Tuning single nucleotide discrimination in polymerase chain reactions (PCRs): synthesis of primer probes bearing polar 4'-C-modifications and their application in allele-specific PCR

There are many methods available for the detection of nucleotide variations in genetic material. Most of these methods are applied after amplification of the target genome sequence by the polymerase chain reaction (PCR). Many efforts are currently underway to develop techniques that can detect single nucleotide variations in genes either by means of, or without the need for, PCR. Allele-specific PCR (asPCR), which reports nucleotide variations based on either the presence or absence of a PCR-amplified DNA product, has the potential to combine target amplification and analysis in one single step. The principle of asPCR is based on the formation of matched or mismatched primer-target complexes by using allele-specific primer probes. PCR amplification by a DNA polymerase from matched 3'-primer termini proceeds, whereas a mismatch should obviate amplification. Given the recent advancements in real-time PCR, this technique should, in principle, allow single nucleotide variations to be detected online. However, this method is hampered by low selectivity, which necessitates tedious and costly manipulations. Recently, we reported that the selectivity of asPCR can be significantly increased through the employment of chemically modified primer probes. Here we report further significant advances in this area. We describe the synthesis of various primer probes that bear polar 4'-C-modified nucleotide residues at their 3' termini, and their evaluation in real-time asPCR. We found that primer probes bearing a 4'-C-methoxymethylene modification have superior properties in the discrimination of single nucleotide variations by PCR.     

Synthesis and DNA binding properties of pyrrole amino acid-containing peptides

Dimers of the pyrrole amino acid (Paa), 5-(aminomethyl)pyrrole-2-carboxylic acid, and its derivatives having Lys anchored on N- and C-termini bind in the minor groove of DNA with considerable apparent binding affinities. When the Lys unit is attached to the C-terminus, the resulting ligand binds to ds-DNA with twice the affinity, of the order of 10⁵, than the one carrying two positive charges at the same end.     

配体形状对多吡啶铜(Ⅱ)配合物与DNA作用的影响

合成了一系列含有平面配体的Cu(Ⅱ)多吡啶配合物[Cu(IP)₂]²⁺、[Cu(PIP)₂]²⁺、[Cu(DPPZ)₂]²⁺和[Cu(HPIP)₂]²⁺，用吸收光谱、CD光谱和粘度等方法研究了这些配合物与小牛胸腺DNA的作用。结果表明配体上的取代基及配体的平面性对这些四面体配合物与DNA的结合强弱产生一定的影响。[Cu(DPPZ)₂]²⁺与DNA的结合较强，而[Cu(HPIP)₂]²⁺与DNA的结合较弱。CD光谱显示配合物[Cu(DPPZ)₂]²⁺、[Cu(PIP)₂]²⁺和[Cu(HPIP)₂]²⁺的加入会导致DNA的CD光谱减弱。而[Cu(IP)₂]²⁺的加入则会使DNA的CD光谱增强。同时，[Cu(IP)₂]²⁺与DNA结合后，还会引起一定程度的DNA构型转换，即DNA从B型转换成Z型。     

Characterization of the monovalent ion position and hydrogen-bond network in guanine quartets by DFT calculations of NMR parameters

Conformational stability of G-quartets found in telomeric DNA quadruplex structures requires the coordination of monovalent ions. Here, an extensive Hartree-Fock and density functional theory analysis of the energetically favored position of Li+, Na+, and K+ ions is presented. The calculations show that at quartet-quartet distances observed in DNA quadruplex structures (3.3 A), the Li+ and Na+ ions favor positions of 0.55 and 0.95 A outside the plane of the G-quartet, respectively. The larger K+ ion prefers a central position between successive G-quartets. The energy barrier separating the minima in the quartet-ion-quartet model are much smaller for the Li+ and Na+ ions compared with the K+ ion; this suggests that K+ ions will not move as freely through the central channel of the DNA quadruplex. Spin-spin coupling constants and isotropic chemical shifts in G-quartets extracted from crystal structures of K+- and Na+-coordinated DNA quadruplexes were calculated with B3LYP/6-311G(d). The results show that the sizes of the trans-hydrogen-bond couplings are influenced primarily by the hydrogen bond geometry and only slightly by the presence of the ion. The calculations show that the R(N2N7) distance of the N2-H2...N7 hydrogen bond is characterized by strong correlations to both the chemical shifts of the donor group atoms and the (h2)J(N2N7) couplings. In contrast, weaker correlations between the (h3)J(N1C6') couplings and single geometric factors related to the N1-H1...O6=C6 hydrogen bond are observed. As such, deriving geometric information on the hydrogen bond through the use of trans-hydrogen-bond couplings and chemical shifts is more complex for the N1-H1...O6=C6 hydrogen bond than for the N2-H2...N7 moiety. The computed trans-hydrogen-bond couplings are shown to correlate with the experimentally determined couplings. However, the experimental values do not show such strong geometric dependencies.     

