公开(公告)号：WO2002095059A2

公开(公告)日：2002-11-28

申请号：PCT/US2002/018532

申请日：2002-05-15

Applicant: THE PUBLIC HEALTH RESEARCH INSTITUTE OF THE CITY OF NEW YORK, INC. ,  DRLICA, Karl ,  WANG, Jian-Ying

Inventor： DRLICA, Karl ,  WANG, Jian-Ying

IPC: C12Q

CPC classification number: C12N15/113 ,  G06F19/18

Abstract: Nucleic acid hybridization under steady-state conditions is described by a kinetic model in which the intermediate state is assumed to be locally single stranded. An expression was derived that relates nucleic acid secondary structure to the rate of oligonucleotide-RNA hybridization. The model assumes that the hybridization of nucleic acids occurs through an intermediate state in which the region to be hybridized has a single-stranded conformation prior to binding the antisense oligonucleotide. In the derivation, a steady-state condition is assumed. The model is applicable to the steady-state condition in living cells and the initial stage of single-tube hybridization when full-length hybrid has not significantly accumulated and the concentration of nucleation complex is approximately constant. The model allows the calculation of a rate factor that is proportional to the rate constant for hybridization between complementary nucleic acids. When rate factors were calculated using a commercially available algorithm for estimating RNA secondary structure, they correlated well with rates for hybridization of antisense oligodeoxynucleotides (ODNs) to a 101-nucleotide artificial RNA that has been published and of molecular beacons to HIV-1 tat mRNA. For RNA-RNA annealing, the locations of 11-nucleotide long regions that have the maximum rate factor coincide with experimentally determined nucleation sites. Dependence of the maximum rate factor on the length of antisense RNA is in agreement with observed relationship between hybridization rates and antisense lengths. Rate factors calculated for 32-sites in HIV-1 integrase mRNA also correlated with hybridization of antisense ODN to each site when measured by ODN-mediated, ribonuclease H-dependent cleavage of RNA. The model identified sites that hybridized readily over a range of magnesium ion concentration expected to affect RNA tertiary structure, suggesting that tertiary structure was either absent or was not an important impediment to hybridization. Calculated target site rate factors also corresponded to published data for antisense oligonucleotide hybridization with mRNAs of human genes encoding multidrug resistance, angiotensin type-1 receptor, c-myb, acetylcholinesterase, and hepatitis C virus. These results support the general applicability of the kinetic model and its potential utility for rapid identification of sites for antisense attack of mRNA.

Abstract translation: 在稳态条件下的核酸杂交通过动力学模型描述，其中假定中间状态是局部单链的。 得出了将核酸二级结构与寡核苷酸 - RNA杂交速率相关联的表达。 该模型假设核酸的杂交通过中间状态发生，其中待结合的区域在结合反义寡核苷酸之前具有单链构象。 在推导中，假设稳态条件。 该模型适用于活体细胞的稳态条件，当全长杂交体未显着积累且成核络合物的浓度近似恒定时，单管杂交的初始阶段。 该模型允许计算与互补核酸之间杂交的速率常数成比例的速率因子。 当使用商业上可用的估计RNA二级结构的算法计算速率因子时，它们与反义寡脱氧核苷酸（ODN）与已经公布的101核苷酸人造RNA和HIV-1 tat mRNA的分子信标的杂交率很好地相关 。 对于RNA-RNA退火，具有最大速率因子的11个核苷酸长的区域的位置与实验确定的成核位点重合。 最大速率因子对反义RNA长度的依赖性与观察到的杂交率和反义长度的关系一致。 计算出的HIV-1整合酶mRNA的32个位点的速率因子与通过ODN介导的核糖核酸酶H依赖性切割RNA测量的反义ODN与每个位点的杂交相关。 该模型鉴定了一系列预期影响RNA三级结构的镁离子浓度范围内容易杂交的位点，表明三级结构不存在或不是杂交的重要障碍。 计算的靶位点率因子也对应于与编码多药耐药性，血管紧张素1型受体，c-myb，乙酰胆碱酯酶和丙型肝炎病毒的人基因的mRNA反义寡核苷酸杂交的公开数据。 这些结果支持动力学模型的一般适用性及其用于快速鉴定mRNA反义位点的潜在效用。

