The formation of DNA triple helices offers the possibility of selectively targeting specific genes to control their expression in vivo. This anti-gene strategy provides powerful tools for the development of therapeutics (anti-cancer drugs, drugs for viral infections) at the transcriptional level. DNA triplexes are formed when an oligonucleotide binds to the major groove of double helical DNA; the third strand can bind in either a parallel motif, or an anti-parallel motif. The requirement of low pH for the protonation of cytosine in the parallel binding motif makes the formation of triple helices difficult under physiological conditions. Described in this thesis is a novel method for the synthesis of the deoxycytidine analogue, 2-amino-3-methyl-5-(2’-deoxy-β-D-ribofuranosyl)pyridine (MeP). The phosphoramidite monomer of MeP was synthesised and incorporated as a “protonated” cytidine analogue into triplex forming oligonucleotides (TFOs). It was compared with other cytosine analogues, 5-methyl-(2’-deoxy-β-D-ribofuranosyl)cytosine (MeC), 2’-Omethyl MeP (MePOMe), and 2’-O-aminoethyl MeC (MeCAE). Triplex stability studies indicate that over the pH range 6.2-8.0, the general trend observed in terms of melting temperature (Tm) was as follows: MeP > MeC > MePOMe > MeCAE. DNase I footprinting studies indicate that at pH 7.5, MeP, when incorporated into the TFO, enhances the stability of the triplex by three-fold relative to MeC. In addition, UV melting, DNase I footprinting, and gel electrophoresis studies were carried out on a triplex formed by the binding of a TFO containing MeP and a 5’-Psoralen to a target duplex. This revealed the benefits of the combined modifications on the stability of the resultant triplex. “Soaking” experiments (in vivo) were also performed with this TFO on the organism C. elegans (the worms were soaked in solutions of the TFO for TFO delivery), to observe whether the TFO would induce loss-of-function phenotypes. Tm measurements indicated that in the pH range 6.6-8.0, photo-crosslinking of the TFO to the duplex created a shift in the triplex Tm of ~ + 26 °C when compared to the un-crosslinked triplexEThOS - Electronic Theses Online ServiceGBUnited Kingdo

Darakchieva, V.

Heuken, M.

Monemar, B.

Paskov, P.P.

Paskova, T.

