Viruses are globally abundant and extremely diverse in their genetic make-up and in the hosts they infect. Although they influence the abundance, diversity and evolution of their hosts, current methods are inadequate for gaining a quantitative understanding of their impact on these processes. Here we report the adaptation of the solid-phase single-molecule PCR polony method for the quantification of taxonomically relevant groups of diverse viruses. Using T7-like cyanophages as our model, we found the polony method to be far superior to regular quantitative PCR methods and droplet digital PCR when degenerate primers were used to encompass the group's diversity. This method revealed that T7-like cyanophages were highly abundant in the Red Sea in spring 2013, reaching 770,000 phages ml, and displaying a similar depth distribution pattern to cyanobacteria. Furthermore, the abundances of two major clades within the T7-like cyanophages differed dramatically throughout the water column: clade B phages that carry the psbA photosynthesis gene and infect either Synechococcus or Prochlorococcus were at least 20-fold more abundant than clade A phages that lack psbA and infect Synechococcus hosts. Such measurements are of paramount importance for understanding virus population dynamics and the impact of viruses on different microbial taxa and for modelling viral influence on ecosystem functioning on a global scale.

To study the meclhanism of arrest of DNA synthesis at d(TC ,ug of DNA, before addition of the polymerase. These assays were performed at pH 7.5.Synthesis of Single-Stranded DNA Containing 7-deaza A or 7-deaza G. DNA strands containing 7-deaza A were synthesized by a polymerase chain reaction using single-stranded mpTC27 phage DNA (at 2.5 ,ug/ml) as a template and the M13 17-mer (at 2.5 ug/ml) as a (single) primer. The reaction mixtures also contained 300 ,uM (each) 7-deaza dATP, dCTP, dGTP, and dTTP, 50 units of the Taq DNA polymerase (Thermus aquaticus DNA polymerase) per ml (New England Abbreviation: SSB, single-strand binding protein.

Telomerase is a cellular reverse transcriptase, which utilizes an integral RNA template to extend single-stranded telomeric DNA. We used site-specific photocrosslinking to map interactions between DNA primers and the catalytic protein subunit (tTERT) of Tetrahymena thermophila telomerase in functional enzyme complexes. Our assays reveal contact of the single-stranded DNA adjacent to the primer-template hybrid and tTERT residue W187 at the periphery of the N-terminal domain. This contact was detected in complexes with three different registers of template in the active site, suggesting that it is maintained throughout synthesis of a complete telomeric repeat. Substitution of nearby residue Q168, but not W187, alters the K m for primer elongation, implying that it plays a role in the DNA recognition. These findings are the first to directly demonstrate the physical location of TERT-DNA contacts in catalytically active telomerase and to identify amino acid determinants of DNA binding affinity. Our data also suggest a movement of the TERT active site relative to the templateadjacent single-stranded DNA binding site within a cycle of repeat synthesis.specific cleavage of proteins ͉ telomerase-primer interaction ͉ UV crosslinking T elomerase is a unique reverse transcriptase (RT) that extends the single-stranded 3Ј overhangs of telomeres by copying a template within the integral RNA component of the enzyme (1). Some telomerase enzymes can also use this internal template to direct the synthesis of telomeres at nontelomeric sites of chromosome fragmentation (2). In addition to the telomerase RNA subunit (TER), the enzyme contains a catalytic protein subunit, designated telomerase RT (TERT), and accessory proteins (3, 4).Telomerase was first discovered in extracts of the ciliate Tetrahymena thermophila (5), and telomerase from this organism remains an excellent model system for studies of enzyme structure and function. Its RNA subunit (tTER) of 159 nt contains the repeat-complementary sequence 3Ј-AACCCCAAC-5Ј and other motifs required for ribonucleoprotein (RNP) assembly and activity (1, 3). T. thermophila TERT (tTERT) consists of 1,117 amino acids, including a region between residues 518 and 881 that is conserved among RTs and designated as the RT domain (6). The N-terminal half of TERT contains motifs conserved among TERTs but not viral RTs. It constitutes two independently folded domains: the TERT essential N-terminal domain (TEN) and the TERT high-affinity TER binding domain (TRBD). In tTERT, residues 1-195 can be considered to constitute the TEN domain, whereas residues 196-528 comprise the TRBD (7-9).Telomerase specificity of interaction with single-stranded DNA has been studied by monitoring the elongation of primers of varying lengths, sequences and concentrations. Differences in the primer concentration-dependence and repeat addition processivity of product synthesis indirectly suggest that extensive contacts to the enzyme are made by primer regions 5Ј of the template hybrid (2). More direct physical assays have...

We describe a novel activity of the SV40 large T-ag helicase, the unwinding of four stranded DNA structures linked by stacked G-quartets, namely stacked groups of four guanine bases bound by Hoogsteen hydrogen bonds. The structures unwound by the helicase were of two types: (i) quadruplexes comprising four parallel strands that were generated by annealing oligonucleotides including clustered G residues in a buffer containing Na+ions. Each parallel quadruplex consisted of four oligonucleotide molecules. (ii) Complexes comprising two parallel and two antiparallel strands that were generated by annealing the above oligonucleotides in a buffer containing K+ions. Each antiparallel complex consisted of two folded oligonucleotide molecules. Unwinding of these unusual DNA structures by the T-ag was monitored by gel electrophoresis. The unwinding process required ATP and at least one single stranded 3'-tail extending beyond the four stranded region. These data indicated that the T-ag first binds the 3'-tail and moves in a 3'-->5'direction, using energy provided by ATP hydrolysis; then it unwinds the four stranded DNA into single strands. This helicase activity may affect processes such as recombination and telomere extension, in which four stranded DNA could play a role.

Previous in vivo studies have indicated that (dT-dC)n.(dG-dA)n tracts (referred to here as (TC)n.(GA)n), which are widely dispersed in vertebrate genomes, may serve as pause or arrest signals for DNA replication and amplification. To determine whether these repeat elements act as stop signals for DNA replication in vitro, single stranded DNAs including (TC)n or (GA)n tracts of various lengths, were prepared by cloning such tracts into phage M13 vectors, and were replicated with the Klenow fragment of the E. coli DNA polymerase I, or with the calf thymus DNA polymerase alpha, by extension of an M13 primer. Gel electrophoresis of the reaction products revealed that the replication was specifically arrested around the middle of both (TC)n and (GA)n tracts of n greater than or equal to 16. However, whereas in the (TC)n tracts the arrests were less prominent at pH = 8.0 than at pH = 6.5-7.5, and were completely eliminated at pH = 8.5, the arrests in the (GA)n tracts were stronger at the higher pH values. These results, and previous data, suggest that the arrests were caused by formation of unusual DNA structures, possibly triple helices between partially replicated (TC)n or (GA)n tracts, and unreplicated portions of these sequences.