Statistical mechanics of supercoils and the torsional stiffness of the DNA double helix.

The distribution of closed unknotted polymer chains over the writhing number is calculated by the Monte-Carlo method. For circular duplex DNA the variance of the distribution equals approximately half the observed variance of equilibrium distribution over the linking number. The balance which arises from fluctuations in DNA twisting makes it possible to estimate the torsional stiffness of the double helix.     

The conformation of the DNA double helix in the crystal is dependent on its environment

Studies of the crystal structures of more than 30 synthetic DNA fragments have provided structural information about three basic forms of the double helix: A-, B- and Z-form DNA. These studies have demonstrated that the DNA double helix adopts a highly variable structure which is related to its base sequence. The extent to which such observed structures are influenced by the crystalline environment can be found by studying the same molecule in different crystalline forms. We have recently crystallized one particular oligomer in various crystal forms. Here we report the results of structural analyses of the different crystal structures and demonstrate that the DNA double helix can adopt a range of conformations in the crystalline state depending on hydration, molecular packing and temperature. These results have implications on our understanding of the influence of the environment on DNA structure, and on the modes of DNA recognition by proteins.     

Single-site enzymatic cleavage of yeast genomic DNA mediated by triple helix formation.

Physical mapping of chromosomes would be facilitated by methods of breaking large DNA into manageable fragments, or cutting uniquely at genetic markers of interest. Key issues in the design of sequence-specific DNA cleaving reagents are the specificity of binding, the generalizability of the recognition motif, and the cleavage yield. Oligonucleotide-directed triple helix formation is a generalizable motif for specific binding to sequences longer than 12 base pairs within DNA of high complexity. Studies with plasmid DNA show that triple helix formation can limit the operational specificity of restriction enzymes to endonuclease recognition sequences that overlap oligonucleotide-binding sites. Triple helix formation, followed by methylase protection, triple helix-disruption, and restriction endonuclease digestion produces near quantitative cleavage at the single overlapping triple helix-endonuclease site. As a demonstration that this technique may be applicable to the orchestrated cleavage of large genomic DNA, we report the near quantitative single-site enzymatic cleavage of the Saccharomyces cerevisiae genome mediated by triple helix formation. The 340-kilobase yeast chromosome III was cut uniquely at an overlapping homopurine-EcoRI target site 27 base pairs long to produce two expected cleavage products of 110 and 230 kilobases. No cleavage of any other chromosome was detected. The potential generalizability of this technique, which is capable of near quantitative cleavage at a single site in at least 14 megabase pairs of DNA, could enable selected regions of chromosomal DNA to be isolated without extensive screening of genomic libraries.     

Molecular structure of r(GCG)d(TATACGC): a DNA--RNA hybrid helix joined to double helical DNA

The molecule r(GCG)d(TATACGC) is self-complementary and forms two DNA--RNA hybrid segments surrounding a central region of double helical DNA; its molecular structure has been solved by X-ray analysis. All three parts of the molecule adopt a conformation which is close to that seen in the 11-fold RNA double helix. The conformation of the ribonucleotides is partly determined by water molecules bridging between the ribose O2' hydroxyl group and cytosine O2. The hybrid-DNA duplex junction contains no structural discontinuities. However, the central DNA TATA sequence has some structural irregularities.     

High-resolution structure of a DNA helix containing mismatched base pairs

The concept of complementary base pairing, integral to the double-helical structure of DNA, provides an effective and elegant mechanism for the faithful transmission of genetic information. Implicit in this model, however, is the potential for incorporating non-complementary base pairs (mismatches) during replication or subsequently, for example, during genetic recombination. As such errors are usually damaging to the organism, they are generally detected and repaired. Occasionally, however, the propagation of erroneous copies of the genome confers a selective advantage, leading to genetic variation and evolutionary change. An understanding of the nature of base-pair mismatches at a molecular level, and the effect of incorporation of such errors on the secondary structure of DNA is thus of fundamental importance. We now report the first single-crystal X-ray analysis of a DNA fragment, d(GGGGCTCC), which contains two non-complementary G X T base pairs, and discuss the implications of the results for the in vivo recognition of base-pair mismatches.     

Crystal structure of an RNA double helix incorporating a track of non-Watson-Crick base pairs

The crystal structure of the RNA dodecamer duplex (r-GGACUUCGGUCC)2 has been determined. The dodecamers stack end-to-end in the crystal, simulating infinite A-form helices with only a break in the phosphodiester chain. These infinite helices are held together in the crystal by hydrogen bonding between ribose hydroxyl groups and a variety of donors and acceptors. The four noncomplementary nucleotides in the middle of the sequence did not form an internal loop, but rather a highly regular double-helix incorporating the non-Watson-Crick base pairs, G.U and U.C. This is the first direct observation of a U.C (or T.C) base pair in a crystal structure. The U.C pairs each form only a single base-base hydrogen bond, but are stabilized by a water molecule which bridges between the ring nitrogens and by four waters in the major groove which link the bases and phosphates. The lack of distortion introduced in the double helix by the U.C mismatch may explain its low efficiency of repair in DNA. The G.U wobble pair is also stabilized by a minor-groove water which bridges between the unpaired guanine amino and the ribose hydroxyl of the uracil. This structure emphasizes the importance of specific hydrogen bonding between not only the nucleotide bases, but also the ribose hydroxyls, phosphate oxygens and tightly bound waters in stabilization of the intramolecular and intermolecular structures of double helical RNA.     