ESE - Salento University Publishing

In−plane strain anisotropy and lattice parameters of GaN films grown on a−planesapphire by metalorganic vapor phase epitaxyV. Darakchieva 1) ,  P. P. Paskov 1) ,  T. Paskova 1) ,  M. Heuken 2) ,  B. Monemar 1)1) IFM, Linkoping University, S−58183 Linkoping, Sweden ,  2) Aixtron AG, D−52072 Aachen, GermanyDue to the lack of native substrate the III−V nitrides are typically grown on foreign substrates such as sapphire,SiC and Si. As a result of the different thermal expansion coefficients and lattice parameters of the substrate andthe film, the film is strained. The effect of strain on the fundamental properties of III−V nitrides, in particularGaN, has been extensively studied in the case of growth on c−plane sapphire [1], while little is known in the caseof growth on a−plane sapphire. The in−plane strain of III−V nitride layers grown on a−plane sapphire is expectedto be anisotropic due to the different thermal expansion coefficients of sapphire in the directions parallel andperpendicular to its c−axis [2], as well as to the nonequal lattice mismatches along the two directions.Manifestations of anisotropic strain have been reported so far in the emission and reflectance spectra of GaN layers[3, 4].In this work we report on the effect of the anisotropic strain on the lattice parameters of GaN layers grown ona−plane sapphire by metalorganic vapor phase epitaxy (MOVPE). High resolution x−ray diffraction (HRXRD) isused to determine the lattice parameters and the epitaxial relationships between the films and the substrates. Thein−plane lattice parameter was determined from sets of equivalent interplanar distances in six different directions.It is found that the obtained six values of the in−plane lattice parameter can be discriminated into two groups. It issuggested that this result is a consequence of the presence of anisotropic in−plane strain in the films. The in−planestrain anisotropy in the films is determined in the crystal coordinate system, and it is compared with a theoreticalestimation.GaN layers with thickness of 2 µm were grown on a−plane sapphire in an Aixtron planetary reactor at 1170 °Cusing a low temperature GaN buffer layers. The a and c lattice parameters of the GaN films and the epitaxialrelationship between the layers and the sapphire substrate were determined by using a Philips triple axisdiffractometer.The asymmetric {10−12} reflections of GaN and {11−23} of the sapphire substrate were measured in order todetermine the epitaxial relationships.  Figure 1 (a) shows azimuthal phi−scans of GaN {10−12} and sapphire{11−23} planes for one representative sample. It is seen that there is a coincidence of the sapphire peaks with twoof the six GaN reflections. Since the normal to the projection of the sapphire (11−23) plane includes an angle of30° with the sapphire [1−100] direction, and the normal to the projection of the GaN (10−12) plane is parallel tothe GaN [1−100] direction, the angle between the two normals is 30°. It means that the GaN [1−100] is parallel tothe sapphire [0001] and the GaN [11−20] is parallel to the sapphire [1−100]. Such epitaxial relationships have beenreported by Bai et al. for MOVPE−GaN layers on a−plane sapphire [5]. The thermal expansion coefficient alongthe sapphire c−axis is known to be larger than that one along its a−axis [2]. Therefore, the thermal strain in theGaN layers will be higher along the GaN [1−100] than in the perpendicular direction. This is illustrated in Fig.1(b), where the distortion of the GaN basal plane under anisotropic strain is schematically shown. The presence ofanisotropic in−plane strain would result in a distortion of the hexagonal symmetry, reflected by two differentlattice parameters a' and a'' . In contrast, the undistorted hexagon has two equal lattice parameters a (Fig. 1 (b)).The distortion of the GaN basal plane under anisotropic strain (see Fig. 1 (b)) should be reflected in the2theta−omega asymmetric  peak positions, since the interplanar distance d i.e. the values of the lattice parametersare directly related to the scattering angle 2theta via the Bragg law , where  is the x−rayradiation wavelength and n is an integer.10th European Workshop on MOVPE, Lecce (Italy) 8−11 June 2003 PS.VII.03V. Darakchieva et al Therefore, we measured 2theta−omega for the asymmetric peaks at each six phi positions, since in this way theinterplanar distances of all six equivalent planes were obtained. The 10−15 2theta−omega diffraction peakpositions of the representative MOVPE−GaN layer at each of the phi positions are shown in Fig. 2. It is clearlyseen that the 2theta−omega peak appears at different positions reflecting a distortion of the hexagonal symmetry −two of the 2theta−omega positions appear at higher (squares) and four at lower (dots) scattering angles and thesame trend is observed for all asymmetric peaks measured. The values of the interplanar distances derived fromthese peak positions can be discriminated accordingly into two groups (two smaller and four larger). Consequently,the in−plane lattice parameter also has two values: a smaller value − a' and a larger value − a''. The c lattice parameter of the films was determined from the 0002, 0004 and 0006 2theta−omega diffraction peaksfor four different azimuthal positions. Each azimuthal position is achieved by a rotation of the sample around itsnormal by 90°. The asymmetric 10−14, 10−15, 20−24 and 20−25 reflections  and the average value of the c latticeparameter were used for the determination of the a lattice parameter. The c and a lattice parameters of the filmswere calculated taking the refraction correction into account (for calculation details see Ref. 6). As a resultwe obtained the following values for the lattice parameters: c = 5.18973(2) Å, a' = 3.1820(1) Å and a'' = 3.1841(2)Å. The values of the lattice parameters of the GaN film show that the films are compressively strained, as can beexpected due to the difference in thermal expansion coefficients and lattice mismatch of sapphire and GaN. Wenote that the two in−plane lattice parameters − a' and a'' appear smaller than the unstrained one a0 .The determination of two different values for the in−plane lattice parameter can be  related to the presence ofin−plain strain anisotropy (see Fig. 1(a)). The same result has been obtained for hydride vapor phase epitaxial (HVPE) GaN films grown on a−plane sapphire [6]. We note that the distortion of the hexagonal symmetry is alsomanifested in the polarized photoluminescence spectra of the MOVPE− and HVPE− GaN films grown on a−planesapphire  (not shown here) and as a result a splitting of the A free exciton peak has been observed [3].  