Dna Structure And Recognition

Question 0

What is the monomeric unit of DNA and RNA?

Answer 0

A nucleotide.

This contains a nitrogenous base, sugar unit and one or more phosphate groups

Question 1

What are the nucleic acids?

Answer 1

Deoxyribonucleic and ribonucleic acid.

These are polymeric materials

Question 2

What are nitrogenous bases?

Answer 2

DNA uses 4 of these:
Adenine - thymine
Guanine - cytosine

RNA uses uracil instead of thymine

Question 3

What is the general structure of DNA?

Answer 3

Nucleotides join together in DNA by following a phosphate ester bond between the 5’OH group on one nucleotide and 3’OH group on sugar of another nucleotide

Question 4

What does the 1:1 ratio of A:T and C:G in the genetic code indicate?

Answer 4

DNA consists of 2 helical strands wrapped around each other but running in opposite directions.
The strands are held together by hydrogen bonding between pairs of bases G-C and A-T

Question 5

What area the major and minor grooves of the double helix?

Answer 5

Duplex b-DNA possesses two distinct groups in its structure.

Major:12Angstrom wide and 8.5Angstrom deep

Minor: 6Angstrom wide and 7.5Angstrom deep

Question 6

What is present on the floor of the major and minor grooves?

Answer 6

The base pairs that express the genetic material are exposed and can interact with various small molecules

Question 7

What is the significance of the polar sugar phosphate backbone on the outside of the DNA strcture?

Answer 7

It can form polar interactions with water

Question 8

What makes DNA a valid target for drug action?

Answer 8

DNA is important for cell replication and the transfer of genetic information
Involved in protein coding via RNA
Many diseases are associated with DNA malfunction/alteration
Inhibition of DNA function selectively can treat a vast array of disorders
Most current treatments of cancer rely on inhibition of DNA function

Question 9

What drugs act on DNA?

Answer 9

Intercalating cytostatic agents
Alkylating agents
Chain cutters
Non-covalent groove binders
Antigene/antisense triple helix compounds

Question 10

What are Intercalating agents?

Answer 10

Compounds that are able to slip between the layers of the nucleic acid base pairs and disrupt the shape of the double helix

Question 11

What are the criteria for Intercalating agents?

Answer 11

They must be flat, (aromatic or heteroaromatic in nature)

Examples include several natural compounds such as antitumour and antibiotics
E.g. Daunomycin, Adriamycin and Antimalarial Chloroquine

Question 12

What are alkylating agents?

Answer 12

Highly electrophilic compounds that react with a nucleophile to form a covalent bond

Question 13

What do alkylating reagents react with in DNA?

Answer 13

N7 of guanine and adenine,
O6 of guanine,
N3 of adenine and PO4-

Question 14

What can react with nucleophilic nitrogens to form DNA substrate covalent bonds?

Answer 14

Electrophilic functional groups like epoxides, cyclopropanes

E.g. CC1065 natural product derived from streptomyces zelensis is a known DNA binder and potent anti tumour drug

Question 15

How do alkylating agents work?

Answer 15

They can cross link two DNA strands and prevent dissociation during transcription or they could link two guanines in the same chain to prevent protein access.

Question 16

What is the effect of alkylation?

Answer 16

Weakens N-glycosidic bond, leading to depurinarion and strand breakage e.g. Mechlorethamine which is a member of the nitrogen mustards.

Question 17

How can the high activity and poor specificity of Mechlorethamine be corrected?

Answer 17

Compounds such as phenyl mustards which have a lower activity, and the uracil mustards which have a higher selectivity, have been developed

Question 18

What is the significance of aziridinylbemzoquinones?

Answer 18

AZQ
Undergone clinical trials as antitumour agent resulting in efficacy against brain tumours,
Forms DNA inter strand x links resulting in efficient cross linking and cell death.
Aziridines critical for activity

Question 19

What is DNA platination?

Answer 19

Cis-diammonia dichloroplatinum (II) aka cisplatin is an antitumour agent for treatment of testicular and ovarian tumours.

It binds to DNA bifunctionally to form intra strand and interstrand cross links.
GN7-GN7 intra strand cross link between neighbouring guanines is a major adduct

Question 20

What are chain cutters?

Answer 20

Neocarzinostatin chromophore which is a natural product able to intercalated into DNA
Once intercalated the enediyne function is located within the DNA minor groove and undergoes Bergman-type cyclisation

Question 21

What does the Berman type cyclisation involve?

Answer 21

The formation of highly energetic free radicals which abstract from hydrogen atoms from the surrounding DNA chains resulting in strand scission

Question 22

What are non covalent groove binders?

Answer 22

The bind non covalently to the DNA minor and major grooves.
These are generally long, usually curved, and possess hydrogen bonding sites and charged groups along their length complementary to the DNA

Question 23

What do the major and minor grooves differ in?

Answer 23

Electrostatic potential
Hydrogen bonding characterstics
Steric effects
Hydration

Question 24

What predominantly binds to major groove?

Answer 24

Proteins

Question 25

What predominantly binds to minor groove?

Answer 25

Small molecules

Question 26

What are the contributions to minor groove binding?

Answer 26

Van der Waals contacts through sugar phosphate backbone
H bonding (bridging bonds between O2 thymine and N3 adenine)
Selective for AT rich sequences e,g, Netropsin for minor groove binding

Question 27

What are antigene/antisense oligonucleotides?

Answer 27

Homopyridine oligodeoxynucleotides (~20 bases in length) can bind to homopurine sites on duplex DNA via the formation of Hoogstein-based hydrogen bonds in the major groove.

This results in severe structure distortion in the binding region causing inability of DNA proteins to mediate cell function leading to cell death