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DNA, duplex

To date, a number of simulation studies have been performed on nucleic acids and proteins using both AMBER and CHARMM. A direct comparison of crystal simulations of bovine pancreatic trypsin inliibitor show that the two force fields behave similarly, although differences in solvent-protein interactions are evident [24]. Side-by-side tests have also been performed on a DNA duplex, showing both force fields to be in reasonable agreement with experiment although significant, and different, problems were evident in both cases [25]. It should be noted that as of the writing of this chapter revised versions of both the AMBER and CHARMM nucleic acid force fields had become available. Several simulations of membranes have been performed with the CHARMM force field for both saturated [26] and unsaturated [27] lipids. The availability of both protein and nucleic acid parameters in AMBER and CHARMM allows for protein-nucleic acid complexes to be studied with both force fields (see Chapter 20), whereas protein-lipid (see Chapter 21) and DNA-lipid simulations can also be performed with CHARMM. [Pg.13]

Figure 1 The course of energy minimization of a DNA duplex with different choices of coordinates. The rate of convergence is monitored by the decrease of the RMSD from the final local minimum structure, which was very similar in all three cases, with the number of gradient calls. The RMSD was normalized by its initial value. CC, IC, and SG stand for Cartesian coordinates, 3N internal coordinates, and standard geometry, respectively. Figure 1 The course of energy minimization of a DNA duplex with different choices of coordinates. The rate of convergence is monitored by the decrease of the RMSD from the final local minimum structure, which was very similar in all three cases, with the number of gradient calls. The RMSD was normalized by its initial value. CC, IC, and SG stand for Cartesian coordinates, 3N internal coordinates, and standard geometry, respectively.
Figure 4 Time step dependence of the average total energy for two models of a partially hydrated dodecamer DNA duplex. Thinner traces show results for virtually harmonic conditions when temperature was lowered to 1 K. The DNA molecule has fixed bond lengths, rigid bases, and fixed valence angles except for the mtra- and extracyclic bond angles m sugars, (a) No modifications of inertia (b) inertia modified as explained m the text. (From Ref. 54.)... Figure 4 Time step dependence of the average total energy for two models of a partially hydrated dodecamer DNA duplex. Thinner traces show results for virtually harmonic conditions when temperature was lowered to 1 K. The DNA molecule has fixed bond lengths, rigid bases, and fixed valence angles except for the mtra- and extracyclic bond angles m sugars, (a) No modifications of inertia (b) inertia modified as explained m the text. (From Ref. 54.)...
In our last example we return to the issue of the possible damaging effects of the standard geometry constraints. Two long trajectories have been computed for a partially hydrated dodecamer DNA duplex of the previous example, first by using ICMD and second with Cartesian coordinate molecular dynamics without constraints [54]. Both trajectories started from the same initial conformation with RMSD of 2.6 A from the canonical B-DNA form. Figure 5 shows the time evolution of RMSD from the canonical A and B conformations. Each point in the figure corresponds to a 15 ps interval and shows an average RMSD value. We see that both trajectories approach the canonical B-DNA, while the RMSD... [Pg.128]

Although experimental studies of DNA and RNA structure have revealed the significant structural diversity of oligonucleotides, there are limitations to these approaches. X-ray crystallographic structures are limited to relatively small DNA duplexes, and the crystal lattice can impact the three-dimensional conformation [4]. NMR-based structural studies allow for the determination of structures in solution however, the limited amount of nuclear overhauser effect (NOE) data between nonadjacent stacked basepairs makes the determination of the overall structure of DNA difficult [5]. In addition, nanotechnology-based experiments, such as the use of optical tweezers and atomic force microscopy [6], have revealed that the forces required to distort DNA are relatively small, consistent with the structural heterogeneity observed in both DNA and RNA. [Pg.441]