The A freeexciton peak position in the MOVPE−GaN films appear at higher energy in [1−100] polarization implying a highercompressive strain in this direction. This finding is in agreement with the determined epitaxial relationships. It isworth noting that for GaN films grown on c−plane sapphire (isotropically stressed) only one a−lattice parameter isdetermine when the above described HRXRD procedure is applied, and no splitting in the polarized PL spectra10th European Workshop on MOVPE, Lecce (Italy) 8−11 June 2003 PS.VII.03V. Darakchieva et al from these films is observed [3, 7].We also estimated the in−plane strain anisotropy  in the films to be 6.6(5)x10−4. As unstrained in−planelattice parameters we used a0 = 3.18935 Å determined for a 130 µm−thick GaN layer grown by HVPE on c−planesapphire [7].  In principle, the strain anisotropy in GaN films on a−plane sapphire could originate from: (i)different lattice mismatches between the film and the substrate in the [1−100] and [11−20]  directions;  (ii) adifference in the thermal expansion coefficients of sapphire in the two directions which will result in differentthermal strain, and (iii) an anisotropic distribution of defects in the film which will lead to different film elasticityin the two perpendicular directions and a different ability to release the strain.We estimated lattice mismatches of −6.3% and −16% along the GaN [11−20] and [1−100] directions forthe obtained epitaxial relationships (Fig. 1 (b)) and using the values for the sapphire lattice constants reported inRef. 8. It is believed that the lattice mismatch induced strain is relieved during the initial stage of growth[9], however there are some reports that MOVPE−GaN films are strained at the growth temperature [10].  In orderto infer which is the dominant distribution to the strain anisotropy we estimated its value in the case of thermalstrain. It can be easily shown that on the assumption of total relaxation of the lattice mismatch induced strainbefore the cooling down starts, the strain anisotropy at room temperature, TRT   is determined by, where and  are the sapphire thermal expansioncoefficients in the [1−100] and [0001] directions, respectively and Tgr  is the growth temperature. We note that inthe calculations it is assumed that the distortion of the hexagonal symmetry is not very large and the angles arekept close to their non−distorted values of 120°. Using the values for the thermal expansion coefficients reportedby Maruska and Tietjen [2] we obtained a value of 1.10x10−3 for the strain anisotropy in the film, being somewhatlarger than the experimentally determined value. The estimated value is in a very good agreement with theexperimentally determined strain anisotropy, having in mind that there is a considerable uncertainty in the valuesof the thermal expansion coefficients of sapphire. Moreover, the unstrained lattice parameter of GaN is also not10th European Workshop on MOVPE, Lecce (Italy) 8−11 June 2003 PS.VII.03V. Darakchieva et al well established. This agreement shows that the strain anisotropy is mainly governed by the difference in thethermal expansion coefficients of sapphire. However, a contribution to the strain anisotropy from the latticemismatch induced strain in [1−100] and [11−20] directions and from an anisotropic defect distribution can not beexcluded. In this respect it is worth mentioning that recently we have reported that the strain anisotropy hasdifferent values in HVPE− and MOVPE−GaN films [6].In conclusion, we have reported on the HRXRD determination of two different values of the in−plane latticeparameter of MOVPE−GaN layers grown on a−plane sapphire. We suggest that the observed distortion of thehexagonal symmetry can be attributed to the presence of anisotropic in−plane strain in the films. The strainanisotropy is determined in the crystal coordinate system, and it is compared with a estimation in the case ofthermal strain. It is suggested that the difference in the thermal strain in the [1−100] and [11−20] directions has adominant contribution to the strain anisotropy, although the lattice mismatch induced strain and an anisotropicdefect distribution can also affect its value.[1] B. Gill, in "Semiconductors and Semimetals" vol. 57 (eds. J. I. Pankove and T. D. Moustakas)  p. 209 (1999).[2] H. P. Maruska and J. J. Tietjen, Appl. Phys. Lett. 15, 327 (1969) [3] P. P. Paskov, T. Paskova, P. O. Holtz, and B. Monemar, Phys. Status Solidi A 190, 75 (2002).[4] A. Alemu, B. Gil, M. Julier, and S. Nakamura, Phys. Rev. B 57, 3761 (1998).[5] J. Bai, T. Wang, H. D. Li, N. Jiang, and S. Sakai, J. Cryst. Growth 231, 41 (2001).[6] V. Darakchieva, P. P. Paskov, T. Paskova, E. Valcheva, B. Monemar and M. Heuken, Appl. Phys. Lett. 82, 703(2003).[7] V. Darakchieva, T. Paskova, P. P. Paskov, B. Monemar, N. Ashkenov, and M. Schubert, Phys. Status Solidi A195, 516 (2003)[8] M. Leszczynski, T. Suski, H. Teisseyre, P. Perlin, I. Grzegory, J. Jun, S. Porowski, and T. D. Moustakas, J.Appl. Phys. 76, 4909 (1994).[9] H. Amano, K. Hiramatsu, and I. Akasaki, Jpn. J. Appl. Phys. 27, L1384 (1998)[10] S. Hearne, E. Chason, J. Han, J. A. Floro, J. Figiel, J. Hunter, H. Amano, and I. S. T. Tsong, Appl. Phys. Lett.74, 356 (1999).10th European Workshop on MOVPE, Lecce (Italy) 8−11 June 2003 PS.VII.03V. Darakchieva et al 

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