公开(公告)号：WO2012018867A1

公开(公告)日：2012-02-09

申请号：PCT/US2011/046337

申请日：2011-08-02

Applicant: UNIVERSITY OF MEDICINE AND DENTISTRY OF NEW JERSEY ,  ZHAO, Xilin ,  DRLICA, Karl

Inventor： ZHAO, Xilin ,  DRLICA, Karl

IPC: A01N37/18

CPC classification number: A61K33/00 ,  A01N59/00 ,  A61M16/12 ,  A01N2300/00 ,  A61K2300/00

Abstract: A gas mixture for treatment of a mycobacterial infection and methods thereof, wherein the gas mixture comprises hydrogen. In certain applications, the gas mixture further comprises oxygen and optionally an inert or anaerobic gas, preferably selected from the group consisting of nitrogen, helium, argon, carbon dioxide, and mixtures thereof. The methods for treatment comprise direct inhalation of the gas mixture comprising hydrogen and oxygen, intubation of a patient with a double lumen endotracheal tube thereby supplying one lung with an anaerobic gas, and administration of a gas mixture comprising hydrogen and oxygen in a hyperbaric setting. Also provided is a method of sterilization of a mycobacterium-contaminated surface comprising administration of the hydrogen-containing gas mixture.

Abstract translation: 一种用于治疗分枝杆菌感染的气体混合物及其方法，其中所述气体混合物包含氢气。 在某些应用中，气体混合物还包含氧气和任选的惰性或厌氧气体，优选选自氮气，氦气，氩气，二氧化碳及其混合物。 治疗方法包括直接吸入包含氢气和氧气的气体混合物，将患者插入双腔气管插管，从而向厌氧气体供应一个肺，以及在高压环境中施用包含氢气和氧气的气体混合物。 还提供了包含施用含氢气体混合物的分枝杆菌污染表面的灭菌方法。

公开(公告)号：WO2002095059A3

公开(公告)日：2002-11-28

申请号：PCT/US2002/018532

申请日：2002-05-15

Applicant: THE PUBLIC HEALTH RESEARCH INSTITUTE OF THE CITY OF NEW YORK, INC. ,  DRLICA, Karl ,  WANG, Jian-Ying

Inventor： DRLICA, Karl ,  WANG, Jian-Ying

IPC: G01N33/48

Abstract: Nucleic acid hybridization under steady-state conditions is described by a kinetic model in which the intermediate state is assumed to be locally single stranded. An expression was derived that relates nucleic acid secondary structure to the rate of oligonucleotide-RNA hybridization. The model assumes that the hybridization of nucleic acids occurs through an intermediate state in which the region to be hybridized has a single-stranded conformation prior to binding the antisense oligonucleotide. In the derivation, a steady-state condition is assumed. The model is applicable to the steady-state condition in living cells and the initial stage of single-tube hybridization when full-length hybrid has not significantly accumulated and the concentration of nucleation complex is approximately constant. The model allows the calculation of a rate factor that is proportional to the rate constant for hybridization between complementary nucleic acids. When rate factors were calculated using a commercially available algorithm for estimating RNA secondary structure, they correlated well with rates for hybridization of antisense oligodeoxynucleotides (ODNs) to a 101-nucleotide artificial RNA that has been published and of molecular beacons to HIV-1 tat mRNA. For RNA-RNA annealing, the locations of 11-nucleotide long regions that have the maximum rate factor coincide with experimentally determined nucleation sites. Dependence of the maximum rate factor on the length of antisense RNA is in agreement with observed relationship between hybridization rates and antisense lengths. Rate factors calculated for 32-sites in HIV-1 integrase mRNA also correlated with hybridization of antisense ODN to each site when measured by ODN-mediated, ribonuclease H-dependent cleavage of RNA. The model identified sites that hybridized readily over a range of magnesium ion concentration expected to affect RNA tertiary structure, suggesting that tertiary structure was either absent or was not an important impediment to hybridization. Calculated target site rate factors also corresponded to published data for antisense oligonucleotide hybridization with mRNAs of human genes encoding multidrug resistance, angiotensin type-1 receptor, c-myb, acetylcholinesterase, and hepatitis C virus. These results support the general applicability of the kinetic model and its potential utility for rapid identification of sites for antisense attack of mRNA.