Nuclear magnetic resonance investigation of lysine–oligopeptides and a complex with d(pA)3pGpC(pT)3

We report proton magnetic resonance studies of a series of lysine oligopeptides in H₂O solution. At pH 5 the protonated ε-amino groups are seen as broad resonances; the peptide NH proton resonances are split by spin–spin coupling with the C^α-H proton, and appear at positions which depend on position in the chain and on chain length. Assignments were made by the europium shift method, and we observed the expected effect of catalysis by the terminal —NH₃⁺ of exchange of the adjacent peptide NH. Coupling constants and the temperature coefficient of chemical shift values were consistent with a non-hydrogen-bonded structure for the oligolysines. The rate and mechanism of NH hydrogen exchange were investigated by line-broadening measurements of the peptide protons as a function of pH. Exchange was found to be OH^? catalyzed, with large differences in the rate depending on position in the chain. Preliminary studies of the complex between double-helical d(pA)₃pGpC(pT)₃ and tetra(L -lysine) were performed using ¹H- and ³¹P-nmr techniques. Pmr spectra of the complex at pH values ranging from 3.98 to 8.15 showed very complicated patterns. Downfield shifts and reduction in exchange rates were observed for several tetra(L -lysine) protons. ³¹P-nmr spectra of the complex reveal an upfield shift of 1 ppm for 3′-5′ phosphate diester resonances on complexation. ³¹P T₁ relaxation times change little on complex formation at low temperature but are altered at higher temperature.     

Cellular and gene expression responses involved in the rapid growth inhibition of human cancer cells by RNA interference-mediated depletion of telomerase RNA

Inhibition of the up-regulated telomerase activity in cancer cells has previously been shown to slow cell growth but only after prior telomere shortening. Previously, we have reported that, unexpectedly, a hairpin short interfering RNA specifically targeting human telomerase RNA rapidly inhibits the growth of human cancer cells independently of p53 or telomere length and without bulk telomere shortening (Li, S., Rosenberg, J. E., Donjacour, A. A., Botchkina, I. L., Hom, Y. K., Cunha, G. R., and Blackburn, E. H. (2004) Cancer Res. 64, 4833-4840). Here we have demonstrated that such telomerase RNA knockdown in cancer cells does not cause telomere uncapping but rather induces changes in the global gene expression profile indicative of a novel response pathway, which includes suppression of specific genes implicated in angiogenesis and metastasis, and is distinct from the expression profile changes induced by telomere-uncapping mutant template telomerase RNAs. These cellular responses to depleting telomerase in human cancer cells together suggest that cancer cells are "telomerase-addicted" and uncover functions of telomerase in tumor growth and progression in addition to telomere maintenance.     

Statistical-mechanical theory of DNA looping

The lack of a rigorous analytical theory for DNA looping has caused many DNA-loop-mediated phenomena to be interpreted using theories describing the related process of DNA cyclization. However, distinctions in the mechanics of DNA looping versus cyclization can have profound quantitative effects on the thermodynamics of loop closure. We have extended a statistical mechanical theory recently developed for DNA cyclization to model DNA looping, taking into account protein flexibility. Notwithstanding the underlying theoretical similarity, we find that the topological constraint of loop closure leads to the coexistence of multiple classes of loops mediated by the same protein structure. These loop topologies are characterized by dramatic differences in twist and writhe; because of the strong coupling of twist and writhe within a loop, DNA looping can exhibit a complex overall helical dependence in terms of amplitude, phase, and deviations from uniform helical periodicity. Moreover, the DNA-length dependence of optimal looping efficiency depends on protein elasticity, protein geometry, and the presence of intrinsic DNA bends. We derive a rigorous theory of loop formation that connects global mechanical and geometric properties of both DNA and protein and demonstrates the importance of protein flexibility in loop-mediated protein-DNA interactions.     

Measurement of diffusion constants for nucleic acids by NMR

Pulsed field-gradient NMR experiments can be used to measure thediffusion constants of nucleic acids. The diffusion constants measured inthis way for double-helical DNAs of defined length agree well both withtheory and with measurements done using other techniques. When applied toRNAs, this experi- ment easily distinguishes duplex RNAs from RNA hairpinsand thus it can solve one of the perennial problems faced by RNAspectroscopists, i.e. assessing whether their samples are monomeric or not.     

Localization of the structural change induced in tRNA fMET (Escherichia coli) by acidic pH.

We have compared the molecular mechanism of thermal unfolding for native tRNA fMet (Escherichia coli) and the denatured species produced by annealing at pH 4.3. Relaxation kinetic measurements reveal that the transitions assigned to melting of TphiC, anticodon, and acceptor stem helices at neutral pH remain essentially unaltered at pH 4.3, but the transition corresponding to coupled melting of tertiary structure and dihydrouridine helix is greatly affected. The Tm of this region is more than 20 degrees higher at pH 4.3 and it has a larger enthalpy formation than in the native state. The transition dynamics are also considerably changed. In contrast to the native structure, tRNA fMet1 and tRNA fMet3 have similar tertiary structure stabilities at pH 4.3. We conclude that the structural difference between native and acid-denatured forms is localized in the tertiary structure-dihydrouridine helix cooperative interaction region of the molecule.     

Variation in the ribosomal internal transcribed spacers and 5.8S rDNA among five species of Acropora (Cnidaria; Scleractinia): patterns of variation consistent with reticulate evolution

The ITS sequences of Acropora spp. are the shortest so far identified in any metazoan and are among the shortest seen in eukaryotes; ITS1 was 70-80 bases, and ITS2 was 100-112 bases. The ITS sequences were also highly variable, but base composition and secondary structure prediction indicate that divergent sequence variants are unlikely to be pseudogenes. The pattern of variation was unusual in several other respects: (1) two distinct ITS2 types were detected in both A. hyacinthus and A. cytherea, species known to hybridize in vitro with high success rates, and a putative intermediate ITS2 form was also detected in A. cytherea; (2) A. valida was found to contain highly (29%) diverged ITS1 variants; and (3) A. longicyathus contained two distinct 5.8S rDNA types. These data are consistent with a reticulate evolutionary history for the genus Acropora.