Hairpin and Pin

A hairpin is a sequence of consecutive turns on a particular section of road. The road includes at least fourteen of these turns. Hairpin turns are notorious for their difficulty, as the margin for error is extremely small. A recent race in Tuscany was won by Max Gordon, son of Robby Gordon, who passed Robert Stout at a hairpin and won his first Super Trucks Series race. Although Merriam-Webster’s dictionary has no opinion on the topic, the words hairpin and pin do have a corresponding definition.

RNAP recognizes hairpin promoters

RNAP recognizes hairpin promoter DNA via a sequence-specific interaction. RNAP recognizes a phosphate backbone containing the bases -4 to +2. The Fingers residues of RNAP bind to this sequence at the -11 and -13 positions and form salt-bridges. This RNAP is capable of directing template DNA towards the active site. These two types of interaction are critical to gene regulation.

The CGG and GGA mutations form more stable secondary structures than the wild-type counterparts. The CGA mutation destabilizes these secondary structures. In order to confirm whether these two mutations are related, the mini-vRNAP K176C and CGA mutants were used to make the proteins. Once purified, the proteins were subjected to energy minimization, right-body refinement, and individual B-factor refinements. Finally, the binary complex structure was determined using the resulting models.

Molecular analyses of RNAP have revealed that the N4 mini-vRNAP recognizes a hairpin DNA promoter and forms a salt-resistant binary complex. Interestingly, this protein switches from its apo-form to its binary complex upon binding to the hairpin DNA promoter. This transition highlights subtle differences in RNAP binding affinity. Further, it highlights the importance of the phage’s life cycle in determining the DNA-protein interactions with hairpin promoters.

RNAP synthesizes an RNA primer

RNAP is a ribonucleoprotein polymerase, which synthesizes an RNA primer for the hairpin strand of DNA. Primers vary in length from ten to sixteen nucleotides. Primers are made of RNA and contain three hydroxyl groups, which serve as a DNA primer. They are produced in the presence of DnaB helicase, which stabilizes the 3′-end hairpin conformation of the template.

To measure RNAP, we used two types of RNAP: KP34 RNAP and T7 RNAP. Both the strong and weak promoter DNA template encodes a 37-nt RNA and were incubated with 100 nM of each RNAP. RNAP was purified using a Monarch(r) RNA Cleanup Kit (Implen and New England BioLabs). Each reaction mixture contained 1.5 U/ml of RNaseOUTTM recombinant ribonuclease inhibitor. The samples were separated on a 12% TBE native gel.

The RNA primer is removed through several mechanisms. The short flap pathway involves RNase H2 and FEN-1. RNase H2 degrades most of the annealed primer. Then, FEN-1 cleaves off the flaps. The long flap pathway involves a number of enzymes and a 5′ to 3′ helicase. The RNA primer is then removed, leaving a gap region.

RNAP primes replication on hairpin DNA

RNAP primes replication on hairpin strands of DNA by locating a sequence-specific nuclease at the 3′ end of parental strands. It is located approximately 11,000 bp downstream of the OH site. The RNAP primes replication by providing a b-hydroxy group for DNA polymerase to elongate. In many plasmids, the RNAP primes replication on hairpin DNA.

After RNAP primes replication on hairpin strands, the lagging strand is repaired by the activity of DNA polymerase I. A small amount of adjacent DNA from the previous fragment is also removed from the lagging strand, which may enhance replication accuracy. In addition to removing RNA primers from the hairpin strand, RNA polymerase also removes DNA from its adjacent fragments.

RNAP recognizes hairpin promoters in plasmids

RNAP, or RNA Polymerase, is a bacterial transcriptional activator that recognizes hairpin promoters in cDNA and plasmid DNA. Hairpins are branched DNA sequences with intrastrand base pairing. These sequences can be essential for horizontal gene transfer between bacteria. RNAP recognizes hairpin promoters and synthesizes a RNA primer to initiate replication.

DNA double-stranded RNAP has a lifetime of about a second. Large perfect IRs are genetically unstable and do not promote gene expression. RNAP recognizes these promoters, which are genetically unstable and are frequently found on plasmid DNA. In addition, large perfect IRs form the basis for dsDNA replication and may cause slippage or mismatched alignment of strands.

RNAP recognizes hairpin promoter sequences in plasmid DNA to prime replication. RNAP recognizes the hairpin promoter in the F-plasmid origin of replication and synthesizes RNA primer in E. coli. Other plasmid ssi’s have been isolated and are shown to use the phX174-type priming mechanism.