User:Shudadoff3/sandbox

RLL comments
Overall I like this. Good work.

Hey, what's up. I'm drafting improvements to the Triple Helix page. If you have any input to the stuff I have going, let me know on my talk page or something.

In geometry, a triple helix (plural triple helices) is a set of three congruent geometrical helices with the same axis, differing by a translation along the axis. This means that each of the helices keeps the same distance from the central axis. As with a single helix, a triple helix may be characterized by its pitch and diameter. Examples of triple helices include triplex DNA, RNA , collagen and collagen-like proteins.

General Structure
A triple helix is named such because it is made up of three separate helices. Each of these helices shares the same axis, but they do not take up the same space because each helix is translated angularly around the axis. Generally, the identity of a triple helix depends on the type of helices that make it up. For example: a triple helix made of three strands of collagen protein is a collagen triple helix, and a triple helix made of three strands of DNA is a DNA triple helix.

As with other types of helices, triple helices have handedness: right-handed or left-handed. A right-handed helix moves around its axis in a clockwise direction from beginning to end. A left-handed helix is the right-handed helix's mirror image, and it moves around the axis in a counterclockwise direction from beginning to end. The beginning and end of a helical molecule are defined based on certain markers in the molecule that do not change easily. For example: the beginning of a helical protein is its N terminus, and the beginning of a single strand of DNA is its 5' end. "Peer Review AJL: It would be nice to have a citation for this general stuff in the preceding two paragraphs."The collagen triple helix is made of three collagen peptides, each of which forms its own left-handed polyproline helix. When the three chains combine, the triple helix adopts a right-handed orientation. The collagen peptide is composed of repeats of Gly-X-Y, with the second residue (X) usually being Pro and the third (Y) being hydroxyproline.

A DNA triple helix is made up of three separate DNA strands, each oriented with the sugar/phosphate backbone on the outside of the helix and the bases on the inside of the helix. The bases are the part of the molecule closest to the triple helix's axis, and the backbone is the part of the molecule farthest away from the axis. The third strand occupies the major groove of relatively normal duplex DNA. The bases in triplex DNA are arranged to match up according to a Hoogsteen base pairing scheme. Similarly, RNA triple helices are formed as a result of a single stranded RNA forming hydrogen bonds with an RNA duplex; the duplex consists of Watson-Crick base pairing while the third strand binds via Hoogsteen base pairing.

Stabilizing Factors
The collagen triple helix has several characteristics that increase its stability. When proline is incorporated into the Y position of the Gly-X-Y sequence, it is post-translationally modified to hydroxyproline. The hydroxyproline can enter into favorable interactions with water, which stabilizes the triple helix because the Y residues are solvent-accessible in the triple helix structure. The individual helices are also held together by an extensive network of amide-amide hydrogen bonds formed between the strands, each of which contributes approximately -2 kcal/mol to the overall free energy of the triple helix. The formation of the superhelix protects the critical glycine residues on the interior of the helix in addition to protecting the overall protein from proteolysis. "Peer Review AJL: Maybe change the wording of the last sentence to make more sense. Perhaps 'The formation of the superhelix not only protects the critical glycine residues on the interior of the helix, but also protects the overall protein from proteolysis.'"Triple helix DNA and RNA are stabilized by many of the same forces that stabilize double-stranded DNA helices. With nucleotide bases oriented to the inside of the helix, closer to its axis, bases engage in hydrogen bonding with other bases. The bonded bases in the center exclude water, so the hydrophobic effect is particularly important in the stabilization of DNA triple helices. "PR AJL: You should include a source here that talks about the hydrophobic effect or hydrogen bonding stabilizing either double or triple helices."

Proteins
Members of the collagen superfamily are major contributors to the extracellular matrix. The triple helical structure provides strength and stability to collagen fibers by providing great resistance to tensile stress. The rigidity of the collagen fibers is an important factor that can withstand most mechanical stress, making it an ideal protein for macromolecular transport and overall structural support throughout the body.

DNA
There are some oligonucleotide sequences, called triplet-forming oligonucleotides (TFOs) that can bind to form a triplex with a longer molecule of double-stranded DNA; TFOs can inactivate a gene or help to induce mutations. TFOs can only bind to certain sites in a larger molecule, so researchers must first determine whether a TFO can bind to the gene of interest.

RNA
In recent years, the biological function of triplex RNA has become more studied. Some roles include increasing stability, translation, influencing ligand binding, and catalysis. One example of ligand binding being influenced by a triple helix is in the SAM-II riboswitch where the triple helix creates a binding site that will uniquely accept S-adenosylmethionine (SAM). The ribonucleoprotein complex telomerase, responsible for replicating the tail-ends of DNA (telomeres) also contains triplex RNA believed to be necessary for proper telomerase functioning. The triple helix at the 3' end of MALAT1 serves to stabilize the RNA by protecting the Poly-A tail from proteolysis as well as increases translation efficiency, which is ultimately detrimental to humans as MALAT1 is related to lung cancer malignancy.