M13 RF IV DNA where phosphorothioate groups are incorporated at restriction endonuclease Nci I recognition sites in the (-)strand is efficiently nicked by the action of this enzyme. Incubation of such nicked DNA with exonuclease III produces gapped DNA. The gap can be filled by reaction with deoxynucleoside triphosphates and DNA polymerase I. When this sequence of reactions is performed with DNA containing a mismatch oligonucleotide primer in the (-)-strand mutational frequencies of 70-90% can be obtained upon transformation. The general nature of this methodology has been further shown to be applicable to other restriction enzymes such as Hind II, Pst I and Fsp I. The mutational frequency obtained using these enzymes is between 40-80% mainly because of less efficient nicking and gapping. Studies on inhibition of Nci I cleavage show that in addition to a phosphorothioate group at the position of cleavage an additional group in the 5'-neighbouring position is necessary for complete inhibition.

The direct sequencing of DNA generated by the polynucleotide chain reaction, via the incorporation of phosphorothioate nucleotides and followed by treatment with an alkylating reagent that cleaves specifically at the phosphorothioate positions, is described. The Taq polymerase used in the amplification reaction incorporates the Sp-diastereomer of the deoxynucleoside 5'-O-(1-thiotriphosphates) as efficiently as the natural nucleotides. Chemical degradation of the phosphorothioate-containing DNA fragment can be performed with either 2-iodoethanol or 2,3-epoxy-1-propanol. The higher reactivity of 2,3-epoxy-1-propanol allows less reagent to be used to obtain the same amount of degradation as with 2-iodoethanol.

In order to find a ribozyme which can cleave the AUA triplet efficiently, the specificities and rates of intermolecular cleavage by the ribozyme of the satellite RNA of the barley yellow dwarf virus have been determined. Although it cleaves the AUA triplet in the plus strand of the viroid RNA, cleavage of AUC and AUU is more efficient, and AUG is essentially not cleaved. Attempts were made to increase cleavage efficiency by in vitro selection with randomization at positions 7, 10.1, and 11.1 in the core region. Fifteen clones were analyzed, two of which showed increased AUA cleavage efficiency. They have a G10.1.C11.1 base pair and a pyrimidine at position 7. This corresponds to the sequence of the consensus hammerhead ribozyme. Attempts to further increase cleavage efficiency by in vitro selection of the consensus hammerhead ribozyme with randomization of the 10 nucleotides in the core region or of the sBYDV ribozyme with 12 core nucleotides randomized were not successful.

A facile and high-yield synthesis of a new ATP analogue, 2-[(4-azido-2-nitrophenyl)amino]ethyl triphosphate (NANTP), is described. NANTP and ATP are hydrolyzed by skeletal myosin subfragment 1 (SF1) at comparable rates in the presence of Ca2+, Mg2+, or NH4+-EDTA. NANTP is also cleaved but less readily by mitochondrial F1-ATPase and by (Na+ + K+)-ATPase from dog brain and hog kidney. F-Actin markedly activates NANTP cleavage by SF1 in the presence of Mg2+, suggesting that the diphosphate product NANDP is slow to be released from the enzyme. [alpha-32P]NANDP binds to a single site on SF1 (KA = 1 X 10(6) M-1) with an affinity identical with that of ADP. The absorption maximum of NANDP was shifted from 474 to 467 nm upon binding to SF1, suggesting that the purine binding site has a dielectric constant of about 45. NANDP was trapped in nearly stoichiometric amounts at the active site by cross-linking SH1 and SH2 with N,N'-p-phenylenedimaleimide (pPDM) or by chelation with cobalt (III) phenanthroline [Wells, J., & Yount, R. (1979) Proc. Natl. Acad. Sci. U.S.A. 76, 4966]. The trapped [beta-32P]NANDP X SF1 complex, like the comparable ADP X SF1 complex, was stable for days at 0 degree C and could be purified free of extraneous analogue by ammonium sulfate precipitation and gel filtration. Photolysis of the purified complex gave greater than 50% covalent incorporation of the trapped NANDP into the 95-kilodalton (kDa) heavy chain of SF1. Limited trypsinization and analysis by gel electrophoresis showed that greater than 95% of the bound label was associated with the 25-kDa NH2-terminal peptide. Without trapping, NANDP labeling of SF1 was nonspecific and was not prevented by addition of a large excess of ATP. This new approach of trapping photoaffinity analogues by cross-linking agents before photolysis may prove to be of general usefulness in increasing the specificity and extent of labeling of enzymes that undergo substrate-induced conformation changes.

We have investigated the ability of the photoaffinity, nonnucleotide ATP analogues, 2-[(4-azido-2-nitrophenyl) amino] ethyl triphosphate (NANTP) and 2-[(4-azido-2-nitrophenyl) amino] propyl triphosphate (PrNANTP), to support active contraction in glycerinated rabbit psoas fibers. At millimolar concentrations, in the absence of calcium, both analogues relaxed fibers. In the presence of calcium, MgNANTP produced isometric tension and stiffness that were one-half to two-thirds the values obtained in MgATP. Maximum shortening velocity and the calcium-activated, myofibrillar catalyzed rate of hydrolysis were approximately the same for MgNANTP as for MgATP. With MgNANTP as the substrate, increasing concentrations of the diphosphate analogue, MgNANDP, inhibited shortening velocity but did not change isometric tension. The addition of increased concentrations of orthophosphate (P) decreased tension while shortening velocity increased. Thus, the effects of the hydrolysis products of NANTP were quite similar to those observed previously for ADP and P in the presence of MgATP. Taken together, these observations show that MgNANTP binds to, and functions in the active site of myosin in a manner quite analogous to MgATP. Thus, the aryl azido group should serve as a valid photoaffinity label for the purine portion of the active site. In contrast, MgPrNANTP, which differs from MgNANTP only in an extra CH2 spacer between the nitrophenyl ring and the triphosphate moiety did not support isometric tension or active shortening in the presence of calcium. Fiber stiffness increased in the presence of calcium and MgPrNANTP, with a calcium-activated, myofibrillar MgPrNANTPase which was about half that obtained with MgATP. Thus, in the presence of MgPrNANTP, cross-bridges appeared to be cycling through states that were attached to actin, but not producing force.