Effect of sulphur crosslinking on the stability and transition of triple helical DNA

177-187In continuation to our work on order-order and order-disorder transition in triple stranded DNA when it is bounded to netropsin, we report in this communication the stabilizing / destabilizing effect of disulphide linkage on the phase dynamics of the triplex using the amended Zimm-Bragg theory. <span style="font-size:14.0pt;font-family:Arial; mso-fareast-font-family:" times="" new="" roman";mso-ansi-language:en-us;mso-fareast-language:="" en-us;mso-bidi-language:ar-sa"="">It <span style="font-size:14.0pt; font-family:" times="" new="" roman";mso-fareast-font-family:"times="" roman";="" mso-ansi-language:en-us;mso-fareast-language:en-us;mso-bidi-language:ar-sa"="">is observed that in contrast to the sequential triplex → <span style="font-size:14.0pt; font-family:" times="" new="" roman";mso-fareast-font-family:"times="" roman";="" mso-ansi-language:en-us;mso-fareast-language:en-us;mso-bidi-language:ar-sa"="">duplex →<span style="font-size:14.0pt;font-family:HiddenHorzOCR;mso-hansi-font-family: " times="" new="" roman";mso-bidi-font-family:hiddenhorzocr;mso-ansi-language:en-us;="" mso-fareast-language:en-us;mso-bidi-language:ar-sa"=""> single strand melting of the uncrosslinked triplex, crosslinking causes the triplex state to melt directly to the single stranded state, with no apparent intermediary of a duplex state. Since there is no overall difference in the enthalpy of crosslinked and uncrosslinked triplexes, the transition is entropy driven.</span

Synthesis, conformation and vibrational dynamics of apolipoprotein B fragment, -Asn-Cys-Lys-Val-Glu-Leu-

318-333It is assumed that all biological processes are dynamical in nature and the low frequency collective modes, particularly the skeletal modes arising from the main chain and the side chain play an important role in such processes. To identify these a complete normal mode analysis of the hexapeptide -Asn-Cys-Lys-Yal-Glu-Leu-, a fragment of apolipoprotein B has been carried out. The assignment of modes is greatly assisted by similar studies on the tetra -Cys-Lys-Val-Glu- and tripeptides (-Asn-Cys-Lys-, -Yal-Glu-Leu-) fragments of the hexapeptide. All the four peptides have been synthesized by the solid phase peptide method using 9-flurrenyl methyloxycarbonyl (Fmoc) on 4-methyl benzhyldrylamine (MBHA) and Wang's resins. Their conformation is determined from the Ramachandran Maps which are based on the global energy minimization method. It is supported by the propensity parameters for the amino acids

A theoretical study of the stability of DNA binding with cis/trans platin

305-310Both cis- and trans-platins are known to form intra- and interstrand cross-linking with DNA. Since the nature and strength of binding is different, it makes their efficacy as anti-tumour drug different. In the present communication, we report theoretical analysis by using an amended Zimm and Bragg theory, to explain the melting behaviour and heat capacity of DNA with and without platin binding. The sharpness of transition has been examined in terms of half width and sensitivity parameter (ΔH/σ). The experimental measurements of Pilch et al (J Mol Biol 2000, 296, 803) and Ctirad and Brabec (J Biol Chem 2001, 276, 9655) have been used

Vibrational dynamics and heat capacity in polyglycine II

240-246The earlier works on the vibrational dynamics of polyglycine II (PG II) suffer from several infirmities, which not only suppress the dynamical nature of normal modes, but also lead to several incorrect assignments and interactive constants of the potential field. In this study, we have re-examined the phonon dispersion profiles of PG II using Higgs method for evaluation of phase-related normal modes and have attempted to remove the infirmities, as far as possible. The Wilson’s GF matrix method combined with the Urey-Bradley force field has been used for normal mode analysis. This potential field leads to correct assignments of Raman, infrared and inelastic neutron scattering frequencies. Characteristic features of the dispersion curve (ν versus δ/π plot), such as repulsion and regions of high density-of-states have been interpreted. In addition, the heat capacity as a function of temperature has been obtained via density-of-states. It agrees well with the experimental data and is being reported for the first time

Synthesis, conformation and vibrational dynamics of the peptide -Ser-Cys-Lys-Leu- Asp- Phe-, a fragment of apolipoprotein B

410-418The collective normal modes of the hexapeptide -Ser-Cys-Lys-Leu-Asp-Phe-, a fragment of apolipoprotein B (apo B), have been obtained. They reflect the dynamic nature and are atleast partly responsible for energy input in autolytic activity. Further, on energetic considerations based on the measurements reported by Sim & Sim, it has been shown that of the two such fragments only one induces autolysis, while the other remains anchored to the coated pit