Dependence of DNA helix flexibility on base composition

We have used triplet anisotropy decay techniques to study the flexibility of synthetic DNA fragments with different base pair compositions. We have found major differences in the torsional and bending stiffness of poly(dG) . poly(dC), poly(dA) . poly(dT) and poly(dA-dC) . poly(dT-dG). Poly(dG) . poly(dC) has a torsional modulus more than 40 times larger than poly(dA-dC) . poly(dT-dG), and approximately 20 times larger than poly(dA) . poly(dT). These differences imply that the torsional stiffness of DNA can vary greatly with base composition. The Young's modulus (bending stiffness) we have measured for poly(dG) . poly(dC) is at least twice that of poly(dA-dC) . poly(dT-dG) or random sequence DNA, and is at least threefold greater than that of poly(dA) . poly(dT). This implies that the bending stiffness of DNA is also strongly dependent on base composition. In light of this dramatic base composition dependence, we suggest here that such stiffness variation may lead to local variations in the stability of chromatin or other protein complexes that require bending or twisting of the DNA helix.     

Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet.

A new Watson-Crick base pair, with a hydrogen bonding pattern different from that in the A.T and G.C base pairs, is incorporated into duplex DNA and RNA by DNA and RNA polymerases and expands the genetic alphabet from 4 to 6 letters. This expansion could lead to RNAs with greater diversity in functional groups and greater catalytic potential.     

叶片宽度比对同心双螺旋静态混合器混合性能的影响

同心双螺旋静态混合器是一种新型的静态混合装置,能够实现流体在混合管内的同心反向螺旋流动。为探究同心双螺旋元件内外叶片宽度比对混合效果的影响规律,利用Fluent中多相流混合模型对低雷诺数状态下该混合器内的混合过程进行了数值模拟,研究结果表明：在较低雷诺数下,同心双螺旋静态混合器与对应尺寸的传统Kenics型混合器相比混合效果明显提升,在叶片宽度比e为0~3/2时混合效果提升6.9%~28%;随着内外叶片宽度比的增大,混合效果呈现先增后减的规律,当e=2/3时混合效果最好;在不同的宽度比下,流体的分离强度沿混合管轴向变化规律相同,即在第一个混合元件内分离强度下降缓慢,第二、三个元件内下降迅速,第四个元件内几乎保持不变而处于维持混合状态,说明本文所研究的混合器使用较少的混合元件即可达到较好的混合效果。     

Carcinogenesis of asbestos switched on by inducing cross-linkage between DNA complementary pair bases

Since the beginning of the 1980s, Dai Qianhuan predicted based upon his di-region theory that the carcinogenesis switched on by the so-called physical carcinogenic factors including radiation, asbestos and foreign matter implantation, is just initiated through the cross-linking between DNA complementary pair bases induced by them. In this note, it was evidenced with the DNA filter elution method that the oxygenase activated by asbestos induces the cross-linking between DNA inter-strands and DNA-protein with dosage correlation, in which over 80% of DNA inter-strand cross-link ratio account for the total cross-link ratio. Obviously, both of the cross-linkages are just induced by hydroxyl free radical, HO ·, because the ferrous ion increased the cross-link ratios up to several times through Fenton reaction and vitamin C inhibited the cross-link ratios with factors of 8–9 by destroying the hydroxyl radical. Non-carcinogen but with lower free radical formation energy, pyrene, by culturing with asbestos gave 3–4 times cross-link ratios than the original ratios induced by asbestos only. Estradiol, an endogenous carcinogen, as a bio-electrophilic species but with higher free radical formation energy by culturing with asbestos, gave only 1.2 time cross-link ratios than expected ones. Ferrous ion which can increase HO · concentration through Fenton reaction, increased the ratios to 2–2.5 times in the former case but only 1.2 time in the latter case. Vitamin C, a free radical scavenger, gave a powerful inhibition to the cross-linking with a factor of 8–11 in the former case but a weak inhibition with a factor of 1.2 only in the latter case. So, it is evidenced further that the cross-linkages induced by asbestos are originated from hydroxyl radical. Reasonable structures of the cross-linking products induced by asbestos or hydroxyl radical have been depicted based upon AMI MO theory. These structures have been verified further by a reasonable explanation of the mutational spectrum induced by hydroxyl radical.     

Local conformation transitions of linear DNA induced by cisplatin

Cisplatin is the most successful anti-tumor drug, and its pharmacological property is generally considered to derive from the modification of DNA molecules. Structural modifications of short DNA induced by cisplatin have already been investigated. However, the conformation transitions induced by cisplatin are not clear. In the present letter, we have studied the effect of low-concentration cisplatin on DNA conformation by using AFM imaging. We observed formations of micro-rod structures of linear DNA induced by cisplatin. A method is presented to quantitatively analyze the occurrence of micro-rod structures. We found that the formation of micro-rod structures depends on the DNA sequence. Based on the results, we proposed a physical mechanism to explain the local conformation transitions of DNA molecules under the influence of cisplatin.     

Primary structure of helix C to helix G of a new retinal protein in H.sp.xz515

The gene fragment encoding the retinal protein from helix C to helix G in a new strain of halobacteria, H.sp.xz515 has been amplified by PCR method. The nucleotide sequence of this fragment has been determined. The deduced amino acid sequence has been compared with halobium br and other two br-like proteins, ar-1 and ar-2. Results show that those amino acid residues in br, essential for proton pumping and binding to retinal, are conserved. The residue M145 in br may be important for isomerization reaction of retinal.