The general transcription factor TFllD is believed to be the key link between specific transcription factors and the general preinitiation complex. However, the purification and molecular characterization of TFllD from higher eucaryotes have been hampered by its instability and heterogeneity. All preparations of TFllD contain the TATA box-binding protein in combination with a variety of different proteins called TBP-associated factors, TAFs. When the preinitiation complex has been assembled, strand separation of the DNA duplex occurs at the transcription start site, and RNA polymerase II is released from the promoter to initiate transcription. However, TFIID can remain bound to the core promoter and support rapid reinitiation of transcription by recruiting another molecule of RNA polymerase. [Pg.152]

UACGGUCUAAGCUGA. What is the corresponding nucleotide sequence (5 —> 3 ) of the template strand in a DNA duplex that might be introduced into these cells so that an antisense RNA could be transcribed from it ... [Pg.355]

FIGURE 12.1 DNA replication yields two daughter DNA duplexes identical to the parental DNA molecule. Each original strand of the double helix serves as a template, and the sequence of nucleotides in each of these strands is copied to form a new complementary strand by the enzyme DNA polymerase. By this process, biosynthesis yields two daughter DNA duplexes from the parental double helix. [Pg.357]

DNA duplex of 400 bp, L is 40 (assuming 10 bp per turn in B-DNA). The linking number for relaxed DNA is usually taken as the reference parameter and is written as Lq. L can be equated to the twist (T) and writhe (W) of the duplex, where twist is the number of helical turns and writhe is the number of supercoils ... [Pg.376]

Saito et al. achieved the first direct confirmation of double alkylation of purine bases by azinomycin B [140]. They incubated azinomycin B with the self-comple-mentary DNA duplex d(TAGCTA)2 and monitored the reaction by HPLC and ion spray MS. They observed initial formation of a monoadduct that was then converted into a crosslinked bisadduct. The crosslink position was identified as between the guanine of one strand and the 5 -adenine on the other strand by thermo-lytic depurination. Further decomposition prevented structural analysis of the azi-... [Pg.417]

Barton and coworkers have shown that proteins can in fact modulate the DNA electron transfer [168]. Methyltransferases are enzymes that recognize distinct DNA sequences, e.g., 5 -G CGC-3, and effect methylation by extrading the target base cytosine ( C) completely out of the DNA duplex while the remainder of the double helix is left intact. The methyltransferase Hha 1-DNA complex is a well-characterized example, revealing that the structure of the DNA is significantly but locally distorted [169,170]. In a recent study, Raj ski et al. used DNA duplex 20 containing the M.Hha I binding site between two oxidizable 5 -GG-3 sites [168] (Fig. 20). The duplex contains a complementary strand, selectively 5 -modified with a Rh intercalator that can function as a photooxidant. Upon... [Pg.421]

FIG. 20 DNA duplex 20 used for studies regarding the protein-modulated DNA electron transfer. Methyltransferase M.Hhal is capable of binding to the shadowed recognition site between two oxidizable 5 -GG-3 sites (outlined letters). The complementary strand of the duplex contains the Rh intercalator, [Rh(phi)2bpy ], at its 5 end, which can function as a photooxidant. (Adapted from Ref. 168.)... [Pg.421]

Autoradiography The detection of radioactive molecules (eg, DNA, RNA, protein) by visualization of their effects on photographic film. Bacteriophage A virus that infects a bacterium. Blunt-ended DNA Two strands of a DNA duplex having ends that are flush with each other. cDNA A single-stranded DNA molecule that is complementary to an mRNA molecule and is synthesized from it by the action of reverse transcriptase. [Pg.413]

Stichy-ended DNA Complementary single strands of DNA that protrude from opposite ends of a DNA duplex or from the ends of different duplex molecules (see also Blunt-ended DNA, above). [Pg.414]


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See also in sourсe #XX -- [ Pg.406 ]

See also in sourсe #XX -- [ Pg.315 ]




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Circular duplex DNA

DNA duplex formation

DNA, duplex, stabilization

DNA-RNA duplexes

DNA/RNA hybrids duplex

DNAs Exist as Double-Helix (Duplex) Structures

DUPLEX

Duplex B DNA

Duplex DNA structures

Duplexe

Duplexer

PNA/DNA duplex

Recognizing Specific Regions in the DNA Duplex

Single duplex DNA

Structure of DNA Duplexes with Mismatched Base Pairs

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