A transcription bubble is a molecular structure formed during DNA

transcription Transcription refers to the process of converting sounds (voice, music etc.) into letters or musical notes, or producing a copy of something in another medium, including: Genetics * Transcription (biology), the copying of DNA into RNA, the fir ...

when a limited portion of the DNA double helix is unwound. The size of a transcription bubble ranges from 12-14 base pairs. A transcription bubble is formed when the RNA polymerase enzyme binds to a promoter and causes two DNA strands to detach. It presents a region of unpaired DNA, where a short stretch of

nucleotides Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules w ...

are exposed on each strand of the

double helix A double is a look-alike or doppelgänger; one person or being that resembles another. Double, The Double or Dubble may also refer to: Film and television * Double (filmmaking), someone who substitutes for the credited actor of a character * ...

RNA polymerase

The bacterial RNA polymerase, a leading

enzyme Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. A ...

involved in formation of a transcription bubble, uses DNA template to guide RNA synthesis. It is present in two main forms: as a core enzyme, when it is inactive, and as a holoenzyme , when it is activated. A sigma (σ) factor is a subunit that assists the process of transcription and it stabilizes the transcription bubble when it binds to unpaired bases. These two components, RNA polymerase and sigma factor, when paired together, build RNA polymerase holoenzyme which is then in its active form and ready to bind to a promoter and initiate

DNA transcription Transcription is the process of copying a segment of DNA into RNA. The segments of DNA transcribed into RNA molecules that can encode proteins are said to produce messenger RNA (mRNA). Other segments of DNA are copied into RNA molecules called ...

. Once it binds to the DNA, RNA polymerase turns from a closed to an open complex, forming the transcription bubble. RNA polymerase synthesizes the new RNA in the

5' to 3' Directionality, in molecular biology and biochemistry, is the end-to-end chemical orientation of a single strand of nucleic acid. In a single strand of DNA or RNA, the chemical convention of naming carbon atoms in the nucleotide Pentose, pentose-s ...

direction by adding complementary bases to the 3' end of a new strand. The holoenzyme composition dissociates after transcription initiation, where the σ factor disengages the complex and the RNA polymerase, in its core form, slides along the DNA molecule.

The transcription cycle of bacterial RNA polymerase

The RNA polymerase holoenzyme binds to a promoter of an exposed DNA strand and begins to synthesize the new strand of

RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...

. The double helix DNA is unwound and a short nucleotide sequence is accessible on each strand. The transcription bubble is a region of unpaired bases on one of the exposed DNA strands. The starting transcription point is determined by the place where the

holoenzyme Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. ...

binds to a promoter. The DNA is unwound and single-stranded at the start site. The DNA promoter interaction is interrupted as the RNA polymerase moves down the template DNA strand and the sigma factor is released. The σ factor is required for the initiation but not for the remaining steps of the DNA transcription. Once the σ factor dissociates from the RNA polymerase, the transcription continues. About 10 synthesized

of a new RNA strand are required for this to proceed to the elongation step. The process of transcribing during elongation is very fast. Elongation takes place until the RNA polymerase comes across a termination signal (terminator) which arrests the process and causes the release of both the DNA template and the new RNA molecule. The DNA usually encodes the termination signal.

Eukaryotic transcription

The majority of eukaryotic genes are transcribed by

RNA polymerase II RNA polymerase II (RNAP II and Pol II) is a multiprotein complex that transcribes DNA into precursors of messenger RNA (mRNA) and most small nuclear RNA (snRNA) and microRNA. It is one of the three RNAP enzymes found in the nucleus of eukaryo ...

, proceeding in the

direction. In eukaryotes, specific subunits within the RNA polymerase II complex allow it to carry out multiple functions. General transcription factors help binding RNA polymerase II to DNA. Promoters are cites where RNA polymerase II binds to start transcription and, in eukaryotes, transcription starting point is positioned at +1 nucleotide. Like all

RNA polymerases In molecular biology, RNA polymerase (abbreviated RNAP or RNApol), or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that synthesizes RNA from a DNA template. Using the enzyme helicase, RNAP locally opens the ...

, it travels along the template DNA, in the 3' to 5' direction and synthesizes a new RNA strand in the 5' to 3' direction, by adding new bases to the 3' end of the new RNA. A transcription bubble occurs as a result of the double stranded DNA unwinding. After about 25 base pairs of the DNA double strand are unwound, RNA synthesis takes place within the transcription bubble region. Supercoiling is also part of this process since DNA regions in front of the RNA polymerase II are unwinding, while DNA regions behind it are rewinding, forming a double helix again. The RNA polymerase carries out the majority of the steps during the

cycle, especially in maintaining the transcription bubble open for the complementary

base pairing A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA ...

. There are some steps of the

cycle that require more proteins, such as the Rpb4/7 complex and the RNA polymerase attached to the elongation factor transcription factor IIS (TFIIS).

References

{{DEFAULTSORT:Transcription Bubble Genetics Gene expression

RNA polymerase

The transcription cycle of bacterial RNA polymerase

Eukaryotic transcription

See also

References