Design of photoactivated DNA oxidizing agents: synthesis and study of photophysical properties and DNA interactions of novel viologen-linked acridines

A new series of photoactivated DNA oxidizing agents in which an acridine moiety is covalently linked to viologen by an alkylidene spacer was synthesized, and their photophysical properties and interactions with DNA, including DNA cleaving properties, were investigated. The fluorescence quantum yields of the viologen-linked acridines were found to be lower than that of the model compound 9-methylacridine (MA). The changes in free energy for the electron transfer reactions were found to be favorable, and the fluorescence quenching observed in these systems is explained by an electron transfer mechanism. Intramolecular electron transfer rate constants were calculated from the observed fluorescence quantum yields and singlet lifetime of MA and are in the range from 1.06x10(10) s(-1) for 1 a (n=1) to 6x10(8) s(-1) for 1 c (n=11), that is, the rate decreases with increasing spacer length. Nanosecond laser flash photolysis of these systems in aqueous solutions showed no transient absorption, but in the presence of guanosine or calf thymus DNA, transient absorption due to the reduced viologen radical cation was observed. Studies on DNA binding demonstrated that the viologen-linked acridines bind effectively to DNA in both intercalative and electrostatic modes. Results of PM2 DNA cleavage studies indicate that, on photoexcitation, these molecules induce DNA damage that is sensitive to formamidopyrimidine DNA glycosylase. These viologen-linked acridines are quite stable in aqueous solutions and oxidize DNA efficiently and hence can be useful as photoactivated DNA-cleaving agents which function purely by the co-sensitization mechanism.     

DNA为模板的铂纳米团簇沉积

Platinum nanoclusters were deposited along the supercoiled DNA strands after incubation of cis-(trans-1R，2R-diaminocyclohexane)(dl-camphorato)platinum(Ⅱ) (Cdp)， an analogue of the anti-tumor drug-carboplatin， with DNA and K₂PtCl₄ for 600 min and then through reduction of dimethylaminoborane (DMAB). The decrease of absorption of DNA at 260 nm indicates the coordination of Cdp and DNA. TEM and AFM were employed to characterize the morphologies and structures of platinum nanoclusters.     

Styrene oxide DNA adducts: quantitative determination using <Superscript>31</Superscript>P monitoring

The reaction of styrene oxide, a potential carcinogen in humans, with DNA constituents has been used to develop an improved method for quantification of DNA adducts. To enable monitoring of DNA adducts caused by xenobiotics at physiological relevant levels, a robust, reliable and powerful method based on monitoring of phosphorus in nucleotides is described. An efficient enzymatic digestion step and a sample-preconcentration procedure are essential, and enable separation of alkylated nucleotides from the large excess of native nucleotides. The adducts are detected by means of the phosphorus signal measured at mass m/z=31 with an inductively-coupled-plasma mass spectrometer. Bis(4-nitrophenyl)phosphate (BNPP) serves as internal standard for quantification of the adducts. The absolute limit of detection, 45 fmol, corresponds to detection of three modified nucleotides among 10⁷ native nucleotides (the calculation is based on use of 50 g calf thymus DNA). An adduct formation ratio at the DNA of 3.6 adducts per 1000 nucleotides was measured, which is 75% lower than for reaction with monomeric 2-deoxy-nucleotides. In addition, a substantial amount of phosphate adducts were detected, but in DNA the rate of phosphate formation was lower than with monomeric nucleotides. Most probably these adducts escaped unnoticed when ³¹P-post-labelling was employed.     

Ultrafast proton-coupled electron-transfer dynamics in pyrene-modified pyrimidine nucleosides: model studies towards an understanding of reductive electron transport in DNA.

5-(Pyren-1-yl)-2'-deoxyuridine (PydU) and 5-(Pyren-1-yl)-2'-deoxycytidine (PydC) were used as model nucleosides for DNA-mediated reductive electron transport (ET) in steady-state fluorescence and femtosecond time-resolved transient absorption spectroscopy studies. Excitation of the pyrene moiety in PydU and PydC leads to an intramolecular electron transfer that yields the pyrenyl radical cation and the corresponding pyrimidine radical anion (dU.- and dC.-. By comparing the excited state dynamics of PydC and PydU, we derived information about the energy difference between the two pyrimidine radical anion states. To determine the influence of protonation on the rates of photoinduced intramolecular ET, the spectroscopic investigations were performed in acetonitrile, MeCN, and in water at different pH values. The results show a significant difference in the basicity of the generated pyrimidine radical anions and imply an involvement of proton transfer during electron hopping in DNA. Our studies revealed that the radical anion dC.- is being protonated even in basic aqueous solution on a picosecond time scale (or faster). These results suggest that protonation of dC.- may also occur in DNA. In contrast, efficient ET in PydU could only be observed at low pH values (< 5). In conclusion, we propose--based on the free energy differences and the different basicities--that only dT.- but not dC.- can participate as an intermediate charge carrier for excess electron migration in DNA.     

可改变DNA构象的非离子糖基表面活性剂

通过Zeta电位及粒径分析考察发现随着体系中辛基葡萄糖多苷表面活性剂质量 农度的增加，DNA分子在溶液中的构趋于缩拢。通过DNA-C_8APG复合物的UV吸收及 CD谱图进一步考察了DNA二级结构变化。随后的扫描电子显微镜（SEM）照片也证实 DNA分子在水溶液中的构象缩拢。通过表面张力UV图谱分析，推测非离子糖基表面 活性剂与DNA分子复合物结合的可能结构是表面活性剂与DNA之间的疏水作用及 多羟基的糖类的亲水头基结构与DNA带负电的核酸磷酸骨架以氢健的方式结合。     

A furan ring expansion approach to the synthesis of novel pyridazino-psoralen derivatives

A convenient preparation of the parent tetrahydrobenzodifuran 2 was developed from resorcinol. The oxidation of one or both furan rings of this key intermediate was accomplished with DDQ and the resulting benzodifuran was subsequently reacted with 3,6-dimethoxycarbonyl-1,2,4,5-tetrazine to afford the expected pyridazino-psoralen derivative in good yield. This simple method allowed the efficient preparation of a pyridazino-psoralen derivative with a formyl group at C-7, which was introduced by directed ortho-lithiation in the intermediate 2. An aminoalkyl side-chain was also introduced to the tetracyclic skeleton through the aldehyde functionality in a reductive amination process, which was accompanied by an unprecedented reduction of the pyridazine ring.