to be small, interrelations are derived among masses, mixing angles and the amount of CP-violation.Comment: To be published in the Springer Proceedings in the Physics Series under the heading of the XXI DAE-BRNS Symposium (Guwahati, India

Effect of dietary supplementation of Bacillus subtilis on haematological and immunological parameters of Catla catla (Hamilton)

Effect of dietary supplementation of a Gram-positive, aerobic, probiotic bacterium Bacillus subtilis on the immunohaematological indices during pre- and post-challenge in Indian major carp, catla (Catla catla), was studied. The B. subtilis was administered orally at four different doses 1.0 × 106 (T1), 1.0 × 107 (T2), 1.0 × 108 (T3), and 1.0 × 109 (T4) cfu g−1 feed to C. catla for 90 days. The positive control (Cp) and negative control (Cn) were fed with feed without B. subtilis for the same period. On the 60th day, blood and serum were sampled to determine various haematological and serum parameters. Fish were challenged intraperitoneally with Aeromonas hydrophila after 60 days in all the treatment groups and Cp, while the Cn was challenged with phosphate-buffered saline (PBS, pH 7.2) only. Dietary supplementation of B. subtilis leads to the rise of various immunological and haematological parameters in catla during the pre- and post-challenge. During pre-challenge, the highest TEC (1.30 ± 0.02 × 106 cells mm−3), haemoglobin (7.43 ± 0.25 g %), total serum protein (3.89 ± 0.08 g dL−1), and serum lysozyme activity (8.39 ± 0.01 µg ml−1) were recorded in fishes fed feed containing B. subtilis at 1 × 109 cfu/g feed (T4). The highest survival percentage (86.33 %) was also observed in T4 group. The significantly increased survival percentage (P < 0.05) of B. subtilis-treated groups in comparison with control group (Cp) suggests that dietary supplementation of this probiotic bacterium can protect catla from A. hydrophila infection by enhancing innate immunity