Re: What is a dinucleotide, what are dinucleotides?

First, let's define the term "nucleotide". You already know that DNA has these four bases - Adenine, Cytosine, Guanine, and Thymine (or Uracil in RNA) - and that the sequence of these bases forms the information stored in the DNA; and you probably know that these bases are attached to a "backbone" composed of sugar (ribose in RNA; deoxy-ribose in DNA) and phosphates. Well, the actual building blocks of DNA and RNA are each composed of a base attached to a single sugar attached to phosphates, so the bases are rarely used or seen alone. Instead, they are found bound to ribose (or deoxy-ribose) forming "nucleosides", e.g. adenine (a base) + ribose = adenosine (a nucleoside); thymine + deoxyribose = thymidine. A nucleoside that is attached to one or more phosphates is called a nucleotide.
Here is a picture of the nucleotide, adenosine monophosphate (AMP). At the top is the double-ring of adenine, and below it is the pentagonal ribose. The phosphate (PO₄) is attached to the ribose to the left.

Now, let's completely switch directions for the next set of definitions - macromolecules. As the name suggests, macro-molecules are very large molecules that are composed of much smaller subunits, like DNA, proteins, starch, etc. When discussing macromolecules, we commonly use the suffix "-mer" to refer to the subunits in general. We then use prefixes to denote about how many subunits are present in a molecule: e.g. a monomer is a single subunit; a dimer is two atttached subunits; a trimer is made of three subunits; an oligomer is made of several (10 - 50) subunits; and a polymer has many, many subunits (over 50). So, a dimer of DNA or RNA would be a molecule containing two attached subunits, which we have already defined as nucleotides; therefore a "dinucleotide" is a single piece of DNA or RNA that is two nucleotides long.

The example you give of a thymidine dinucleotide would be two thymidine nucleotides attached by a phosphate bridge - in this case, the 5'-phophate of one thymidine bonds to the 3'-hydroxyl group of the other thymidine, just as the bonding occurs in complete DNA and RNA molecules. This kind of dinucleotide is often abbreviated as NpN, where N is any nucleotide and "p" indicates the phosphate bridge; thus, thymidine dinucleotide would be abbreviated, TpT. This abbreviation is important to distinguish dinucleotides from basepairs in double- stranded DNA, where CG is an interacting pair of bases on opposite strands, but CpG is a dinucleotide within one strand (for longer stretches, like trimers and above, the p's are dropped). There is another group of dinucleotides that are essential for energy transfer, which bind phosphate-to-phosphate, creating a 5'- 5' diphosphate bridge. The most common of these are NAD+, which is niacin-adenosine dinucleotide, and FAD, which is riboflavin-adenosine dinucleotide (it is interesting that some of the most important co-enzymes are B-complex vitamins bound to adenosine). To sum up: a dinucleotide is a single molecule composed of two, linked nucleotides - the building blocks of DNA and RNA.